diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 899cf187c09..f4445f16948 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -27,7 +27,7 @@ jobs: path: ~/.cache/pip key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }} - name: Install Python dependencies - run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning awscli + run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning - name: Add Google Analytics to doc/source/conf.py run: | sed -i -e "/html_theme_options = {/a\ @@ -50,6 +50,7 @@ jobs: AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} run: | + pip install awscli case "$TARGET_BRANCH" in release_[[:digit:]][[:digit:]].[[:digit:]][[:digit:]]|master) UPLOAD_DIR=$TARGET_BRANCH diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index 2e45eb3b7fe..6b196a0f4c4 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -200,7 +200,7 @@ Conda Dependency Resolver The ``conda`` directive can be used to configure a conda dependency resolver. This resolver can be configured with the following options. For a very detailed -discussion of Conda dependency resolution, check out the :ref:`Conda FAQ `. +discussion of Conda dependency resolution, check out the :doc:`Conda FAQ `. prefix The conda_prefix used to locate dependencies in (default: ``/_conda``). diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md index fdaf363f7d6..c323c96b9fc 100644 --- a/doc/source/admin/python.md +++ b/doc/source/admin/python.md @@ -1,6 +1,6 @@ # Supported Python versions -Galaxy's core functionality is currently supported on Python **>=3.5** . +Galaxy's core functionality is currently supported on Python **>=3.6** . If Galaxy complains about the version of Python you are using: diff --git a/doc/source/admin/special_topics/mulled_containers.rst b/doc/source/admin/special_topics/mulled_containers.rst index a9b6a9be43c..a10d6b631b9 100644 --- a/doc/source/admin/special_topics/mulled_containers.rst +++ b/doc/source/admin/special_topics/mulled_containers.rst @@ -3,7 +3,7 @@ Containers for Tool Dependencies ================================ Galaxy tools (also called wrappers) are able to use Conda packages -(see more information in our `Galaxy Conda documentation`_) and Docker containers as dependency resolvers. +(see more information in our :doc:`Galaxy Conda documentation <../conda_faq>`) and Docker containers as dependency resolvers. The IUC_ recommends to use Conda packages as the primary dependency resolver, mainly because Docker is not available on every (HPC-) system. Conda on the other hand can be installed by Galaxy and maintained entirely in user-space. Nevertheless, Docker and containers in general have some unique features and @@ -159,7 +159,6 @@ Containers, once generated, should be tested. This can be achieved by affixing ` $ mulled-singularity-testing --container-list list.txt --filepath /tmp/sing/ --installation /usr/local/bin/singularity --logfile test-output.txt -.. _Galaxy Conda documentation: ./conda_faq.rst .. _IUC: https://galaxyproject.org/iuc/ .. _container annotation: https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4 .. _BioContainers: https://github.com/biocontainers diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index 6bef88c7bc6..a1229c02b41 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -2,9 +2,9 @@ galaxy.actions package ====================== .. automodule:: galaxy.actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.actions.admin module --------------------------- .. automodule:: galaxy.actions.admin - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.actions.library module ----------------------------- .. automodule:: galaxy.actions.library - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index 2a5a44ea5bf..aad52165d4d 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -2,9 +2,9 @@ galaxy.auth.providers package ============================= .. automodule:: galaxy.auth.providers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,30 @@ galaxy.auth.providers.alwaysreject module ----------------------------------------- .. automodule:: galaxy.auth.providers.alwaysreject - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.auth.providers.ldap\_ad module ------------------------------------- .. automodule:: galaxy.auth.providers.ldap_ad - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.auth.providers.localdb module ------------------------------------ .. automodule:: galaxy.auth.providers.localdb - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.auth.providers.pam\_auth module -------------------------------------- .. automodule:: galaxy.auth.providers.pam_auth - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst index ac0af26959e..8df09f1c809 100644 --- a/doc/source/lib/galaxy.auth.rst +++ b/doc/source/lib/galaxy.auth.rst @@ -2,16 +2,17 @@ galaxy.auth package =================== .. automodule:: galaxy.auth - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.auth.providers + galaxy.auth.providers Submodules ---------- @@ -20,8 +21,6 @@ galaxy.auth.util module ----------------------- .. automodule:: galaxy.auth.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.authnz.rst b/doc/source/lib/galaxy.authnz.rst index 156c62d7961..63096b0f1a5 100644 --- a/doc/source/lib/galaxy.authnz.rst +++ b/doc/source/lib/galaxy.authnz.rst @@ -2,9 +2,9 @@ galaxy.authnz package ===================== .. automodule:: galaxy.authnz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.authnz.custos\_authnz module ----------------------------------- .. automodule:: galaxy.authnz.custos_authnz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.authnz.managers module ----------------------------- .. automodule:: galaxy.authnz.managers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.authnz.psa\_authnz module -------------------------------- .. automodule:: galaxy.authnz.psa_authnz - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.config.rst b/doc/source/lib/galaxy.config.rst index b09517518ab..08c750a26fe 100644 --- a/doc/source/lib/galaxy.config.rst +++ b/doc/source/lib/galaxy.config.rst @@ -2,9 +2,9 @@ galaxy.config package ===================== .. automodule:: galaxy.config - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.config.config\_manage module ----------------------------------- .. automodule:: galaxy.config.config_manage - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.config.schema module --------------------------- .. automodule:: galaxy.config.schema - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.config.script module --------------------------- .. automodule:: galaxy.config.script - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.containers.rst b/doc/source/lib/galaxy.containers.rst index 8d61cd41340..6a1a6952015 100644 --- a/doc/source/lib/galaxy.containers.rst +++ b/doc/source/lib/galaxy.containers.rst @@ -2,9 +2,9 @@ galaxy.containers package ========================= .. automodule:: galaxy.containers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,30 @@ galaxy.containers.docker module ------------------------------- .. automodule:: galaxy.containers.docker - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.containers.docker\_decorators module ------------------------------------------- .. automodule:: galaxy.containers.docker_decorators - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.containers.docker\_model module -------------------------------------- .. automodule:: galaxy.containers.docker_model - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.containers.docker\_swarm module -------------------------------------- .. automodule:: galaxy.containers.docker_swarm - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index b307e892729..e62c824cf74 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -2,9 +2,9 @@ galaxy.datatypes.converters package =================================== .. automodule:: galaxy.datatypes.converters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,232 +13,230 @@ galaxy.datatypes.converters.bed\_to\_gff\_converter module ---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bed_to_gff_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.bgzip module ---------------------------------------- .. automodule:: galaxy.datatypes.converters.bgzip - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.cram\_to\_bam module ------------------------------------------------ .. automodule:: galaxy.datatypes.converters.cram_to_bam - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.fasta\_to\_len module ------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_len - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.fasta\_to\_tabular\_converter module ---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.fastq\_to\_fqtoc module --------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.fastqsolexa\_to\_fasta\_converter module -------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.fastqsolexa\_to\_qual\_converter module ------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.gff\_to\_bed\_converter module ---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_bed_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.gff\_to\_interval\_index\_converter module ---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.interval\_to\_bed\_converter module --------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bed_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.interval\_to\_bedstrict\_converter module --------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.interval\_to\_fli module ---------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_fli - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.interval\_to\_interval\_index\_converter module --------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.interval\_to\_tabix\_converter module ----------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.lped\_to\_fped\_converter module ------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_fped_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.lped\_to\_pbed\_converter module ------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.maf\_to\_fasta\_converter module ------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.maf\_to\_interval\_converter module --------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.maf_to_interval_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.pbed\_ldreduced\_converter module ------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.pbed\_to\_lped\_converter module ------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.picard\_interval\_list\_to\_bed6\_converter module ------------------------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.pileup\_to\_interval\_index\_converter module ------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.ref\_to\_seq\_taxonomy\_converter module -------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.ref_to_seq_taxonomy_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.tabular\_csv module ----------------------------------------------- .. automodule:: galaxy.datatypes.converters.tabular_csv - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.tabular\_to\_dbnsfp module ------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.tabular_to_dbnsfp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.vcf\_to\_interval\_index\_converter module ---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.vcf\_to\_vcf\_bgzip module ------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.converters.wiggle\_to\_simple\_converter module ---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst index cd85ef190df..570981adedb 100644 --- a/doc/source/lib/galaxy.datatypes.dataproviders.rst +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -2,9 +2,9 @@ galaxy.datatypes.dataproviders package ====================================== .. automodule:: galaxy.datatypes.dataproviders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,72 +13,70 @@ galaxy.datatypes.dataproviders.base module ------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.chunk module ------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.chunk - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.column module -------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.dataset module --------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.dataset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.decorators module ------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.decorators - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.exceptions module ------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.exceptions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.external module ---------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.external - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.hierarchy module ----------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.hierarchy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.dataproviders.line module ------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.line - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index acbf8fd2f9c..8329f13e076 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -2,9 +2,9 @@ galaxy.datatypes.display\_applications package ============================================== .. automodule:: galaxy.datatypes.display_applications - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.datatypes.display\_applications.application module --------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.application - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.display\_applications.parameters module -------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.parameters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.display\_applications.util module -------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index b34c4e24783..11fcfd910db 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -2,19 +2,20 @@ galaxy.datatypes package ======================== .. automodule:: galaxy.datatypes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.datatypes.converters - galaxy.datatypes.dataproviders - galaxy.datatypes.display_applications - galaxy.datatypes.util + galaxy.datatypes.converters + galaxy.datatypes.dataproviders + galaxy.datatypes.display_applications + galaxy.datatypes.util Submodules ---------- @@ -23,296 +24,310 @@ galaxy.datatypes.annotation module ---------------------------------- .. automodule:: galaxy.datatypes.annotation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.anvio module ----------------------------- .. automodule:: galaxy.datatypes.anvio - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.assembly module -------------------------------- .. automodule:: galaxy.datatypes.assembly - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.binary module ------------------------------ .. automodule:: galaxy.datatypes.binary - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.blast module ----------------------------- .. automodule:: galaxy.datatypes.blast - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.checkers module -------------------------------- .. automodule:: galaxy.datatypes.checkers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.chrominfo module --------------------------------- .. automodule:: galaxy.datatypes.chrominfo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.constructive\_solid\_geometry module ----------------------------------------------------- .. automodule:: galaxy.datatypes.constructive_solid_geometry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.coverage module -------------------------------- .. automodule:: galaxy.datatypes.coverage - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.data module ---------------------------- .. automodule:: galaxy.datatypes.data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.genetics module -------------------------------- .. automodule:: galaxy.datatypes.genetics - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.gis module --------------------------- .. automodule:: galaxy.datatypes.gis - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.graph module ----------------------------- .. automodule:: galaxy.datatypes.graph - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.images module ------------------------------ .. automodule:: galaxy.datatypes.images - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.interval module -------------------------------- .. automodule:: galaxy.datatypes.interval - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.isa module --------------------------- .. automodule:: galaxy.datatypes.isa - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.media module +----------------------------- + +.. automodule:: galaxy.datatypes.media + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.metadata module -------------------------------- .. automodule:: galaxy.datatypes.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.microarrays module ----------------------------------- .. automodule:: galaxy.datatypes.microarrays - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.molecules module --------------------------------- .. automodule:: galaxy.datatypes.molecules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.mothur module ------------------------------ .. automodule:: galaxy.datatypes.mothur - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.msa module --------------------------- .. automodule:: galaxy.datatypes.msa - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.neo4j module ----------------------------- .. automodule:: galaxy.datatypes.neo4j - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.ngsindex module -------------------------------- .. automodule:: galaxy.datatypes.ngsindex - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.phylip module ------------------------------ .. automodule:: galaxy.datatypes.phylip - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.plant\_tribes module ------------------------------------- .. automodule:: galaxy.datatypes.plant_tribes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.proteomics module ---------------------------------- .. automodule:: galaxy.datatypes.proteomics - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.qualityscore module ------------------------------------ .. automodule:: galaxy.datatypes.qualityscore - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.registry module -------------------------------- .. automodule:: galaxy.datatypes.registry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.sequence module -------------------------------- .. automodule:: galaxy.datatypes.sequence - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.sniff module ----------------------------- .. automodule:: galaxy.datatypes.sniff - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.spaln module ----------------------------- .. automodule:: galaxy.datatypes.spaln - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.speech module +------------------------------ + +.. automodule:: galaxy.datatypes.speech + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.tabular module ------------------------------- .. automodule:: galaxy.datatypes.tabular - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.text module ---------------------------- .. automodule:: galaxy.datatypes.text - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.tracks module ------------------------------ .. automodule:: galaxy.datatypes.tracks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.triples module ------------------------------- .. automodule:: galaxy.datatypes.triples - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.upload\_util module ------------------------------------ .. automodule:: galaxy.datatypes.upload_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.xml module --------------------------- .. automodule:: galaxy.datatypes.xml - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 9812c396a99..8b507bf028a 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -2,9 +2,9 @@ galaxy.datatypes.util package ============================= .. automodule:: galaxy.datatypes.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.datatypes.util.generic\_util module ------------------------------------------ .. automodule:: galaxy.datatypes.util.generic_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.util.gff\_util module -------------------------------------- .. automodule:: galaxy.datatypes.util.gff_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.datatypes.util.maf\_utilities module ------------------------------------------- .. automodule:: galaxy.datatypes.util.maf_utilities - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.dependencies.rst b/doc/source/lib/galaxy.dependencies.rst index 16ce685cbc1..a1915f48d56 100644 --- a/doc/source/lib/galaxy.dependencies.rst +++ b/doc/source/lib/galaxy.dependencies.rst @@ -2,7 +2,6 @@ galaxy.dependencies package =========================== .. automodule:: galaxy.dependencies - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index 6331aa38fdd..2c4bf2f535a 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -2,7 +2,6 @@ galaxy.eggs package =================== .. automodule:: galaxy.eggs - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index 8f118c6aa45..fbd65bbf861 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -2,9 +2,9 @@ galaxy.exceptions package ========================= .. automodule:: galaxy.exceptions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.exceptions.error\_codes module ------------------------------------- .. automodule:: galaxy.exceptions.error_codes - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.files.rst b/doc/source/lib/galaxy.files.rst new file mode 100644 index 00000000000..e5d3cda4660 --- /dev/null +++ b/doc/source/lib/galaxy.files.rst @@ -0,0 +1,15 @@ +galaxy.files package +==================== + +.. automodule:: galaxy.files + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + galaxy.files.sources diff --git a/doc/source/lib/galaxy.files.sources.rst b/doc/source/lib/galaxy.files.sources.rst new file mode 100644 index 00000000000..bee1d7000d1 --- /dev/null +++ b/doc/source/lib/galaxy.files.sources.rst @@ -0,0 +1,50 @@ +galaxy.files.sources package +============================ + +.. automodule:: galaxy.files.sources + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.files.sources.dropbox module +----------------------------------- + +.. automodule:: galaxy.files.sources.dropbox + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.galaxy module +---------------------------------- + +.. automodule:: galaxy.files.sources.galaxy + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.posix module +--------------------------------- + +.. automodule:: galaxy.files.sources.posix + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.s3 module +------------------------------ + +.. automodule:: galaxy.files.sources.s3 + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.webdav module +---------------------------------- + +.. automodule:: galaxy.files.sources.webdav + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst index 088d52bcb9c..557cf96d8ab 100644 --- a/doc/source/lib/galaxy.forms.rst +++ b/doc/source/lib/galaxy.forms.rst @@ -2,9 +2,9 @@ galaxy.forms package ==================== .. automodule:: galaxy.forms - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.forms.forms module ------------------------- .. automodule:: galaxy.forms.forms - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_execution.ports.rst b/doc/source/lib/galaxy.job_execution.ports.rst index 269584f9d36..fabbe62802b 100644 --- a/doc/source/lib/galaxy.job_execution.ports.rst +++ b/doc/source/lib/galaxy.job_execution.ports.rst @@ -2,9 +2,9 @@ galaxy.job\_execution.ports package =================================== .. automodule:: galaxy.job_execution.ports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.job\_execution.ports.view module --------------------------------------- .. automodule:: galaxy.job_execution.ports.view - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_execution.rst b/doc/source/lib/galaxy.job_execution.rst index 86c4e3019fe..4e144d62cda 100644 --- a/doc/source/lib/galaxy.job_execution.rst +++ b/doc/source/lib/galaxy.job_execution.rst @@ -2,16 +2,17 @@ galaxy.job\_execution package ============================= .. automodule:: galaxy.job_execution - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.job_execution.ports + galaxy.job_execution.ports Submodules ---------- @@ -20,24 +21,22 @@ galaxy.job\_execution.datasets module ------------------------------------- .. automodule:: galaxy.job_execution.datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_execution.output\_collect module -------------------------------------------- .. automodule:: galaxy.job_execution.output_collect - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_execution.setup module ---------------------------------- .. automodule:: galaxy.job_execution.setup - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_metrics.collectl.rst b/doc/source/lib/galaxy.job_metrics.collectl.rst index 74c5ee89df1..d302c9f9f5b 100644 --- a/doc/source/lib/galaxy.job_metrics.collectl.rst +++ b/doc/source/lib/galaxy.job_metrics.collectl.rst @@ -2,9 +2,9 @@ galaxy.job\_metrics.collectl package ==================================== .. automodule:: galaxy.job_metrics.collectl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,30 @@ galaxy.job\_metrics.collectl.cli module --------------------------------------- .. automodule:: galaxy.job_metrics.collectl.cli - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.collectl.processes module --------------------------------------------- .. automodule:: galaxy.job_metrics.collectl.processes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.collectl.stats module ----------------------------------------- .. automodule:: galaxy.job_metrics.collectl.stats - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.collectl.subsystems module ---------------------------------------------- .. automodule:: galaxy.job_metrics.collectl.subsystems - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_metrics.instrumenters.rst b/doc/source/lib/galaxy.job_metrics.instrumenters.rst index 232ba437a5a..54615895b99 100644 --- a/doc/source/lib/galaxy.job_metrics.instrumenters.rst +++ b/doc/source/lib/galaxy.job_metrics.instrumenters.rst @@ -2,9 +2,9 @@ galaxy.job\_metrics.instrumenters package ========================================= .. automodule:: galaxy.job_metrics.instrumenters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,64 +13,62 @@ galaxy.job\_metrics.instrumenters.cgroup module ----------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.cgroup - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.collectl module ------------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.collectl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.core module --------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.cpuinfo module ------------------------------------------------ .. automodule:: galaxy.job_metrics.instrumenters.cpuinfo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.env module -------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.env - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.hostname module ------------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.hostname - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.meminfo module ------------------------------------------------ .. automodule:: galaxy.job_metrics.instrumenters.meminfo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.job\_metrics.instrumenters.uname module ---------------------------------------------- .. automodule:: galaxy.job_metrics.instrumenters.uname - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.job_metrics.rst b/doc/source/lib/galaxy.job_metrics.rst index 9419d2aebd1..c51c202b505 100644 --- a/doc/source/lib/galaxy.job_metrics.rst +++ b/doc/source/lib/galaxy.job_metrics.rst @@ -2,17 +2,18 @@ galaxy.job\_metrics package =========================== .. automodule:: galaxy.job_metrics - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.job_metrics.collectl - galaxy.job_metrics.instrumenters + galaxy.job_metrics.collectl + galaxy.job_metrics.instrumenters Submodules ---------- @@ -21,8 +22,6 @@ galaxy.job\_metrics.formatting module ------------------------------------- .. automodule:: galaxy.job_metrics.formatting - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst index 7ec9a937d81..849f193f77e 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -2,9 +2,9 @@ galaxy.jobs.actions package =========================== .. automodule:: galaxy.jobs.actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.jobs.actions.post module ------------------------------- .. automodule:: galaxy.jobs.actions.post - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index 900a19d1680..bb09c301003 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -2,19 +2,20 @@ galaxy.jobs package =================== .. automodule:: galaxy.jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.jobs.actions - galaxy.jobs.rules - galaxy.jobs.runners - galaxy.jobs.splitters + galaxy.jobs.actions + galaxy.jobs.rules + galaxy.jobs.runners + galaxy.jobs.splitters Submodules ---------- @@ -23,64 +24,62 @@ galaxy.jobs.command\_factory module ----------------------------------- .. automodule:: galaxy.jobs.command_factory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.dynamic\_tool\_destination module --------------------------------------------- .. automodule:: galaxy.jobs.dynamic_tool_destination - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.handler module -------------------------- .. automodule:: galaxy.jobs.handler - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.manager module -------------------------- .. automodule:: galaxy.jobs.manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.mapper module ------------------------- .. automodule:: galaxy.jobs.mapper - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.rule\_helper module ------------------------------- .. automodule:: galaxy.jobs.rule_helper - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.stock\_rules module ------------------------------- .. automodule:: galaxy.jobs.stock_rules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.transfer\_manager module ------------------------------------ .. automodule:: galaxy.jobs.transfer_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.rules.rst b/doc/source/lib/galaxy.jobs.rules.rst index 29f0510c5a9..6a52cab0889 100644 --- a/doc/source/lib/galaxy.jobs.rules.rst +++ b/doc/source/lib/galaxy.jobs.rules.rst @@ -2,7 +2,6 @@ galaxy.jobs.rules package ========================= .. automodule:: galaxy.jobs.rules - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index 937787d586c..41419f7b41a 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -2,17 +2,18 @@ galaxy.jobs.runners package =========================== .. automodule:: galaxy.jobs.runners - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.jobs.runners.state_handlers - galaxy.jobs.runners.util + galaxy.jobs.runners.state_handlers + galaxy.jobs.runners.util Submodules ---------- @@ -21,104 +22,102 @@ galaxy.jobs.runners.chronos module ---------------------------------- .. automodule:: galaxy.jobs.runners.chronos - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.cli module ------------------------------ .. automodule:: galaxy.jobs.runners.cli - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.condor module --------------------------------- .. automodule:: galaxy.jobs.runners.condor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.drmaa module -------------------------------- .. automodule:: galaxy.jobs.runners.drmaa - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.godocker module ----------------------------------- .. automodule:: galaxy.jobs.runners.godocker - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.kubernetes module ------------------------------------- .. automodule:: galaxy.jobs.runners.kubernetes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.local module -------------------------------- .. automodule:: galaxy.jobs.runners.local - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.pbs module ------------------------------ .. automodule:: galaxy.jobs.runners.pbs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.pulsar module --------------------------------- .. automodule:: galaxy.jobs.runners.pulsar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.slurm module -------------------------------- .. automodule:: galaxy.jobs.runners.slurm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.state\_handler\_factory module -------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handler_factory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.tasks module -------------------------------- .. automodule:: galaxy.jobs.runners.tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.univa module -------------------------------- .. automodule:: galaxy.jobs.runners.univa - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst index 1e71d735662..f1b37fe7acb 100644 --- a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -2,9 +2,9 @@ galaxy.jobs.runners.state\_handlers package =========================================== .. automodule:: galaxy.jobs.runners.state_handlers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.jobs.runners.state\_handlers.resubmit module --------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handlers.resubmit - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst index 11813c7a0d1..b931eb319b4 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -2,9 +2,9 @@ galaxy.jobs.runners.util.cli.job package ======================================== .. automodule:: galaxy.jobs.runners.util.cli.job - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,30 @@ galaxy.jobs.runners.util.cli.job.lsf module ------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.lsf - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.cli.job.slurm module --------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.cli.job.slurm\_torque module ----------------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.cli.job.torque module ---------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.torque - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst index dadd626718b..4813fc60084 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -2,17 +2,18 @@ galaxy.jobs.runners.util.cli package ==================================== .. automodule:: galaxy.jobs.runners.util.cli - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.jobs.runners.util.cli.job - galaxy.jobs.runners.util.cli.shell + galaxy.jobs.runners.util.cli.job + galaxy.jobs.runners.util.cli.shell Submodules ---------- @@ -21,8 +22,6 @@ galaxy.jobs.runners.util.cli.factory module ------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.factory - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst index 42e5c7ffe73..2e0017399b1 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -2,9 +2,9 @@ galaxy.jobs.runners.util.cli.shell package ========================================== .. automodule:: galaxy.jobs.runners.util.cli.shell - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.jobs.runners.util.cli.shell.local module ----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.local - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.cli.shell.rsh module --------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.rsh - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst index 823ea51ac3e..86bcd81aba2 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.condor.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -2,7 +2,6 @@ galaxy.jobs.runners.util.condor package ======================================= .. automodule:: galaxy.jobs.runners.util.condor - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst index 28119d40f7d..ab905e51043 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -2,7 +2,6 @@ galaxy.jobs.runners.util.job\_script package ============================================ .. automodule:: galaxy.jobs.runners.util.job_script - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst index 702f20bb351..b0b138fd8a2 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -2,18 +2,19 @@ galaxy.jobs.runners.util package ================================ .. automodule:: galaxy.jobs.runners.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.jobs.runners.util.cli - galaxy.jobs.runners.util.condor - galaxy.jobs.runners.util.job_script + galaxy.jobs.runners.util.cli + galaxy.jobs.runners.util.condor + galaxy.jobs.runners.util.job_script Submodules ---------- @@ -22,48 +23,46 @@ galaxy.jobs.runners.util.env module ----------------------------------- .. automodule:: galaxy.jobs.runners.util.env - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.external module ---------------------------------------- .. automodule:: galaxy.jobs.runners.util.external - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.kill module ------------------------------------ .. automodule:: galaxy.jobs.runners.util.kill - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.process\_groups module ----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.process_groups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.pykube\_util module -------------------------------------------- .. automodule:: galaxy.jobs.runners.util.pykube_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.runners.util.sudo module ------------------------------------ .. automodule:: galaxy.jobs.runners.util.sudo - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst index d8af934e1be..6818d339d28 100644 --- a/doc/source/lib/galaxy.jobs.splitters.rst +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -2,9 +2,9 @@ galaxy.jobs.splitters package ============================= .. automodule:: galaxy.jobs.splitters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.jobs.splitters.basic module ---------------------------------- .. automodule:: galaxy.jobs.splitters.basic - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.jobs.splitters.multi module ---------------------------------- .. automodule:: galaxy.jobs.splitters.multi - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index 72f6ad26206..4d9b071fedc 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -2,9 +2,9 @@ galaxy.managers package ======================= .. automodule:: galaxy.managers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,296 +13,302 @@ galaxy.managers.annotatable module ---------------------------------- .. automodule:: galaxy.managers.annotatable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.api\_keys module -------------------------------- .. automodule:: galaxy.managers.api_keys - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.base module --------------------------- .. automodule:: galaxy.managers.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.citations module -------------------------------- .. automodule:: galaxy.managers.citations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.cloud module ---------------------------- .. automodule:: galaxy.managers.cloud - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.cloudauthzs module ---------------------------------- .. automodule:: galaxy.managers.cloudauthzs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.collections module ---------------------------------- .. automodule:: galaxy.managers.collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.collections\_util module ---------------------------------------- .. automodule:: galaxy.managers.collections_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.configuration module ------------------------------------ .. automodule:: galaxy.managers.configuration - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.containers module --------------------------------- .. automodule:: galaxy.managers.containers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.context module ------------------------------ .. automodule:: galaxy.managers.context - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.datasets module ------------------------------- .. automodule:: galaxy.managers.datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.deletable module -------------------------------- .. automodule:: galaxy.managers.deletable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.executables module ---------------------------------- .. automodule:: galaxy.managers.executables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.folders module ------------------------------ .. automodule:: galaxy.managers.folders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.hdas module --------------------------- .. automodule:: galaxy.managers.hdas - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.hdcas module ---------------------------- .. automodule:: galaxy.managers.hdcas - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.histories module -------------------------------- .. automodule:: galaxy.managers.histories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.history\_contents module ---------------------------------------- .. automodule:: galaxy.managers.history_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.interactivetool module -------------------------------------- .. automodule:: galaxy.managers.interactivetool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.jobs module --------------------------- .. automodule:: galaxy.managers.jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.lddas module ---------------------------- .. automodule:: galaxy.managers.lddas - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.libraries module -------------------------------- .. automodule:: galaxy.managers.libraries - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.library\_datasets module ---------------------------------------- .. automodule:: galaxy.managers.library_datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.managers.licenses module +------------------------------- + +.. automodule:: galaxy.managers.licenses + :members: + :undoc-members: + :show-inheritance: galaxy.managers.markdown\_parse module -------------------------------------- .. automodule:: galaxy.managers.markdown_parse - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.markdown\_util module ------------------------------------- .. automodule:: galaxy.managers.markdown_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.pages module ---------------------------- .. automodule:: galaxy.managers.pages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.ratable module ------------------------------ .. automodule:: galaxy.managers.ratable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.rbac\_secured module ------------------------------------ .. automodule:: galaxy.managers.rbac_secured - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.roles module ---------------------------- .. automodule:: galaxy.managers.roles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.secured module ------------------------------ .. automodule:: galaxy.managers.secured - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.sharable module ------------------------------- .. automodule:: galaxy.managers.sharable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.taggable module ------------------------------- .. automodule:: galaxy.managers.taggable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.tools module ---------------------------- .. automodule:: galaxy.managers.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.users module ---------------------------- .. automodule:: galaxy.managers.users - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.visualizations module ------------------------------------- .. automodule:: galaxy.managers.visualizations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.managers.workflows module -------------------------------- .. automodule:: galaxy.managers.workflows - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.metadata.rst b/doc/source/lib/galaxy.metadata.rst index 43f1a71c0e2..6ffb662b2fe 100644 --- a/doc/source/lib/galaxy.metadata.rst +++ b/doc/source/lib/galaxy.metadata.rst @@ -2,9 +2,9 @@ galaxy.metadata package ======================= .. automodule:: galaxy.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.metadata.set\_metadata module ------------------------------------ .. automodule:: galaxy.metadata.set_metadata - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.dataset_collections.rst b/doc/source/lib/galaxy.model.dataset_collections.rst index 688cd5e87e7..4c0a0debd60 100644 --- a/doc/source/lib/galaxy.model.dataset_collections.rst +++ b/doc/source/lib/galaxy.model.dataset_collections.rst @@ -2,16 +2,17 @@ galaxy.model.dataset\_collections package ========================================= .. automodule:: galaxy.model.dataset_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.model.dataset_collections.types + galaxy.model.dataset_collections.types Submodules ---------- @@ -20,48 +21,46 @@ galaxy.model.dataset\_collections.builder module ------------------------------------------------ .. automodule:: galaxy.model.dataset_collections.builder - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.matching module ------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.matching - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.registry module ------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.registry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.structure module -------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.structure - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.subcollections module ------------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.subcollections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.type\_description module ---------------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.type_description - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.dataset_collections.types.rst b/doc/source/lib/galaxy.model.dataset_collections.types.rst index e13a8a83e88..c4d4e12a399 100644 --- a/doc/source/lib/galaxy.model.dataset_collections.types.rst +++ b/doc/source/lib/galaxy.model.dataset_collections.types.rst @@ -2,9 +2,9 @@ galaxy.model.dataset\_collections.types package =============================================== .. automodule:: galaxy.model.dataset_collections.types - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.model.dataset\_collections.types.list module --------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.types.list - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.dataset\_collections.types.paired module ----------------------------------------------------- .. automodule:: galaxy.model.dataset_collections.types.paired - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 2d56bcc2878..0a8f979a501 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -2,16 +2,17 @@ galaxy.model.migrate package ============================ .. automodule:: galaxy.model.migrate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.model.migrate.versions + galaxy.model.migrate.versions Submodules ---------- @@ -20,8 +21,6 @@ galaxy.model.migrate.check module --------------------------------- .. automodule:: galaxy.model.migrate.check - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrate.versions.rst b/doc/source/lib/galaxy.model.migrate.versions.rst index c2a33b575e3..576ea6fb2a4 100644 --- a/doc/source/lib/galaxy.model.migrate.versions.rst +++ b/doc/source/lib/galaxy.model.migrate.versions.rst @@ -2,9 +2,9 @@ galaxy.model.migrate.versions package ===================================== .. automodule:: galaxy.model.migrate.versions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,1328 +13,1374 @@ galaxy.model.migrate.versions.0001\_initial\_tables module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0001_initial_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0002\_metadata\_file\_table module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0002_metadata_file_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0003\_security\_and\_libraries module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0003_security_and_libraries - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0004\_indexes\_and\_defaults module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0004_indexes_and_defaults - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0005\_cleanup\_datasets\_fix module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0005_cleanup_datasets_fix - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0006\_change\_qual\_datatype module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0006_change_qual_datatype - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0007\_sharing\_histories module ------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0007_sharing_histories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0008\_galaxy\_forms module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0008_galaxy_forms - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0009\_request\_table module --------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0009_request_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0010\_hda\_display\_at\_authz\_table module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0010_hda_display_at_authz_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0011\_v0010\_mysql\_index\_fix module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0011_v0010_mysql_index_fix - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0012\_user\_address module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0012_user_address - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0013\_change\_lib\_item\_templates\_to\_forms module ---------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0014\_pages module ------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0014_pages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0015\_tagging module -------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0015_tagging - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0016\_v0015\_mysql\_index\_fix module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0016_v0015_mysql_index_fix - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0017\_library\_item\_indexes module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0017_library_item_indexes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0018\_ordered\_tags\_and\_page\_tags module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0019\_request\_library\_folder module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0019_request_library_folder - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0020\_library\_upload\_job module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0020_library_upload_job - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0021\_user\_prefs module ------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0021_user_prefs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0022\_visualization\_tables module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0022_visualization_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0023\_page\_published\_and\_deleted\_columns module --------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0023_page_published_and_deleted_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0024\_page\_slug\_unique\_constraint module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0024_page_slug_unique_constraint - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0025\_user\_info module ----------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0025_user_info - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0026\_cloud\_tables module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0026_cloud_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0027\_request\_events module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0027_request_events - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0028\_external\_metadata\_file\_override module ----------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0028_external_metadata_file_override - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0029\_user\_actions module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0029_user_actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0030\_history\_slug\_column module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0030_history_slug_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0031\_community\_and\_workflow\_tags module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0031_community_and_workflow_tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0032\_stored\_workflow\_slug\_column module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0032_stored_workflow_slug_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0033\_published\_cols\_for\_histories\_and\_workflows module ------------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0034\_page\_user\_share\_association module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0034_page_user_share_association - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0035\_item\_annotations\_and\_workflow\_step\_tags module --------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0036\_add\_deleted\_column\_to\_library\_template\_assoc\_tables module ----------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0037\_samples\_library module ----------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0037_samples_library - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0038\_add\_inheritable\_column\_to\_library\_template\_assoc\_tables module --------------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0039\_add\_synopsis\_column\_to\_library\_table module ------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0040\_page\_annotations module ------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0040_page_annotations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0041\_workflow\_invocation module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0041_workflow_invocation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0042\_workflow\_invocation\_fix module -------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0042_workflow_invocation_fix - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0043\_visualization\_sharing\_tagging\_annotating module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0044\_add\_notify\_column\_to\_request\_table module ---------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0044_add_notify_column_to_request_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0045\_request\_type\_permissions\_table module ---------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0045_request_type_permissions_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0046\_post\_job\_actions module ------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0046_post_job_actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0047\_job\_table\_user\_id\_column module ----------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0047_job_table_user_id_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0048\_dataset\_instance\_state\_column module --------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0048_dataset_instance_state_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0049\_api\_keys\_table module ----------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0049_api_keys_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0050\_drop\_cloud\_tables module -------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0050_drop_cloud_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0051\_imported\_col\_for\_jobs\_table module -------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0051_imported_col_for_jobs_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0052\_sample\_dataset\_table module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0052_sample_dataset_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0053\_item\_ratings module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0053_item_ratings - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0054\_visualization\_dbkey module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0054_visualization_dbkey - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0055\_add\_pja\_assoc\_for\_jobs module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0056\_workflow\_outputs module ------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0056_workflow_outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0057\_request\_notify module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0057_request_notify - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0058\_history\_import\_export module ------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0058_history_import_export - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0059\_sample\_dataset\_file\_path module ---------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0059_sample_dataset_file_path - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0060\_history\_archive\_import module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0060_history_archive_import - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0061\_tasks module ------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0061_tasks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0062\_user\_openid\_table module -------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0062_user_openid_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0063\_sequencer\_table module ----------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0063_sequencer_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0064\_add\_run\_and\_sample\_run\_association\_tables module ------------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0065\_add\_name\_to\_form\_fields\_and\_values module ----------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0066\_deferred\_job\_and\_transfer\_job\_tables module ------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0067\_populate\_sequencer\_table module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0067_populate_sequencer_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0068\_rename\_sequencer\_to\_external\_services module ------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0069\_rename\_sequencer\_form\_type module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0069_rename_sequencer_form_type - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0070\_add\_info\_column\_to\_deferred\_job\_table module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0071\_add\_history\_and\_workflow\_to\_sample module ---------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0072\_add\_pid\_and\_socket\_columns\_to\_transfer\_job\_table module --------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0073\_add\_ldda\_to\_implicit\_conversion\_table module ------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0074\_add\_purged\_column\_to\_library\_dataset\_table module ------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0075\_add\_subindex\_column\_to\_run\_table module -------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0076\_fix\_form\_values\_data\_corruption module ------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0076_fix_form_values_data_corruption - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0077\_create\_tool\_tag\_association\_table module -------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0077_create_tool_tag_association_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0078\_add\_columns\_for\_disk\_usage\_accounting module ------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0079\_input\_library\_to\_job\_table module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0079_input_library_to_job_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0080\_quota\_tables module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0080_quota_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0081\_add\_tool\_version\_to\_hda\_ldda module ---------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0082\_add\_tool\_shed\_repository\_table module ----------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0082_add_tool_shed_repository_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0083\_add\_prepare\_files\_to\_task module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0083_add_prepare_files_to_task - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0084\_add\_ldda\_id\_to\_implicit\_conversion\_table module ----------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0085\_add\_task\_info module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0085_add_task_info - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0086\_add\_tool\_shed\_repository\_table\_columns module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0087\_tool\_id\_guid\_map\_table module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0087_tool_id_guid_map_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0088\_add\_installed\_changeset\_revison\_column module ------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0089\_add\_object\_store\_id\_columns module -------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0089_add_object_store_id_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0090\_add\_tool\_shed\_repository\_table\_columns module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0091\_add\_tool\_version\_tables module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0091_add_tool_version_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0092\_add\_migrate\_tools\_table module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0092_add_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0093\_add\_job\_params\_col module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0093_add_job_params_col - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0094\_add\_job\_handler\_col module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0094_add_job_handler_col - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0095\_hda\_subsets module ------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0095_hda_subsets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0096\_openid\_provider module ----------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0096_openid_provider - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0097\_add\_ctx\_rev\_column module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0097_add_ctx_rev_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0098\_genome\_index\_tool\_data\_table module --------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0098_genome_index_tool_data_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0099\_add\_tool\_dependency\_table module ----------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0099_add_tool_dependency_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0100\_alter\_tool\_dependency\_table\_version\_column module ------------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0101\_drop\_installed\_changeset\_revision\_column module --------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0102\_add\_tool\_dependency\_status\_columns module --------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0103\_add\_tool\_shed\_repository\_status\_columns module --------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0104\_update\_genome\_downloader\_job\_parameters module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0105\_add\_cleanup\_event\_table module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0105_add_cleanup_event_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0106\_add\_missing\_indexes module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0106_add_missing_indexes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0107\_add\_exit\_code\_to\_job\_and\_task module ------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0108\_add\_extended\_metadata module ------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0108_add_extended_metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0109\_add\_repository\_dependency\_tables module ------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0109_add_repository_dependency_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0110\_add\_dataset\_uuid module ------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0110_add_dataset_uuid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0111\_add\_job\_destinations module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0111_add_job_destinations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0112\_add\_data\_manager\_history\_association\_and\_data\_manager\_job\_association\_tables module --------------------------------------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0113\_update\_migrate\_tools\_table module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0113_update_migrate_tools_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0114\_update\_migrate\_tools\_table\_again module ------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0114_update_migrate_tools_table_again - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0115\_longer\_user\_password\_field module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0115_longer_user_password_field - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0116\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module ----------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0117\_add\_user\_activation module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0117_add_user_activation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0118\_add\_hda\_extended\_metadata module ----------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0118_add_hda_extended_metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0119\_job\_metrics module ------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0119_job_metrics - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0120\_dataset\_collections module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0120_dataset_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0121\_workflow\_uuids module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0121_workflow_uuids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0122\_grow\_mysql\_blobs module ------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0122_grow_mysql_blobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0123\_add\_workflow\_request\_tables module ------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0123_add_workflow_request_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0124\_job\_state\_history module -------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0124_job_state_history - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0125\_workflow\_step\_tracking module ------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0125_workflow_step_tracking - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0126\_password\_reset module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0126_password_reset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0127\_output\_collection\_adjustments module -------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0127_output_collection_adjustments - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0128\_session\_timeout module ----------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0128_session_timeout - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0129\_job\_external\_output\_metadata\_validity module ------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0129_job_external_output_metadata_validity - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0130\_change\_pref\_datatype module ----------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0130_change_pref_datatype - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0131\_subworkflow\_and\_input\_parameter\_modules module -------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0132\_add\_lastpasswordchange\_to\_user module ---------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0133\_add\_dependency\_column\_to\_job module --------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0133_add_dependency_column_to_job - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0134\_hda\_set\_deleted\_if\_purged module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0135\_add\_library\_tags module ------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0135_add_library_tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0136\_collection\_and\_workflow\_state module --------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0136_collection_and_workflow_state - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0137\_add\_copied\_from\_job\_id\_column module ----------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0137_add_copied_from_job_id_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0138\_add\_hda\_version module ------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0138_add_hda_version - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0139\_add\_history\_dataset\_association\_history\_table module --------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0140\_add\_dataset\_version\_to\_job\_to\_input\_dataset\_association\_table module ----------------------------------------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0141\_add\_oidc\_tables module ------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0141_add_oidc_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0142\_change\_numeric\_metric\_precision module ----------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0142_change_numeric_metric_precision - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0143\_add\_cloudauthz\_tables module ------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0143_add_cloudauthz_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0144\_add\_cleanup\_event\_user\_table module --------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0144_add_cleanup_event_user_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0145\_add\_workflow\_step\_input module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0145_add_workflow_step_input - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0146\_workflow\_paths module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0146_workflow_paths - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0147\_job\_messages module -------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0147_job_messages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0148\_add\_checksum\_table module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0148_add_checksum_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0149\_dynamic\_tools module --------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0149_dynamic_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0150\_add\_create\_time\_field\_for\_cloudauthz module ------------------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0151\_add\_worker\_process module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0151_add_worker_process - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0152\_add\_metadata\_file\_uuid module -------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0152_add_metadata_file_uuid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0153\_add\_custos\_authnz\_token\_table module ---------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0153_add_custos_authnz_token_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0154\_created\_from\_basename module ------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0154_created_from_basename - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0155\_job\_galaxy\_version module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0155_job_galaxy_version - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0156\_add\_interactivetools module ---------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0156_add_interactivetools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0157\_rework\_dataset\_validation module ---------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0157_rework_dataset_validation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0158\_workflow\_reports module ------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0158_workflow_reports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0159\_add\_job\_external\_id\_index module ------------------------------------------------------------------------ .. automodule:: galaxy.model.migrate.versions.0159_add_job_external_id_index - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0160\_hda\_set\_deleted\_if\_purged\_again module ------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0161\_add\_workflow\_invocation\_output\_table module ----------------------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0162\_job\_only\_pjas module ---------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0162_job_only_pjas - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0163\_worker\_process\_pid module --------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0163_worker_process_pid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0164\_page\_format module ------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0164_page_format - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.0165\_add\_content\_update\_time module --------------------------------------------------------------------- .. automodule:: galaxy.model.migrate.versions.0165_add_content_update_time - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0166\_job\_state\_summary\_view module +-------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0166_job_state_summary_view + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0167\_add\_job\_to\_input\_dataset\_collection\_element\_association module +--------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0168\_stored\_workflow\_hidden\_col module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0168_stored_workflow_hidden_col + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0169\_add\_missing\_indexes module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0169_add_missing_indexes + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0170\_add\_more\_missing\_indexes module +---------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0170_add_more_missing_indexes + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0171\_schemaorg\_metadata module +-------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0171_schemaorg_metadata + :members: + :undoc-members: + :show-inheritance: galaxy.model.migrate.versions.util module ----------------------------------------- .. automodule:: galaxy.model.migrate.versions.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index c42fe0be8a6..726abd3e20a 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -2,9 +2,9 @@ galaxy.model.orm package ======================== .. automodule:: galaxy.model.orm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,22 @@ galaxy.model.orm.engine\_factory module --------------------------------------- .. automodule:: galaxy.model.orm.engine_factory - :members: - :undoc-members: - :show-inheritance: - -galaxy.model.orm.logging\_connection\_proxy module --------------------------------------------------- - -.. automodule:: galaxy.model.orm.logging_connection_proxy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.orm.now module --------------------------- .. automodule:: galaxy.model.orm.now - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.orm.scripts module ------------------------------- .. automodule:: galaxy.model.orm.scripts - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index 7d2e6e33958..ec0c3266eb8 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -2,20 +2,22 @@ galaxy.model package ==================== .. automodule:: galaxy.model - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.model.dataset_collections - galaxy.model.migrate - galaxy.model.orm - galaxy.model.store - galaxy.model.tool_shed_install + galaxy.model.dataset_collections + galaxy.model.migrate + galaxy.model.orm + galaxy.model.store + galaxy.model.tool_shed_install + galaxy.model.view Submodules ---------- @@ -24,88 +26,86 @@ galaxy.model.base module ------------------------ .. automodule:: galaxy.model.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.custom\_types module --------------------------------- .. automodule:: galaxy.model.custom_types - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.database\_heartbeat module --------------------------------------- .. automodule:: galaxy.model.database_heartbeat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.item\_attrs module ------------------------------- .. automodule:: galaxy.model.item_attrs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.mapping module --------------------------- .. automodule:: galaxy.model.mapping - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.metadata module ---------------------------- .. automodule:: galaxy.model.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.none\_like module ------------------------------ .. automodule:: galaxy.model.none_like - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.search module -------------------------- .. automodule:: galaxy.model.search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.security module ---------------------------- .. automodule:: galaxy.model.security - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.tags module ------------------------ .. automodule:: galaxy.model.tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.triggers module ---------------------------- .. automodule:: galaxy.model.triggers - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.store.rst b/doc/source/lib/galaxy.model.store.rst index 1ab8db02595..84e3b2fcb3f 100644 --- a/doc/source/lib/galaxy.model.store.rst +++ b/doc/source/lib/galaxy.model.store.rst @@ -2,9 +2,9 @@ galaxy.model.store package ========================== .. automodule:: galaxy.model.store - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.model.store.build\_objects module ---------------------------------------- .. automodule:: galaxy.model.store.build_objects - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.model.store.discover module ---------------------------------- .. automodule:: galaxy.model.store.discover - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst index fdd56b65033..1c8d6340e27 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -2,9 +2,9 @@ galaxy.model.tool\_shed\_install.migrate package ================================================ .. automodule:: galaxy.model.tool_shed_install.migrate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.model.tool\_shed\_install.migrate.check module ----------------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.migrate.check - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index d074ead1e89..464c6ec817e 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -2,16 +2,17 @@ galaxy.model.tool\_shed\_install package ======================================== .. automodule:: galaxy.model.tool_shed_install - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.model.tool_shed_install.migrate + galaxy.model.tool_shed_install.migrate Submodules ---------- @@ -20,8 +21,6 @@ galaxy.model.tool\_shed\_install.mapping module ----------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.mapping - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.view.rst b/doc/source/lib/galaxy.model.view.rst new file mode 100644 index 00000000000..98c26055bc8 --- /dev/null +++ b/doc/source/lib/galaxy.model.view.rst @@ -0,0 +1,18 @@ +galaxy.model.view package +========================= + +.. automodule:: galaxy.model.view + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.view.utils module +------------------------------ + +.. automodule:: galaxy.model.view.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index c3937f5ca1b..61b92f89d14 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -2,9 +2,9 @@ galaxy.objectstore package ========================== .. automodule:: galaxy.objectstore - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,56 +13,54 @@ galaxy.objectstore.azure\_blob module ------------------------------------- .. automodule:: galaxy.objectstore.azure_blob - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.cloud module ------------------------------- .. automodule:: galaxy.objectstore.cloud - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.irods module ------------------------------- .. automodule:: galaxy.objectstore.irods - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.pithos module -------------------------------- .. automodule:: galaxy.objectstore.pithos - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.pulsar module -------------------------------- .. automodule:: galaxy.objectstore.pulsar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.s3 module ---------------------------- .. automodule:: galaxy.objectstore.s3 - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.objectstore.s3\_multipart\_upload module ----------------------------------------------- .. automodule:: galaxy.objectstore.s3_multipart_upload - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst index 90031e56aad..86451bafb5e 100644 --- a/doc/source/lib/galaxy.openid.rst +++ b/doc/source/lib/galaxy.openid.rst @@ -2,9 +2,9 @@ galaxy.openid package ===================== .. automodule:: galaxy.openid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.openid.openid\_manager module ------------------------------------ .. automodule:: galaxy.openid.openid_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.openid.providers module ------------------------------ .. automodule:: galaxy.openid.providers - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.quota.rst b/doc/source/lib/galaxy.quota.rst index 36802033ce1..ac75c58da46 100644 --- a/doc/source/lib/galaxy.quota.rst +++ b/doc/source/lib/galaxy.quota.rst @@ -2,7 +2,6 @@ galaxy.quota package ==================== .. automodule:: galaxy.quota - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index 3fae54d86bb..8c559a9dff6 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -2,48 +2,50 @@ galaxy package ============== .. automodule:: galaxy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.actions - galaxy.auth - galaxy.authnz - galaxy.config - galaxy.containers - galaxy.datatypes - galaxy.dependencies - galaxy.eggs - galaxy.exceptions - galaxy.forms - galaxy.job_execution - galaxy.job_metrics - galaxy.jobs - galaxy.managers - galaxy.metadata - galaxy.model - galaxy.objectstore - galaxy.openid - galaxy.quota - galaxy.security - galaxy.selenium - galaxy.tool_shed - galaxy.tool_util - galaxy.tools - galaxy.tours - galaxy.util - galaxy.visualization - galaxy.web - galaxy.web_stack - galaxy.webapps - galaxy.webhooks - galaxy.work - galaxy.workflow + galaxy.actions + galaxy.auth + galaxy.authnz + galaxy.config + galaxy.containers + galaxy.datatypes + galaxy.dependencies + galaxy.eggs + galaxy.exceptions + galaxy.files + galaxy.forms + galaxy.job_execution + galaxy.job_metrics + galaxy.jobs + galaxy.managers + galaxy.metadata + galaxy.model + galaxy.objectstore + galaxy.openid + galaxy.quota + galaxy.security + galaxy.selenium + galaxy.tool_shed + galaxy.tool_util + galaxy.tools + galaxy.tours + galaxy.util + galaxy.visualization + galaxy.web + galaxy.web_stack + galaxy.webapps + galaxy.webhooks + galaxy.work + galaxy.workflow Submodules ---------- @@ -52,48 +54,46 @@ galaxy.app module ----------------- .. automodule:: galaxy.app - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.config\_watchers module ------------------------------ .. automodule:: galaxy.config_watchers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.main module ------------------ .. automodule:: galaxy.main - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.queue\_worker module --------------------------- .. automodule:: galaxy.queue_worker - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.queues module -------------------- .. automodule:: galaxy.queues - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.version module --------------------- .. automodule:: galaxy.version - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index 351ecf61547..62e9f4d264a 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -2,9 +2,9 @@ galaxy.security package ======================= .. automodule:: galaxy.security - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.security.idencoding module --------------------------------- .. automodule:: galaxy.security.idencoding - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.security.passwords module -------------------------------- .. automodule:: galaxy.security.passwords - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.security.validate\_user\_input module -------------------------------------------- .. automodule:: galaxy.security.validate_user_input - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.selenium.rst b/doc/source/lib/galaxy.selenium.rst index db4f0adfa64..7d495ad8f3c 100644 --- a/doc/source/lib/galaxy.selenium.rst +++ b/doc/source/lib/galaxy.selenium.rst @@ -2,16 +2,18 @@ galaxy.selenium package ======================= .. automodule:: galaxy.selenium - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.selenium.scripts + galaxy.selenium.scripts + galaxy.selenium.toolbox Submodules ---------- @@ -20,64 +22,62 @@ galaxy.selenium.cli module -------------------------- .. automodule:: galaxy.selenium.cli - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.components module --------------------------------- .. automodule:: galaxy.selenium.components - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.data module --------------------------- .. automodule:: galaxy.selenium.data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.driver\_factory module -------------------------------------- .. automodule:: galaxy.selenium.driver_factory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.has\_driver module ---------------------------------- .. automodule:: galaxy.selenium.has_driver - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.navigates\_galaxy module ---------------------------------------- .. automodule:: galaxy.selenium.navigates_galaxy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.sizzle module ----------------------------- .. automodule:: galaxy.selenium.sizzle - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.selenium.smart\_components module ---------------------------------------- .. automodule:: galaxy.selenium.smart_components - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.selenium.scripts.rst b/doc/source/lib/galaxy.selenium.scripts.rst index 9b1ca62862e..0e216657687 100644 --- a/doc/source/lib/galaxy.selenium.scripts.rst +++ b/doc/source/lib/galaxy.selenium.scripts.rst @@ -2,9 +2,9 @@ galaxy.selenium.scripts package =============================== .. automodule:: galaxy.selenium.scripts - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.selenium.scripts.dump\_tour module ----------------------------------------- .. automodule:: galaxy.selenium.scripts.dump_tour - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.selenium.toolbox.rst b/doc/source/lib/galaxy.selenium.toolbox.rst new file mode 100644 index 00000000000..32e362a871e --- /dev/null +++ b/doc/source/lib/galaxy.selenium.toolbox.rst @@ -0,0 +1,18 @@ +galaxy.selenium.toolbox package +=============================== + +.. automodule:: galaxy.selenium.toolbox + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.selenium.toolbox.filters module +-------------------------------------- + +.. automodule:: galaxy.selenium.toolbox.filters + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.datatypes.rst index 7022dd4009f..74f341b6a7b 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.datatypes.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.datatypes.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.datatypes package =================================================== .. automodule:: galaxy.tool_shed.galaxy_install.datatypes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.datatypes.custom\_datatype\_manager module ---------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.metadata.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.metadata.rst index 26b4274a3c9..7f1685f4ff9 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.metadata.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.metadata.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.metadata package ================================================== .. automodule:: galaxy.tool_shed.galaxy_install.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.metadata.installed\_repository\_metadata\_mana ------------------------------------------------------------------------------------------ .. automodule:: galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst index e7ff85c03c0..937d4510298 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst @@ -2,16 +2,17 @@ galaxy.tool\_shed.galaxy\_install.migrate package ================================================= .. automodule:: galaxy.tool_shed.galaxy_install.migrate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_shed.galaxy_install.migrate.versions + galaxy.tool_shed.galaxy_install.migrate.versions Submodules ---------- @@ -20,16 +21,14 @@ galaxy.tool\_shed.galaxy\_install.migrate.check module ------------------------------------------------------ .. automodule:: galaxy.tool_shed.galaxy_install.migrate.check - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.common module ------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.common - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst index 3268a6869d0..dea11083e28 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.migrate.versions package ========================================================== .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,96 +13,94 @@ galaxy.tool\_shed.galaxy\_install.migrate.versions.0001\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0002\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0003\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0004\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0005\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0006\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0007\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0008\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0009\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0010\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0011\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.migrate.versions.0012\_tools module --------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.repository_dependencies.rst index 9056483a72c..0f21a7e9442 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.repository_dependencies.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.repository_dependencies.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.repository\_dependencies package ================================================================== .. automodule:: galaxy.tool_shed.galaxy_install.repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.tool\_shed.galaxy\_install.repository\_dependencies.repository\_dependenc ------------------------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst index 080cd61bcb5..e0cbc6d5ac7 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst @@ -2,21 +2,22 @@ galaxy.tool\_shed.galaxy\_install package ========================================= .. automodule:: galaxy.tool_shed.galaxy_install - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_shed.galaxy_install.datatypes - galaxy.tool_shed.galaxy_install.metadata - galaxy.tool_shed.galaxy_install.migrate - galaxy.tool_shed.galaxy_install.repository_dependencies - galaxy.tool_shed.galaxy_install.tool_dependencies - galaxy.tool_shed.galaxy_install.tools + galaxy.tool_shed.galaxy_install.datatypes + galaxy.tool_shed.galaxy_install.metadata + galaxy.tool_shed.galaxy_install.migrate + galaxy.tool_shed.galaxy_install.repository_dependencies + galaxy.tool_shed.galaxy_install.tool_dependencies + galaxy.tool_shed.galaxy_install.tools Submodules ---------- @@ -25,32 +26,30 @@ galaxy.tool\_shed.galaxy\_install.install\_manager module --------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.install_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.installed\_repository\_manager module ----------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.installed_repository_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_migration\_manager module ----------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_migration_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.update\_repository\_manager module -------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.update_repository_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst index de007f7a05a..78eb081a3cd 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe package =================================================================== .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,48 +13,46 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader --------------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module ------------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module --------------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module ---------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module -------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module ------------------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst index 97f9c7abde8..f577255f4ea 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.tool_dependencies.rst @@ -2,16 +2,17 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies package ============================================================ .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_shed.galaxy_install.tool_dependencies.recipe + galaxy.tool_shed.galaxy_install.tool_dependencies.recipe Submodules ---------- @@ -20,8 +21,6 @@ galaxy.tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module ------------------------------------------------------------------------ .. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.tools.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.tools.rst index c21e1ef5123..362501c5c54 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.tools.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.tools.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.galaxy\_install.tools package =============================================== .. automodule:: galaxy.tool_shed.galaxy_install.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.tool\_shed.galaxy\_install.tools.data\_manager module ------------------------------------------------------------ .. automodule:: galaxy.tool_shed.galaxy_install.tools.data_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.galaxy\_install.tools.tool\_panel\_manager module ------------------------------------------------------------------- .. automodule:: galaxy.tool_shed.galaxy_install.tools.tool_panel_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.metadata.rst b/doc/source/lib/galaxy.tool_shed.metadata.rst index 4ad0d660185..7a89d2bf041 100644 --- a/doc/source/lib/galaxy.tool_shed.metadata.rst +++ b/doc/source/lib/galaxy.tool_shed.metadata.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.metadata package ================================== .. automodule:: galaxy.tool_shed.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.tool\_shed.metadata.metadata\_generator module ----------------------------------------------------- .. automodule:: galaxy.tool_shed.metadata.metadata_generator - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.rst b/doc/source/lib/galaxy.tool_shed.rst index 16b905d3498..afc644f3e94 100644 --- a/doc/source/lib/galaxy.tool_shed.rst +++ b/doc/source/lib/galaxy.tool_shed.rst @@ -2,19 +2,20 @@ galaxy.tool\_shed package ========================= .. automodule:: galaxy.tool_shed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_shed.galaxy_install - galaxy.tool_shed.metadata - galaxy.tool_shed.tools - galaxy.tool_shed.util + galaxy.tool_shed.galaxy_install + galaxy.tool_shed.metadata + galaxy.tool_shed.tools + galaxy.tool_shed.util Submodules ---------- @@ -23,16 +24,14 @@ galaxy.tool\_shed.repository\_type module ----------------------------------------- .. automodule:: galaxy.tool_shed.repository_type - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.tool\_shed\_registry module --------------------------------------------- .. automodule:: galaxy.tool_shed.tool_shed_registry - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.tools.rst b/doc/source/lib/galaxy.tool_shed.tools.rst index d0339fd2b26..3b1f7bf3e7d 100644 --- a/doc/source/lib/galaxy.tool_shed.tools.rst +++ b/doc/source/lib/galaxy.tool_shed.tools.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.tools package =============================== .. automodule:: galaxy.tool_shed.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.tool\_shed.tools.data\_table\_manager module --------------------------------------------------- .. automodule:: galaxy.tool_shed.tools.data_table_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.tools.tool\_validator module ---------------------------------------------- .. automodule:: galaxy.tool_shed.tools.tool_validator - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.util.rst b/doc/source/lib/galaxy.tool_shed.util.rst index 8fdff4ba29e..32de4d3b831 100644 --- a/doc/source/lib/galaxy.tool_shed.util.rst +++ b/doc/source/lib/galaxy.tool_shed.util.rst @@ -2,9 +2,9 @@ galaxy.tool\_shed.util package ============================== .. automodule:: galaxy.tool_shed.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,64 +13,62 @@ galaxy.tool\_shed.util.basic\_util module ----------------------------------------- .. automodule:: galaxy.tool_shed.util.basic_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.container\_util module --------------------------------------------- .. automodule:: galaxy.tool_shed.util.container_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.hg\_util module -------------------------------------- .. automodule:: galaxy.tool_shed.util.hg_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.metadata\_util module -------------------------------------------- .. automodule:: galaxy.tool_shed.util.metadata_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.repository\_util module ---------------------------------------------- .. automodule:: galaxy.tool_shed.util.repository_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.shed\_util\_common module ------------------------------------------------ .. automodule:: galaxy.tool_shed.util.shed_util_common - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.tool\_dependency\_util module ---------------------------------------------------- .. automodule:: galaxy.tool_shed.util.tool_dependency_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_shed.util.tool\_util module ---------------------------------------- .. automodule:: galaxy.tool_shed.util.tool_util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.cwl.rst b/doc/source/lib/galaxy.tool_util.cwl.rst index 5049af0a7af..87cd25bd5ac 100644 --- a/doc/source/lib/galaxy.tool_util.cwl.rst +++ b/doc/source/lib/galaxy.tool_util.cwl.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.cwl package ============================= .. automodule:: galaxy.tool_util.cwl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,48 +13,54 @@ galaxy.tool\_util.cwl.cwltool\_deps module ------------------------------------------ .. automodule:: galaxy.tool_util.cwl.cwltool_deps - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.cwl.parser module ----------------------------------- .. automodule:: galaxy.tool_util.cwl.parser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.cwl.representation module ------------------------------------------- .. automodule:: galaxy.tool_util.cwl.representation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.runnable module +------------------------------------- + +.. automodule:: galaxy.tool_util.cwl.runnable + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.cwl.runtime\_actions module --------------------------------------------- .. automodule:: galaxy.tool_util.cwl.runtime_actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.cwl.schema module ----------------------------------- .. automodule:: galaxy.tool_util.cwl.schema - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.cwl.util module --------------------------------- .. automodule:: galaxy.tool_util.cwl.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst b/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst index 3866cb37a3b..631ad34b8cd 100644 --- a/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst +++ b/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.deps.container\_resolvers package =================================================== .. automodule:: galaxy.tool_util.deps.container_resolvers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.tool\_util.deps.container\_resolvers.explicit module ----------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.container_resolvers.explicit - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.container\_resolvers.mulled module --------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.container_resolvers.mulled - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.mulled.rst b/doc/source/lib/galaxy.tool_util.deps.mulled.rst index ec1e12fbcf8..cd84c1ddbe5 100644 --- a/doc/source/lib/galaxy.tool_util.deps.mulled.rst +++ b/doc/source/lib/galaxy.tool_util.deps.mulled.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.deps.mulled package ===================================== .. automodule:: galaxy.tool_util.deps.mulled - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,72 +13,70 @@ galaxy.tool\_util.deps.mulled.get\_tests module ----------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.get_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_build module -------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_build - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_build\_channel module ----------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_build_channel - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_build\_files module --------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_build_files - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_build\_tool module -------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_build_tool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_list module ------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_list - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_search module --------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.mulled\_update\_singularity\_containers module ---------------------------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.mulled_update_singularity_containers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.mulled.util module ----------------------------------------- .. automodule:: galaxy.tool_util.deps.mulled.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.resolvers.rst b/doc/source/lib/galaxy.tool_util.deps.resolvers.rst index 06be31af971..30bdd9ce23b 100644 --- a/doc/source/lib/galaxy.tool_util.deps.resolvers.rst +++ b/doc/source/lib/galaxy.tool_util.deps.resolvers.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.deps.resolvers package ======================================== .. automodule:: galaxy.tool_util.deps.resolvers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,72 +13,70 @@ galaxy.tool\_util.deps.resolvers.brewed\_tool\_shed\_packages module -------------------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.conda module --------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.conda - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.galaxy\_packages module -------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.galaxy_packages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.homebrew module ------------------------------------------------ .. automodule:: galaxy.tool_util.deps.resolvers.homebrew - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.lmod module -------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.lmod - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.modules module ----------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.modules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.resolver\_mixins module -------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.resolver_mixins - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.tool\_shed\_packages module ------------------------------------------------------------ .. automodule:: galaxy.tool_util.deps.resolvers.tool_shed_packages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.resolvers.unlinked\_tool\_shed\_packages module ---------------------------------------------------------------------- .. automodule:: galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.rst b/doc/source/lib/galaxy.tool_util.deps.rst index e763832ecbc..947dddb4f28 100644 --- a/doc/source/lib/galaxy.tool_util.deps.rst +++ b/doc/source/lib/galaxy.tool_util.deps.rst @@ -2,18 +2,19 @@ galaxy.tool\_util.deps package ============================== .. automodule:: galaxy.tool_util.deps - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_util.deps.container_resolvers - galaxy.tool_util.deps.mulled - galaxy.tool_util.deps.resolvers + galaxy.tool_util.deps.container_resolvers + galaxy.tool_util.deps.mulled + galaxy.tool_util.deps.resolvers Submodules ---------- @@ -22,104 +23,110 @@ galaxy.tool\_util.deps.brew\_exts module ---------------------------------------- .. automodule:: galaxy.tool_util.deps.brew_exts - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.brew\_util module ---------------------------------------- .. automodule:: galaxy.tool_util.deps.brew_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.commands module +-------------------------------------- + +.. automodule:: galaxy.tool_util.deps.commands + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.conda\_compat module ------------------------------------------- .. automodule:: galaxy.tool_util.deps.conda_compat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.conda\_util module ----------------------------------------- .. automodule:: galaxy.tool_util.deps.conda_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.container\_classes module ------------------------------------------------ .. automodule:: galaxy.tool_util.deps.container_classes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.containers module ---------------------------------------- .. automodule:: galaxy.tool_util.deps.containers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.dependencies module ------------------------------------------ .. automodule:: galaxy.tool_util.deps.dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.docker\_util module ------------------------------------------ .. automodule:: galaxy.tool_util.deps.docker_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.dockerfiles module ----------------------------------------- .. automodule:: galaxy.tool_util.deps.dockerfiles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.installable module ----------------------------------------- .. automodule:: galaxy.tool_util.deps.installable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.requirements module ------------------------------------------ .. automodule:: galaxy.tool_util.deps.requirements - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.singularity\_util module ----------------------------------------------- .. automodule:: galaxy.tool_util.deps.singularity_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.deps.views module ----------------------------------- .. automodule:: galaxy.tool_util.deps.views - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.linters.rst b/doc/source/lib/galaxy.tool_util.linters.rst index e87307309f8..dde26aa99d3 100644 --- a/doc/source/lib/galaxy.tool_util.linters.rst +++ b/doc/source/lib/galaxy.tool_util.linters.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.linters package ================================= .. automodule:: galaxy.tool_util.linters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,80 +13,78 @@ galaxy.tool\_util.linters.citations module ------------------------------------------ .. automodule:: galaxy.tool_util.linters.citations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.command module ---------------------------------------- .. automodule:: galaxy.tool_util.linters.command - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.cwl module ------------------------------------ .. automodule:: galaxy.tool_util.linters.cwl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.general module ---------------------------------------- .. automodule:: galaxy.tool_util.linters.general - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.help module ------------------------------------- .. automodule:: galaxy.tool_util.linters.help - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.inputs module --------------------------------------- .. automodule:: galaxy.tool_util.linters.inputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.outputs module ---------------------------------------- .. automodule:: galaxy.tool_util.linters.outputs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.stdio module -------------------------------------- .. automodule:: galaxy.tool_util.linters.stdio - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.tests module -------------------------------------- .. automodule:: galaxy.tool_util.linters.tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.linters.xml\_order module ------------------------------------------- .. automodule:: galaxy.tool_util.linters.xml_order - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.locations.rst b/doc/source/lib/galaxy.tool_util.locations.rst index 12de3f42acf..94a218d8be2 100644 --- a/doc/source/lib/galaxy.tool_util.locations.rst +++ b/doc/source/lib/galaxy.tool_util.locations.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.locations package =================================== .. automodule:: galaxy.tool_util.locations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.tool\_util.locations.dockstore module -------------------------------------------- .. automodule:: galaxy.tool_util.locations.dockstore - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.locations.file module --------------------------------------- .. automodule:: galaxy.tool_util.locations.file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.locations.http module --------------------------------------- .. automodule:: galaxy.tool_util.locations.http - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.parser.rst b/doc/source/lib/galaxy.tool_util.parser.rst index f22d99e459d..d2d952b52f8 100644 --- a/doc/source/lib/galaxy.tool_util.parser.rst +++ b/doc/source/lib/galaxy.tool_util.parser.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.parser package ================================ .. automodule:: galaxy.tool_util.parser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,80 +13,78 @@ galaxy.tool\_util.parser.cwl module ----------------------------------- .. automodule:: galaxy.tool_util.parser.cwl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.factory module --------------------------------------- .. automodule:: galaxy.tool_util.parser.factory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.interface module ----------------------------------------- .. automodule:: galaxy.tool_util.parser.interface - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.output\_actions module ----------------------------------------------- .. automodule:: galaxy.tool_util.parser.output_actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.output\_collection\_def module ------------------------------------------------------- .. automodule:: galaxy.tool_util.parser.output_collection_def - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.output\_objects module ----------------------------------------------- .. automodule:: galaxy.tool_util.parser.output_objects - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.stdio module ------------------------------------- .. automodule:: galaxy.tool_util.parser.stdio - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.util module ------------------------------------ .. automodule:: galaxy.tool_util.parser.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.xml module ----------------------------------- .. automodule:: galaxy.tool_util.parser.xml - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.parser.yaml module ------------------------------------ .. automodule:: galaxy.tool_util.parser.yaml - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst index f09d5aa37f5..0d7546a8f4b 100644 --- a/doc/source/lib/galaxy.tool_util.rst +++ b/doc/source/lib/galaxy.tool_util.rst @@ -2,21 +2,22 @@ galaxy.tool\_util package ========================= .. automodule:: galaxy.tool_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_util.cwl - galaxy.tool_util.deps - galaxy.tool_util.linters - galaxy.tool_util.locations - galaxy.tool_util.parser - galaxy.tool_util.verify + galaxy.tool_util.cwl + galaxy.tool_util.deps + galaxy.tool_util.linters + galaxy.tool_util.locations + galaxy.tool_util.parser + galaxy.tool_util.verify Submodules ---------- @@ -25,48 +26,46 @@ galaxy.tool\_util.fetcher module -------------------------------- .. automodule:: galaxy.tool_util.fetcher - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.lint module ----------------------------- .. automodule:: galaxy.tool_util.lint - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.loader module ------------------------------- .. automodule:: galaxy.tool_util.loader - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.loader\_directory module ------------------------------------------ .. automodule:: galaxy.tool_util.loader_directory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.output\_checker module ---------------------------------------- .. automodule:: galaxy.tool_util.output_checker - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.provided\_metadata module ------------------------------------------- .. automodule:: galaxy.tool_util.provided_metadata - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.verify.asserts.rst b/doc/source/lib/galaxy.tool_util.verify.asserts.rst index 7a164fefe94..2a481cce118 100644 --- a/doc/source/lib/galaxy.tool_util.verify.asserts.rst +++ b/doc/source/lib/galaxy.tool_util.verify.asserts.rst @@ -2,9 +2,9 @@ galaxy.tool\_util.verify.asserts package ======================================== .. automodule:: galaxy.tool_util.verify.asserts - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,48 +13,46 @@ galaxy.tool\_util.verify.asserts.archive module ----------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.archive - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.asserts.hdf5 module -------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.hdf5 - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.asserts.size module -------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.size - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.asserts.tabular module ----------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.tabular - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.asserts.text module -------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.text - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.asserts.xml module ------------------------------------------- .. automodule:: galaxy.tool_util.verify.asserts.xml - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.verify.rst b/doc/source/lib/galaxy.tool_util.verify.rst index 99469adf02d..e905a8506a0 100644 --- a/doc/source/lib/galaxy.tool_util.verify.rst +++ b/doc/source/lib/galaxy.tool_util.verify.rst @@ -2,16 +2,17 @@ galaxy.tool\_util.verify package ================================ .. automodule:: galaxy.tool_util.verify - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tool_util.verify.asserts + galaxy.tool_util.verify.asserts Submodules ---------- @@ -20,24 +21,30 @@ galaxy.tool\_util.verify.interactor module ------------------------------------------ .. automodule:: galaxy.tool_util.verify.interactor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.script module -------------------------------------- .. automodule:: galaxy.tool_util.verify.script - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tool\_util.verify.test\_data module ------------------------------------------ .. automodule:: galaxy.tool_util.verify.test_data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: +galaxy.tool\_util.verify.wait module +------------------------------------ +.. automodule:: galaxy.tool_util.verify.wait + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 1ef158180cd..2798891f7ac 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -2,9 +2,9 @@ galaxy.tools.actions package ============================ .. automodule:: galaxy.tools.actions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,56 +13,54 @@ galaxy.tools.actions.data\_manager module ----------------------------------------- .. automodule:: galaxy.tools.actions.data_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.data\_source module ---------------------------------------- .. automodule:: galaxy.tools.actions.data_source - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.history\_imp\_exp module --------------------------------------------- .. automodule:: galaxy.tools.actions.history_imp_exp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.metadata module ------------------------------------ .. automodule:: galaxy.tools.actions.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.model\_operations module --------------------------------------------- .. automodule:: galaxy.tools.actions.model_operations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.upload module ---------------------------------- .. automodule:: galaxy.tools.actions.upload - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.actions.upload\_common module ------------------------------------------ .. automodule:: galaxy.tools.actions.upload_common - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst index 4435ba549f8..b61235b340f 100644 --- a/doc/source/lib/galaxy.tools.data.rst +++ b/doc/source/lib/galaxy.tools.data.rst @@ -2,7 +2,6 @@ galaxy.tools.data package ========================= .. automodule:: galaxy.tools.data - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst index 53e9b630fb9..5b0921d0892 100644 --- a/doc/source/lib/galaxy.tools.data_manager.rst +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -2,9 +2,9 @@ galaxy.tools.data\_manager package ================================== .. automodule:: galaxy.tools.data_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.tools.data\_manager.manager module ----------------------------------------- .. automodule:: galaxy.tools.data_manager.manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.error_reports.plugins.rst b/doc/source/lib/galaxy.tools.error_reports.plugins.rst index 3491c92977c..fc53911c39b 100644 --- a/doc/source/lib/galaxy.tools.error_reports.plugins.rst +++ b/doc/source/lib/galaxy.tools.error_reports.plugins.rst @@ -2,9 +2,9 @@ galaxy.tools.error\_reports.plugins package =========================================== .. automodule:: galaxy.tools.error_reports.plugins - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,56 +13,54 @@ galaxy.tools.error\_reports.plugins.base\_git module ---------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.base_git - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.email module ------------------------------------------------ .. automodule:: galaxy.tools.error_reports.plugins.email - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.github module ------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.github - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.gitlab module ------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.gitlab - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.influxdb module --------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.influxdb - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.json module ----------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.json - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.error\_reports.plugins.sentry module ------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.sentry - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.error_reports.rst b/doc/source/lib/galaxy.tools.error_reports.rst index 7cf8be64e4c..e846514ffec 100644 --- a/doc/source/lib/galaxy.tools.error_reports.rst +++ b/doc/source/lib/galaxy.tools.error_reports.rst @@ -2,14 +2,14 @@ galaxy.tools.error\_reports package =================================== .. automodule:: galaxy.tools.error_reports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tools.error_reports.plugins - + galaxy.tools.error_reports.plugins diff --git a/doc/source/lib/galaxy.tools.expressions.rst b/doc/source/lib/galaxy.tools.expressions.rst index 6c952368f2e..760fce2a368 100644 --- a/doc/source/lib/galaxy.tools.expressions.rst +++ b/doc/source/lib/galaxy.tools.expressions.rst @@ -2,9 +2,9 @@ galaxy.tools.expressions package ================================ .. automodule:: galaxy.tools.expressions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.tools.expressions.evaluation module ------------------------------------------ .. automodule:: galaxy.tools.expressions.evaluation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.expressions.script module -------------------------------------- .. automodule:: galaxy.tools.expressions.script - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.expressions.util module ------------------------------------ .. automodule:: galaxy.tools.expressions.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst index bbea7ec45e4..2c6cae93734 100644 --- a/doc/source/lib/galaxy.tools.filters.rst +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -2,7 +2,6 @@ galaxy.tools.filters package ============================ .. automodule:: galaxy.tools.filters - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.imp_exp.rst b/doc/source/lib/galaxy.tools.imp_exp.rst index 6cefd450f76..9c8cb4f432b 100644 --- a/doc/source/lib/galaxy.tools.imp_exp.rst +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -2,9 +2,9 @@ galaxy.tools.imp\_exp package ============================= .. automodule:: galaxy.tools.imp_exp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.tools.imp\_exp.export\_history module -------------------------------------------- .. automodule:: galaxy.tools.imp_exp.export_history - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.imp\_exp.unpack\_tar\_gz\_archive module ----------------------------------------------------- .. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 568fb0c2c5f..4e846dff4a5 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -2,9 +2,9 @@ galaxy.tools.parameters package =============================== .. automodule:: galaxy.tools.parameters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,88 +13,86 @@ galaxy.tools.parameters.basic module ------------------------------------ .. automodule:: galaxy.tools.parameters.basic - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.dataset\_matcher module ----------------------------------------------- .. automodule:: galaxy.tools.parameters.dataset_matcher - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.dynamic\_options module ----------------------------------------------- .. automodule:: galaxy.tools.parameters.dynamic_options - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.grouping module --------------------------------------- .. automodule:: galaxy.tools.parameters.grouping - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.history\_query module --------------------------------------------- .. automodule:: galaxy.tools.parameters.history_query - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.input\_translation module ------------------------------------------------- .. automodule:: galaxy.tools.parameters.input_translation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.meta module ----------------------------------- .. automodule:: galaxy.tools.parameters.meta - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.sanitize module --------------------------------------- .. automodule:: galaxy.tools.parameters.sanitize - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.validation module ----------------------------------------- .. automodule:: galaxy.tools.parameters.validation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.wrapped module -------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.parameters.wrapped\_json module -------------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped_json - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 7fb4201a49c..1b65b6a1275 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -2,26 +2,27 @@ galaxy.tools package ==================== .. automodule:: galaxy.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tools.actions - galaxy.tools.data - galaxy.tools.data_manager - galaxy.tools.error_reports - galaxy.tools.expressions - galaxy.tools.filters - galaxy.tools.imp_exp - galaxy.tools.parameters - galaxy.tools.search - galaxy.tools.toolbox - galaxy.tools.util + galaxy.tools.actions + galaxy.tools.data + galaxy.tools.data_manager + galaxy.tools.error_reports + galaxy.tools.expressions + galaxy.tools.filters + galaxy.tools.imp_exp + galaxy.tools.parameters + galaxy.tools.search + galaxy.tools.toolbox + galaxy.tools.util Submodules ---------- @@ -30,88 +31,86 @@ galaxy.tools.cache module ------------------------- .. automodule:: galaxy.tools.cache - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.data\_fetch module ------------------------------- .. automodule:: galaxy.tools.data_fetch - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.errors module -------------------------- .. automodule:: galaxy.tools.errors - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.evaluation module ------------------------------ .. automodule:: galaxy.tools.evaluation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.exception\_handling module --------------------------------------- .. automodule:: galaxy.tools.exception_handling - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.execute module --------------------------- .. automodule:: galaxy.tools.execute - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.recommendations module ----------------------------------- .. automodule:: galaxy.tools.recommendations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.repositories module -------------------------------- .. automodule:: galaxy.tools.repositories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.special\_tools module ---------------------------------- .. automodule:: galaxy.tools.special_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.test module ------------------------ .. automodule:: galaxy.tools.test - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.wrappers module ---------------------------- .. automodule:: galaxy.tools.wrappers - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst index edbb5bf3c79..6969e2e02da 100644 --- a/doc/source/lib/galaxy.tools.search.rst +++ b/doc/source/lib/galaxy.tools.search.rst @@ -2,7 +2,6 @@ galaxy.tools.search package =========================== .. automodule:: galaxy.tools.search - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst index a5a81d279fb..1d5157fd251 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -2,7 +2,6 @@ galaxy.tools.toolbox.filters package ==================================== .. automodule:: galaxy.tools.toolbox.filters - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst index e2628fd8bc4..e21361b648e 100644 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -2,9 +2,9 @@ galaxy.tools.toolbox.lineages package ===================================== .. automodule:: galaxy.tools.toolbox.lineages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.tools.toolbox.lineages.factory module -------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.factory - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.lineages.interface module ---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.interface - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst index 9631687f40f..3e8a1628caf 100644 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -2,17 +2,18 @@ galaxy.tools.toolbox package ============================ .. automodule:: galaxy.tools.toolbox - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tools.toolbox.filters - galaxy.tools.toolbox.lineages + galaxy.tools.toolbox.filters + galaxy.tools.toolbox.lineages Submodules ---------- @@ -21,48 +22,46 @@ galaxy.tools.toolbox.base module -------------------------------- .. automodule:: galaxy.tools.toolbox.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.integrated\_panel module --------------------------------------------- .. automodule:: galaxy.tools.toolbox.integrated_panel - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.panel module --------------------------------- .. automodule:: galaxy.tools.toolbox.panel - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.parser module ---------------------------------- .. automodule:: galaxy.tools.toolbox.parser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.tags module -------------------------------- .. automodule:: galaxy.tools.toolbox.tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.tools.toolbox.watcher module ----------------------------------- .. automodule:: galaxy.tools.toolbox.watcher - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst index 4ea949a2fac..2e87810d07f 100644 --- a/doc/source/lib/galaxy.tools.util.galaxyops.rst +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -2,7 +2,6 @@ galaxy.tools.util.galaxyops package =================================== .. automodule:: galaxy.tools.util.galaxyops - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.util.rst b/doc/source/lib/galaxy.tools.util.rst index 588817928fa..594c2af5bdd 100644 --- a/doc/source/lib/galaxy.tools.util.rst +++ b/doc/source/lib/galaxy.tools.util.rst @@ -2,16 +2,17 @@ galaxy.tools.util package ========================= .. automodule:: galaxy.tools.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.tools.util.galaxyops + galaxy.tools.util.galaxyops Submodules ---------- @@ -20,8 +21,6 @@ galaxy.tools.util.maf\_utilities module --------------------------------------- .. automodule:: galaxy.tools.util.maf_utilities - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tours.rst b/doc/source/lib/galaxy.tours.rst index 9729a10a6fe..56232296de6 100644 --- a/doc/source/lib/galaxy.tours.rst +++ b/doc/source/lib/galaxy.tours.rst @@ -2,7 +2,6 @@ galaxy.tours package ==================== .. automodule:: galaxy.tours - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.custom_logging.rst b/doc/source/lib/galaxy.util.custom_logging.rst new file mode 100644 index 00000000000..bb89d3b6b02 --- /dev/null +++ b/doc/source/lib/galaxy.util.custom_logging.rst @@ -0,0 +1,18 @@ +galaxy.util.custom\_logging package +=================================== + +.. automodule:: galaxy.util.custom_logging + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.util.custom\_logging.fluent\_log module +---------------------------------------------- + +.. automodule:: galaxy.util.custom_logging.fluent_log + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.logging.rst b/doc/source/lib/galaxy.util.logging.rst deleted file mode 100644 index b72a2ad0d74..00000000000 --- a/doc/source/lib/galaxy.util.logging.rst +++ /dev/null @@ -1,20 +0,0 @@ -galaxy.util.custom_logging package -=========================== - -.. automodule:: galaxy.util.custom_logging - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.util.custom_logging.fluent\_log module --------------------------------------- - -.. automodule:: galaxy.util.custom_logging.fluent_log - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst index 0a861eb5a4f..1eabd88f0c9 100644 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -2,9 +2,9 @@ galaxy.util.pastescript package =============================== .. automodule:: galaxy.util.pastescript - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.util.pastescript.loadwsgi module --------------------------------------- .. automodule:: galaxy.util.pastescript.loadwsgi - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.pastescript.serve module ------------------------------------ .. automodule:: galaxy.util.pastescript.serve - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.path.rst b/doc/source/lib/galaxy.util.path.rst index c74056d2d89..361acd75a24 100644 --- a/doc/source/lib/galaxy.util.path.rst +++ b/doc/source/lib/galaxy.util.path.rst @@ -2,9 +2,9 @@ galaxy.util.path package ======================== .. automodule:: galaxy.util.path - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.util.path.ntpath module ------------------------------ .. automodule:: galaxy.util.path.ntpath - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.path.posixpath module --------------------------------- .. automodule:: galaxy.util.path.posixpath - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 3237a0f7b47..c9b52ceb3c1 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -2,19 +2,20 @@ galaxy.util package =================== .. automodule:: galaxy.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.util.custom_logging - galaxy.util.pastescript - galaxy.util.path - galaxy.util.tool_shed + galaxy.util.custom_logging + galaxy.util.pastescript + galaxy.util.path + galaxy.util.tool_shed Submodules ---------- @@ -23,376 +24,382 @@ galaxy.util.aliaspickler module ------------------------------- .. automodule:: galaxy.util.aliaspickler - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.bunch module ------------------------ .. automodule:: galaxy.util.bunch - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.bytesize module --------------------------- .. automodule:: galaxy.util.bytesize - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.checkers module --------------------------- .. automodule:: galaxy.util.checkers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.commands module --------------------------- .. automodule:: galaxy.util.commands - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.compression\_utils module ------------------------------------- .. automodule:: galaxy.util.compression_utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.dbkeys module ------------------------- .. automodule:: galaxy.util.dbkeys - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.dictifiable module ------------------------------ .. automodule:: galaxy.util.dictifiable - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.expressions module ------------------------------ .. automodule:: galaxy.util.expressions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.facts module ------------------------ .. automodule:: galaxy.util.facts - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.filelock module --------------------------- .. automodule:: galaxy.util.filelock - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.form\_builder module -------------------------------- .. automodule:: galaxy.util.form_builder - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.getargspec module ----------------------------- .. automodule:: galaxy.util.getargspec - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.hash\_util module ----------------------------- .. automodule:: galaxy.util.hash_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.heartbeat module ---------------------------- .. automodule:: galaxy.util.heartbeat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.image\_util module ------------------------------ .. automodule:: galaxy.util.image_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.inflection module ----------------------------- .. automodule:: galaxy.util.inflection - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.json module ----------------------- .. automodule:: galaxy.util.json - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.jstree module ------------------------- .. automodule:: galaxy.util.jstree - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.lazy\_process module -------------------------------- .. automodule:: galaxy.util.lazy_process - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.monitors module --------------------------- .. automodule:: galaxy.util.monitors - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.object\_wrapper module ---------------------------------- .. automodule:: galaxy.util.object_wrapper - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.odict module ------------------------ .. automodule:: galaxy.util.odict - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.oset module ----------------------- .. automodule:: galaxy.util.oset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.permutations module ------------------------------- .. automodule:: galaxy.util.permutations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.plugin\_config module --------------------------------- .. automodule:: galaxy.util.plugin_config - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.properties module ----------------------------- .. automodule:: galaxy.util.properties - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.renamed\_temporary\_file module ------------------------------------------- .. automodule:: galaxy.util.renamed_temporary_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.rules\_dsl module ----------------------------- .. automodule:: galaxy.util.rules_dsl - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.sanitize\_html module --------------------------------- .. automodule:: galaxy.util.sanitize_html - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.script module ------------------------- .. automodule:: galaxy.util.script - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.search module +------------------------- + +.. automodule:: galaxy.util.search + :members: + :undoc-members: + :show-inheritance: galaxy.util.simplegraph module ------------------------------ .. automodule:: galaxy.util.simplegraph - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.sleeper module -------------------------- .. automodule:: galaxy.util.sleeper - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.sockets module -------------------------- .. automodule:: galaxy.util.sockets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.specs module ------------------------ .. automodule:: galaxy.util.specs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.sqlite module ------------------------- .. automodule:: galaxy.util.sqlite - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.streamball module ----------------------------- .. automodule:: galaxy.util.streamball - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.submodules module ----------------------------- .. automodule:: galaxy.util.submodules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.template module --------------------------- .. automodule:: galaxy.util.template - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.tool\_version module -------------------------------- .. automodule:: galaxy.util.tool_version - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.topsort module -------------------------- .. automodule:: galaxy.util.topsort - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.ucsc module ----------------------- .. automodule:: galaxy.util.ucsc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.validation module ----------------------------- .. automodule:: galaxy.util.validation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.watcher module -------------------------- .. automodule:: galaxy.util.watcher - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.web\_compat module ------------------------------ .. automodule:: galaxy.util.web_compat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.xml\_macros module ------------------------------ .. automodule:: galaxy.util.xml_macros - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.yaml\_util module ----------------------------- .. automodule:: galaxy.util.yaml_util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.util.tool_shed.rst b/doc/source/lib/galaxy.util.tool_shed.rst index 42b92b9bc7e..2f5b45a1153 100644 --- a/doc/source/lib/galaxy.util.tool_shed.rst +++ b/doc/source/lib/galaxy.util.tool_shed.rst @@ -2,9 +2,9 @@ galaxy.util.tool\_shed package ============================== .. automodule:: galaxy.util.tool_shed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.util.tool\_shed.common\_util module ------------------------------------------ .. automodule:: galaxy.util.tool_shed.common_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.tool\_shed.encoding\_util module -------------------------------------------- .. automodule:: galaxy.util.tool_shed.encoding_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.util.tool\_shed.xml\_util module --------------------------------------- .. automodule:: galaxy.util.tool_shed.xml_util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst index 1866488ed19..fbc3636d801 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -2,9 +2,9 @@ galaxy.visualization.data\_providers.phyloviz package ===================================================== .. automodule:: galaxy.visualization.data_providers.phyloviz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,32 +13,30 @@ galaxy.visualization.data\_providers.phyloviz.baseparser module --------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.phyloviz.newickparser module ----------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.phyloviz.nexusparser module ---------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.phyloviz.phyloxmlparser module ------------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index 326f6c75321..717a4eba3a9 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -2,16 +2,17 @@ galaxy.visualization.data\_providers package ============================================ .. automodule:: galaxy.visualization.data_providers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.visualization.data_providers.phyloviz + galaxy.visualization.data_providers.phyloviz Submodules ---------- @@ -20,32 +21,30 @@ galaxy.visualization.data\_providers.basic module ------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.basic - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.cigar module ------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.cigar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.genome module -------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.genome - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.data\_providers.registry module ---------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.registry - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index 9097529321c..63f8e10017b 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -2,7 +2,6 @@ galaxy.visualization.genome package =================================== .. automodule:: galaxy.visualization.genome - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst index 019f744d8b4..6209b4d1398 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -2,9 +2,9 @@ galaxy.visualization.plugins package ==================================== .. automodule:: galaxy.visualization.plugins - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,48 +13,46 @@ galaxy.visualization.plugins.config\_parser module -------------------------------------------------- .. automodule:: galaxy.visualization.plugins.config_parser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.plugins.interactive\_environments module ------------------------------------------------------------- .. automodule:: galaxy.visualization.plugins.interactive_environments - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.plugins.plugin module ------------------------------------------ .. automodule:: galaxy.visualization.plugins.plugin - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.plugins.registry module -------------------------------------------- .. automodule:: galaxy.visualization.plugins.registry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.plugins.resource\_parser module ---------------------------------------------------- .. automodule:: galaxy.visualization.plugins.resource_parser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.visualization.plugins.utils module ----------------------------------------- .. automodule:: galaxy.visualization.plugins.utils - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index 1f334499e29..0b4e8b5011f 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -2,19 +2,20 @@ galaxy.visualization package ============================ .. automodule:: galaxy.visualization - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.visualization.data_providers - galaxy.visualization.genome - galaxy.visualization.plugins - galaxy.visualization.tracks + galaxy.visualization.data_providers + galaxy.visualization.genome + galaxy.visualization.plugins + galaxy.visualization.tracks Submodules ---------- @@ -23,8 +24,6 @@ galaxy.visualization.genomes module ----------------------------------- .. automodule:: galaxy.visualization.genomes - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 2d279399ef6..7ac1498fc94 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -2,7 +2,6 @@ galaxy.visualization.tracks package =================================== .. automodule:: galaxy.visualization.tracks - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst index e0024343c0c..18966a362ca 100644 --- a/doc/source/lib/galaxy.web.framework.helpers.rst +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -2,9 +2,9 @@ galaxy.web.framework.helpers package ==================================== .. automodule:: galaxy.web.framework.helpers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ galaxy.web.framework.helpers.grids module ----------------------------------------- .. automodule:: galaxy.web.framework.helpers.grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.helpers.tags module ---------------------------------------- .. automodule:: galaxy.web.framework.helpers.tags - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index 675615531da..db25934e8d6 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -2,9 +2,9 @@ galaxy.web.framework.middleware package ======================================= .. automodule:: galaxy.web.framework.middleware - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,88 +13,86 @@ galaxy.web.framework.middleware.batch module -------------------------------------------- .. automodule:: galaxy.web.framework.middleware.batch - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.error module -------------------------------------------- .. automodule:: galaxy.web.framework.middleware.error - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.profile module ---------------------------------------------- .. automodule:: galaxy.web.framework.middleware.profile - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.remoteuser module ------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.remoteuser - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.request\_id module -------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.request_id - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.sentry module --------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sentry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.sqldebug module ----------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sqldebug - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.static module --------------------------------------------- .. automodule:: galaxy.web.framework.middleware.static - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.statsd module --------------------------------------------- .. automodule:: galaxy.web.framework.middleware.statsd - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.translogger module -------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.translogger - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.middleware.xforwardedhost module ----------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.xforwardedhost - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index a7dc4812d56..e1cfbbd1ee9 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -2,17 +2,18 @@ galaxy.web.framework package ============================ .. automodule:: galaxy.web.framework - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.web.framework.helpers - galaxy.web.framework.middleware + galaxy.web.framework.helpers + galaxy.web.framework.middleware Submodules ---------- @@ -21,24 +22,14 @@ galaxy.web.framework.base module -------------------------------- .. automodule:: galaxy.web.framework.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.framework.decorators module -------------------------------------- .. automodule:: galaxy.web.framework.decorators - :members: - :undoc-members: - :show-inheritance: - -galaxy.web.framework.webapp module ----------------------------------- - -.. automodule:: galaxy.web.framework.webapp - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst index d69630ba177..80c82226ba1 100644 --- a/doc/source/lib/galaxy.web.proxy.rst +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -2,7 +2,6 @@ galaxy.web.proxy package ======================== .. automodule:: galaxy.web.proxy - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index f1b0144f820..620fa2d94a4 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -2,17 +2,18 @@ galaxy.web package ================== .. automodule:: galaxy.web - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.web.framework - galaxy.web.proxy + galaxy.web.framework + galaxy.web.proxy Submodules ---------- @@ -21,40 +22,38 @@ galaxy.web.buildapp module -------------------------- .. automodule:: galaxy.web.buildapp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.form\_builder module ------------------------------- .. automodule:: galaxy.web.form_builder - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.formatting module ---------------------------- .. automodule:: galaxy.web.formatting - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.params module ------------------------ .. automodule:: galaxy.web.params - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web.statsd\_client module -------------------------------- .. automodule:: galaxy.web.statsd_client - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.web_stack.rst b/doc/source/lib/galaxy.web_stack.rst index 26d7b0e02d6..8ef43b9ffe5 100644 --- a/doc/source/lib/galaxy.web_stack.rst +++ b/doc/source/lib/galaxy.web_stack.rst @@ -2,9 +2,9 @@ galaxy.web\_stack package ========================= .. automodule:: galaxy.web_stack - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ galaxy.web\_stack.handlers module --------------------------------- .. automodule:: galaxy.web_stack.handlers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web\_stack.message module -------------------------------- .. automodule:: galaxy.web_stack.message - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.web\_stack.transport module ---------------------------------- .. automodule:: galaxy.web_stack.transport - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.base.rst b/doc/source/lib/galaxy.webapps.base.rst index 57a5db43038..f8fdff600df 100644 --- a/doc/source/lib/galaxy.webapps.base.rst +++ b/doc/source/lib/galaxy.webapps.base.rst @@ -2,9 +2,9 @@ galaxy.webapps.base package =========================== .. automodule:: galaxy.webapps.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,14 @@ galaxy.webapps.base.controller module ------------------------------------- .. automodule:: galaxy.webapps.base.controller - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: +galaxy.webapps.base.webapp module +--------------------------------- +.. automodule:: galaxy.webapps.base.webapp + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index e188d8b981d..93847b467f5 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -2,9 +2,9 @@ galaxy.webapps.galaxy.api package ================================= .. automodule:: galaxy.webapps.galaxy.api - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,400 +13,422 @@ galaxy.webapps.galaxy.api.annotations module -------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.authenticate module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.cloud module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloud - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.cloudauthz module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloudauthz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.configuration module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.container\_resolution module ------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.container_resolution - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.dataset\_collections module ----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.datasets module ----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.datatypes module ------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.datatypes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.display\_applications module ------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.display_applications - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.dynamic\_tools module ----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dynamic_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.extended\_metadata module --------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.folder\_contents module ------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.folders module ---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.forms module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.genomes module ---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.group\_roles module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.group\_users module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.groups module --------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.histories module ------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.history\_contents module -------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.item\_tags module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.item_tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.job\_files module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.job_files - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.job\_ports module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.job_ports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.jobs module ------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.libraries module ------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.library\_contents module -------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.library\_datasets module -------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.api.licenses module +----------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.licenses + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.metrics module ---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.page\_revisions module ------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.page_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.pages module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.pages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.plugins module ---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.plugins - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.provenance module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.provenance - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.quotas module --------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.remote\_files module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.roles module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.search module --------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tags module ------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tags - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tool\_data module ------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tool\_dependencies module --------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tool\_entry\_points module ---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_entry_points - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tool\_shed\_repositories module --------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tools module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.toolshed module ----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.toolshed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.tours module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tours - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.api.trs\_consumer module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.trs_consumer + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.api.trs\_search module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.trs_search + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.uploads module ---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.uploads - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.users module -------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.visualizations module ----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.webhooks module ----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.webhooks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.api.workflows module ------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index c54cdfba41a..aadf5d94c4e 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -2,9 +2,9 @@ galaxy.webapps.galaxy.controllers package ========================================= .. automodule:: galaxy.webapps.galaxy.controllers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,176 +13,174 @@ galaxy.webapps.galaxy.controllers.admin module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.admin\_toolshed module -------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.async module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.async - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.authnz module ----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.authnz - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.data\_manager module ------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.data_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.dataset module ------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.dataset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.error module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.error - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.forms module ---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.forms - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.history module ------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.history - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.interactive\_environments module ------------------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.interactive_environments - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.interactivetool module -------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.interactivetool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.library module ------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.openid module ----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.openid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.page module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.page - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.root module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.root - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.shed\_tool\_static module ----------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.shed_tool_static - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.tag module -------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tag - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.tool\_runner module ----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tool_runner - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.user module --------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.user - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.userskeys module -------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.userskeys - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.visualization module ------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.visualization - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.galaxy.controllers.workflow module ------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.workflow - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index 5256155b1ed..8147c682540 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -2,17 +2,18 @@ galaxy.webapps.galaxy package ============================= .. automodule:: galaxy.webapps.galaxy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.webapps.galaxy.api - galaxy.webapps.galaxy.controllers + galaxy.webapps.galaxy.api + galaxy.webapps.galaxy.controllers Submodules ---------- @@ -21,8 +22,6 @@ galaxy.webapps.galaxy.buildapp module ------------------------------------- .. automodule:: galaxy.webapps.galaxy.buildapp - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index b6039634602..64909a7408f 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -2,9 +2,9 @@ galaxy.webapps.reports.controllers package ========================================== .. automodule:: galaxy.webapps.reports.controllers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,72 +13,70 @@ galaxy.webapps.reports.controllers.history module ------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.history - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.home module ---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.home - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.jobs module ---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.query module ----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.query - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.root module ---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.root - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.system module ------------------------------------------------ .. automodule:: galaxy.webapps.reports.controllers.system - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.tools module ----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.users module ----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.users - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.controllers.workflows module --------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.workflows - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.reports.framework.rst b/doc/source/lib/galaxy.webapps.reports.framework.rst index 0d4cec5661f..1a39715bd9e 100644 --- a/doc/source/lib/galaxy.webapps.reports.framework.rst +++ b/doc/source/lib/galaxy.webapps.reports.framework.rst @@ -2,9 +2,9 @@ galaxy.webapps.reports.framework package ======================================== .. automodule:: galaxy.webapps.reports.framework - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.webapps.reports.framework.grids module --------------------------------------------- .. automodule:: galaxy.webapps.reports.framework.grids - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index 84dcee28911..1d480541877 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -2,17 +2,18 @@ galaxy.webapps.reports package ============================== .. automodule:: galaxy.webapps.reports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.webapps.reports.controllers - galaxy.webapps.reports.framework + galaxy.webapps.reports.controllers + galaxy.webapps.reports.framework Submodules ---------- @@ -21,24 +22,22 @@ galaxy.webapps.reports.app module --------------------------------- .. automodule:: galaxy.webapps.reports.app - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.buildapp module -------------------------------------- .. automodule:: galaxy.webapps.reports.buildapp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.webapps.reports.config module ------------------------------------ .. automodule:: galaxy.webapps.reports.config - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 55443b8ce3b..e8f02a396c3 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -2,18 +2,19 @@ galaxy.webapps package ====================== .. automodule:: galaxy.webapps - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.webapps.base - galaxy.webapps.galaxy - galaxy.webapps.reports + galaxy.webapps.base + galaxy.webapps.galaxy + galaxy.webapps.reports Submodules ---------- @@ -22,8 +23,6 @@ galaxy.webapps.util module -------------------------- .. automodule:: galaxy.webapps.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webhooks.rst b/doc/source/lib/galaxy.webhooks.rst index 866964ebc4c..71d4534040b 100644 --- a/doc/source/lib/galaxy.webhooks.rst +++ b/doc/source/lib/galaxy.webhooks.rst @@ -2,7 +2,6 @@ galaxy.webhooks package ======================= .. automodule:: galaxy.webhooks - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst index 415a5b881c8..d0ecf8fc302 100644 --- a/doc/source/lib/galaxy.work.rst +++ b/doc/source/lib/galaxy.work.rst @@ -2,9 +2,9 @@ galaxy.work package =================== .. automodule:: galaxy.work - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.work.context module -------------------------- .. automodule:: galaxy.work.context - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.workflow.reports.generators.rst b/doc/source/lib/galaxy.workflow.reports.generators.rst index 21e7af8096d..7df9cf21d19 100644 --- a/doc/source/lib/galaxy.workflow.reports.generators.rst +++ b/doc/source/lib/galaxy.workflow.reports.generators.rst @@ -2,9 +2,9 @@ galaxy.workflow.reports.generators package ========================================== .. automodule:: galaxy.workflow.reports.generators - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.workflow.reports.generators.markdown module -------------------------------------------------- .. automodule:: galaxy.workflow.reports.generators.markdown - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.workflow.reports.rst b/doc/source/lib/galaxy.workflow.reports.rst index 6e26e08430b..3de3d770572 100644 --- a/doc/source/lib/galaxy.workflow.reports.rst +++ b/doc/source/lib/galaxy.workflow.reports.rst @@ -2,14 +2,14 @@ galaxy.workflow.reports package =============================== .. automodule:: galaxy.workflow.reports - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.workflow.reports.generators - + galaxy.workflow.reports.generators diff --git a/doc/source/lib/galaxy.workflow.resources.rst b/doc/source/lib/galaxy.workflow.resources.rst index 30773bc1ce9..2425b5f8012 100644 --- a/doc/source/lib/galaxy.workflow.resources.rst +++ b/doc/source/lib/galaxy.workflow.resources.rst @@ -2,7 +2,6 @@ galaxy.workflow.resources package ================================= .. automodule:: galaxy.workflow.resources - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 1af35e4b995..ad3c925e446 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -2,18 +2,19 @@ galaxy.workflow package ======================= .. automodule:: galaxy.workflow - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy.workflow.reports - galaxy.workflow.resources - galaxy.workflow.schedulers + galaxy.workflow.reports + galaxy.workflow.resources + galaxy.workflow.schedulers Submodules ---------- @@ -22,56 +23,62 @@ galaxy.workflow.extract module ------------------------------ .. automodule:: galaxy.workflow.extract - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.modules module ------------------------------ .. automodule:: galaxy.workflow.modules - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.render module ----------------------------- .. automodule:: galaxy.workflow.render - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.run module -------------------------- .. automodule:: galaxy.workflow.run - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.run\_request module ----------------------------------- .. automodule:: galaxy.workflow.run_request - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.scheduling\_manager module ------------------------------------------ .. automodule:: galaxy.workflow.scheduling_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy.workflow.steps module ---------------------------- .. automodule:: galaxy.workflow.steps - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: +galaxy.workflow.trs\_proxy module +--------------------------------- +.. automodule:: galaxy.workflow.trs_proxy + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst index 43801194aa8..9e1627b2589 100644 --- a/doc/source/lib/galaxy.workflow.schedulers.rst +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -2,9 +2,9 @@ galaxy.workflow.schedulers package ================================== .. automodule:: galaxy.workflow.schedulers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy.workflow.schedulers.core module -------------------------------------- .. automodule:: galaxy.workflow.schedulers.core - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_ext.expressions.rst b/doc/source/lib/galaxy_ext.expressions.rst index 8ddd34f7020..df712ca1542 100644 --- a/doc/source/lib/galaxy_ext.expressions.rst +++ b/doc/source/lib/galaxy_ext.expressions.rst @@ -2,9 +2,9 @@ galaxy\_ext.expressions package =============================== .. automodule:: galaxy_ext.expressions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy\_ext.expressions.handle\_job module ------------------------------------------ .. automodule:: galaxy_ext.expressions.handle_job - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst index f02145f9106..a29461e1e6b 100644 --- a/doc/source/lib/galaxy_ext.metadata.rst +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -2,9 +2,9 @@ galaxy\_ext.metadata package ============================ .. automodule:: galaxy_ext.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ galaxy\_ext.metadata.set\_metadata module ----------------------------------------- .. automodule:: galaxy_ext.metadata.set_metadata - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index 824dc1eaf63..22bf2e82487 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -2,15 +2,15 @@ galaxy\_ext package =================== .. automodule:: galaxy_ext - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy_ext.expressions - galaxy_ext.metadata - + galaxy_ext.expressions + galaxy_ext.metadata diff --git a/doc/source/lib/galaxy_test.api.rst b/doc/source/lib/galaxy_test.api.rst index 30868c7bf41..cfb24861349 100644 --- a/doc/source/lib/galaxy_test.api.rst +++ b/doc/source/lib/galaxy_test.api.rst @@ -2,9 +2,9 @@ galaxy\_test.api package ======================== .. automodule:: galaxy_test.api - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,216 +13,214 @@ galaxy\_test.api.test\_api\_batch module ---------------------------------------- .. automodule:: galaxy_test.api.test_api_batch - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_authenticate module ------------------------------------------ .. automodule:: galaxy_test.api.test_authenticate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_configuration module ------------------------------------------- .. automodule:: galaxy_test.api.test_configuration - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_dataset\_collections module -------------------------------------------------- .. automodule:: galaxy_test.api.test_dataset_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_datasets module -------------------------------------- .. automodule:: galaxy_test.api.test_datasets - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_datatypes module --------------------------------------- .. automodule:: galaxy_test.api.test_datatypes - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_framework module --------------------------------------- .. automodule:: galaxy_test.api.test_framework - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_galaxy\_interactor module ------------------------------------------------ .. automodule:: galaxy_test.api.test_galaxy_interactor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_histories module --------------------------------------- .. automodule:: galaxy_test.api.test_histories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_history\_contents module ----------------------------------------------- .. automodule:: galaxy_test.api.test_history_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_history\_contents\_provenance module ----------------------------------------------------------- .. automodule:: galaxy_test.api.test_history_contents_provenance - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_jobs module ---------------------------------- .. automodule:: galaxy_test.api.test_jobs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_libraries module --------------------------------------- .. automodule:: galaxy_test.api.test_libraries - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_page\_revisions module --------------------------------------------- .. automodule:: galaxy_test.api.test_page_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_pages module ----------------------------------- .. automodule:: galaxy_test.api.test_pages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_roles module ----------------------------------- .. automodule:: galaxy_test.api.test_roles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_search module ------------------------------------ .. automodule:: galaxy_test.api.test_search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_tool\_data module ---------------------------------------- .. automodule:: galaxy_test.api.test_tool_data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_tools module ----------------------------------- .. automodule:: galaxy_test.api.test_tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_tools\_upload module ------------------------------------------- .. automodule:: galaxy_test.api.test_tools_upload - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_tours module ----------------------------------- .. automodule:: galaxy_test.api.test_tours - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_users module ----------------------------------- .. automodule:: galaxy_test.api.test_users - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_visualizations module -------------------------------------------- .. automodule:: galaxy_test.api.test_visualizations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_webhooks module -------------------------------------- .. automodule:: galaxy_test.api.test_webhooks - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_workflow\_extraction module -------------------------------------------------- .. automodule:: galaxy_test.api.test_workflow_extraction - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_workflows module --------------------------------------- .. automodule:: galaxy_test.api.test_workflows - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.api.test\_workflows\_from\_yaml module --------------------------------------------------- .. automodule:: galaxy_test.api.test_workflows_from_yaml - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.base.rst b/doc/source/lib/galaxy_test.base.rst index e597b81b4fd..f3c83ac8519 100644 --- a/doc/source/lib/galaxy_test.base.rst +++ b/doc/source/lib/galaxy_test.base.rst @@ -2,91 +2,113 @@ galaxy\_test.base package ========================= .. automodule:: galaxy_test.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- +galaxy\_test.base.api module +---------------------------- + +.. automodule:: galaxy_test.base.api + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.base.api\_asserts module ------------------------------------- .. automodule:: galaxy_test.base.api_asserts - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.api\_util module ---------------------------------- .. automodule:: galaxy_test.base.api_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.constants module ---------------------------------- .. automodule:: galaxy_test.base.constants - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.base.env module +---------------------------- + +.. automodule:: galaxy_test.base.env + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.instrument module ----------------------------------- .. automodule:: galaxy_test.base.instrument - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.interactor module ----------------------------------- .. automodule:: galaxy_test.base.interactor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.nose\_util module ----------------------------------- .. automodule:: galaxy_test.base.nose_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.populators module ----------------------------------- .. automodule:: galaxy_test.base.populators - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.rules\_test\_data module ------------------------------------------ .. automodule:: galaxy_test.base.rules_test_data - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.ssh\_util module ---------------------------------- .. automodule:: galaxy_test.base.ssh_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.base.testcase module +--------------------------------- + +.. automodule:: galaxy_test.base.testcase + :members: + :undoc-members: + :show-inheritance: galaxy\_test.base.workflow\_fixtures module ------------------------------------------- .. automodule:: galaxy_test.base.workflow_fixtures - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.driver.rst b/doc/source/lib/galaxy_test.driver.rst index f91cc319cce..03abce0b64c 100644 --- a/doc/source/lib/galaxy_test.driver.rst +++ b/doc/source/lib/galaxy_test.driver.rst @@ -2,51 +2,41 @@ galaxy\_test.driver package =========================== .. automodule:: galaxy_test.driver - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- -galaxy\_test.driver.api module ------------------------------- - -.. automodule:: galaxy_test.driver.api - :members: - :undoc-members: - :show-inheritance: - galaxy\_test.driver.driver\_util module --------------------------------------- .. automodule:: galaxy_test.driver.driver_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.driver.integration\_util module -------------------------------------------- .. automodule:: galaxy_test.driver.integration_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.driver.test\_logging module ---------------------------------------- .. automodule:: galaxy_test.driver.test_logging - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.driver.testcase module ----------------------------------- .. automodule:: galaxy_test.driver.testcase - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.rst b/doc/source/lib/galaxy_test.rst index ae9ab1e66d6..756ea47eeb8 100644 --- a/doc/source/lib/galaxy_test.rst +++ b/doc/source/lib/galaxy_test.rst @@ -2,17 +2,17 @@ galaxy\_test package ==================== .. automodule:: galaxy_test - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - galaxy_test.api - galaxy_test.base - galaxy_test.driver - galaxy_test.selenium - + galaxy_test.api + galaxy_test.base + galaxy_test.driver + galaxy_test.selenium diff --git a/doc/source/lib/galaxy_test.selenium.rst b/doc/source/lib/galaxy_test.selenium.rst index 074beee18a4..8732ba7f502 100644 --- a/doc/source/lib/galaxy_test.selenium.rst +++ b/doc/source/lib/galaxy_test.selenium.rst @@ -2,9 +2,9 @@ galaxy\_test.selenium package ============================= .. automodule:: galaxy_test.selenium - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,272 +13,278 @@ galaxy\_test.selenium.framework module -------------------------------------- .. automodule:: galaxy_test.selenium.framework - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_admin\_app module --------------------------------------------- .. automodule:: galaxy_test.selenium.test_admin_app - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_anon\_history module ------------------------------------------------ .. automodule:: galaxy_test.selenium.test_anon_history - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_change\_password module --------------------------------------------------- .. automodule:: galaxy_test.selenium.test_change_password - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_collection\_builders module ------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_collection_builders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_custom\_builds module ------------------------------------------------- .. automodule:: galaxy_test.selenium.test_custom_builds - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_histories\_list module -------------------------------------------------- .. automodule:: galaxy_test.selenium.test_histories_list - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_copy\_elements module ---------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_copy_elements - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_dataset\_state module ---------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_dataset_state - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_multi\_view module ------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_multi_view - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_options module --------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_options - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_panel module ------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_panel - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_panel\_collections module -------------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_panel_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_panel\_pagination module ------------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_panel_pagination - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_history\_sharing module --------------------------------------------------- .. automodule:: galaxy_test.selenium.test_history_sharing - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.selenium.test\_history\_structure module +----------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_history_structure + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_jupyter module ------------------------------------------ .. automodule:: galaxy_test.selenium.test_jupyter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_library\_contents module ---------------------------------------------------- .. automodule:: galaxy_test.selenium.test_library_contents - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_library\_landing module --------------------------------------------------- .. automodule:: galaxy_test.selenium.test_library_landing - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_library\_to\_collections module ----------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_library_to_collections - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_login module ---------------------------------------- .. automodule:: galaxy_test.selenium.test_login - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_navigates\_galaxy module ---------------------------------------------------- .. automodule:: galaxy_test.selenium.test_navigates_galaxy - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_pages module ---------------------------------------- .. automodule:: galaxy_test.selenium.test_pages - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_personal\_information module -------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_personal_information - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_published\_histories\_grid module ------------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_published_histories_grid - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_registration module ----------------------------------------------- .. automodule:: galaxy_test.selenium.test_registration - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_sign\_out module -------------------------------------------- .. automodule:: galaxy_test.selenium.test_sign_out - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_sizzle\_loading module -------------------------------------------------- .. automodule:: galaxy_test.selenium.test_sizzle_loading - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_stock\_tours module ----------------------------------------------- .. automodule:: galaxy_test.selenium.test_stock_tours - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_tool\_describing\_tours module ---------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_tool_describing_tours - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_tool\_form module --------------------------------------------- .. automodule:: galaxy_test.selenium.test_tool_form - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_uploads module ------------------------------------------ .. automodule:: galaxy_test.selenium.test_uploads - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_workflow\_editor module --------------------------------------------------- .. automodule:: galaxy_test.selenium.test_workflow_editor - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_workflow\_management module ------------------------------------------------------- .. automodule:: galaxy_test.selenium.test_workflow_management - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: galaxy\_test.selenium.test\_workflow\_run module ------------------------------------------------ .. automodule:: galaxy_test.selenium.test_workflow_run - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst index a0fec837ad4..2e291cd751a 100644 --- a/doc/source/lib/tool_shed.dependencies.repository.rst +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -2,9 +2,9 @@ tool\_shed.dependencies.repository package ========================================== .. automodule:: tool_shed.dependencies.repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ tool\_shed.dependencies.repository.relation\_builder module ----------------------------------------------------------- .. automodule:: tool_shed.dependencies.repository.relation_builder - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst index d78fa5a2b7b..8bdead91785 100644 --- a/doc/source/lib/tool_shed.dependencies.rst +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -2,17 +2,18 @@ tool\_shed.dependencies package =============================== .. automodule:: tool_shed.dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.dependencies.repository - tool_shed.dependencies.tool + tool_shed.dependencies.repository + tool_shed.dependencies.tool Submodules ---------- @@ -21,8 +22,6 @@ tool\_shed.dependencies.attribute\_handlers module -------------------------------------------------- .. automodule:: tool_shed.dependencies.attribute_handlers - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst index 024726c14b2..01ccf34461c 100644 --- a/doc/source/lib/tool_shed.dependencies.tool.rst +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -2,9 +2,9 @@ tool\_shed.dependencies.tool package ==================================== .. automodule:: tool_shed.dependencies.tool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ tool\_shed.dependencies.tool.tag\_attribute\_handler module ----------------------------------------------------------- .. automodule:: tool_shed.dependencies.tool.tag_attribute_handler - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst index 04e2fc38e54..afa46002510 100644 --- a/doc/source/lib/tool_shed.galaxy_install.grids.rst +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -2,9 +2,9 @@ tool\_shed.galaxy\_install.grids package ======================================== .. automodule:: tool_shed.galaxy_install.grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ tool\_shed.galaxy\_install.grids.admin\_toolshed\_grids module -------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index b0a892fe6cc..aa13a373953 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -2,17 +2,18 @@ tool\_shed.galaxy\_install package ================================== .. automodule:: tool_shed.galaxy_install - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.galaxy_install.grids - tool_shed.galaxy_install.utility_containers + tool_shed.galaxy_install.grids + tool_shed.galaxy_install.utility_containers Submodules ---------- @@ -21,8 +22,6 @@ tool\_shed.galaxy\_install.dependency\_display module ----------------------------------------------------- .. automodule:: tool_shed.galaxy_install.dependency_display - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst index 768dac7ce96..bf34663a199 100644 --- a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -2,7 +2,6 @@ tool\_shed.galaxy\_install.utility\_containers package ====================================================== .. automodule:: tool_shed.galaxy_install.utility_containers - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst index 59ec7e90ad8..0998ba7dc1f 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -2,9 +2,9 @@ tool\_shed.grids package ======================== .. automodule:: tool_shed.grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,40 +13,38 @@ tool\_shed.grids.admin\_grids module ------------------------------------ .. automodule:: tool_shed.grids.admin_grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.grids.repository\_grid\_filter\_manager module --------------------------------------------------------- .. automodule:: tool_shed.grids.repository_grid_filter_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.grids.repository\_grids module ----------------------------------------- .. automodule:: tool_shed.grids.repository_grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.grids.repository\_review\_grids module ------------------------------------------------- .. automodule:: tool_shed.grids.repository_review_grids - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.grids.util module ---------------------------- .. automodule:: tool_shed.grids.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst index 5c7928cf6e1..24ba2192e48 100644 --- a/doc/source/lib/tool_shed.managers.rst +++ b/doc/source/lib/tool_shed.managers.rst @@ -2,9 +2,9 @@ tool\_shed.managers package =========================== .. automodule:: tool_shed.managers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ tool\_shed.managers.groups module --------------------------------- .. automodule:: tool_shed.managers.groups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.managers.repositories module --------------------------------------- .. automodule:: tool_shed.managers.repositories - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst index 8f0215125f6..49d8fa35c56 100644 --- a/doc/source/lib/tool_shed.metadata.rst +++ b/doc/source/lib/tool_shed.metadata.rst @@ -2,9 +2,9 @@ tool\_shed.metadata package =========================== .. automodule:: tool_shed.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ tool\_shed.metadata.metadata\_generator module ---------------------------------------------- .. automodule:: tool_shed.metadata.metadata_generator - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.metadata.repository\_metadata\_manager module -------------------------------------------------------- .. automodule:: tool_shed.metadata.repository_metadata_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst index 55d6b2743bc..4372649f79d 100644 --- a/doc/source/lib/tool_shed.repository_types.rst +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -2,9 +2,9 @@ tool\_shed.repository\_types package ==================================== .. automodule:: tool_shed.repository_types - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,48 +13,46 @@ tool\_shed.repository\_types.metadata module -------------------------------------------- .. automodule:: tool_shed.repository_types.metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.repository\_types.registry module -------------------------------------------- .. automodule:: tool_shed.repository_types.registry - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.repository\_types.repository\_suite\_definition module ----------------------------------------------------------------- .. automodule:: tool_shed.repository_types.repository_suite_definition - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.repository\_types.tool\_dependency\_definition module ---------------------------------------------------------------- .. automodule:: tool_shed.repository_types.tool_dependency_definition - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.repository\_types.unrestricted module ------------------------------------------------ .. automodule:: tool_shed.repository_types.unrestricted - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.repository\_types.util module ---------------------------------------- .. automodule:: tool_shed.repository_types.util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index 0b7e6e7e57f..7610d74557b 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -2,26 +2,27 @@ tool\_shed package ================== .. automodule:: tool_shed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.dependencies - tool_shed.galaxy_install - tool_shed.grids - tool_shed.managers - tool_shed.metadata - tool_shed.repository_types - tool_shed.test - tool_shed.tools - tool_shed.util - tool_shed.utility_containers - tool_shed.webapp + tool_shed.dependencies + tool_shed.galaxy_install + tool_shed.grids + tool_shed.managers + tool_shed.metadata + tool_shed.repository_types + tool_shed.test + tool_shed.tools + tool_shed.util + tool_shed.utility_containers + tool_shed.webapp Submodules ---------- @@ -30,8 +31,6 @@ tool\_shed.repository\_registry module -------------------------------------- .. automodule:: tool_shed.repository_registry - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.test.base.rst b/doc/source/lib/tool_shed.test.base.rst index f3f2f0b91fb..2b9c59afc8e 100644 --- a/doc/source/lib/tool_shed.test.base.rst +++ b/doc/source/lib/tool_shed.test.base.rst @@ -2,9 +2,9 @@ tool\_shed.test.base package ============================ .. automodule:: tool_shed.test.base - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ tool\_shed.test.base.common module ---------------------------------- .. automodule:: tool_shed.test.base.common - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.base.test\_db\_util module ------------------------------------------ .. automodule:: tool_shed.test.base.test_db_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.base.twilltestcase module ----------------------------------------- .. automodule:: tool_shed.test.base.twilltestcase - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.test.functional.rst b/doc/source/lib/tool_shed.test.functional.rst index bc0fe095ec9..557c9a025f0 100644 --- a/doc/source/lib/tool_shed.test.functional.rst +++ b/doc/source/lib/tool_shed.test.functional.rst @@ -2,9 +2,9 @@ tool\_shed.test.functional package ================================== .. automodule:: tool_shed.test.functional - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,480 +13,478 @@ tool\_shed.test.functional.test\_0000\_basic\_repository\_features module ------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0000_basic_repository_features - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0010\_repository\_with\_tool\_dependencies module ---------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0010_repository_with_tool_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0020\_basic\_repository\_dependencies module ----------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0020_basic_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0030\_repository\_dependency\_revisions module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0030_repository_dependency_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0040\_repository\_circular\_dependencies module -------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0040_repository_circular_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0050\_circular\_dependencies\_4\_levels module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0050_circular_dependencies_4_levels - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0070\_invalid\_tool module ----------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0070_invalid_tool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0080\_advanced\_circular\_dependencies module ------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0080_advanced_circular_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0090\_tool\_search module ---------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0090_tool_search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0100\_complex\_repository\_dependencies module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0100_complex_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0110\_invalid\_simple\_repository\_dependencies module --------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0120\_simple\_repository\_dependency\_multiple\_owners module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0130\_datatype\_converters module ------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0130_datatype_converters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0140\_tool\_help\_images module ---------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0140_tool_help_images - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0150\_prior\_installation\_required module --------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0150_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0160\_circular\_prior\_installation\_required module ------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0160_circular_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0170\_complex\_prior\_installation\_required module ------------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0170_complex_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0300\_reset\_all\_metadata module ------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0300_reset_all_metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0310\_hg\_api\_features module --------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0310_hg_api_features - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0400\_repository\_component\_reviews module ---------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0400_repository_component_reviews - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0410\_repository\_component\_review\_access\_control module -------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0410_repository_component_review_access_control - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0420\_citable\_urls\_for\_repositories module ------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0420_citable_urls_for_repositories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0430\_browse\_utilities module --------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0430_browse_utilities - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0440\_deleting\_dependency\_definitions module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0440_deleting_dependency_definitions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0460\_upload\_to\_repository module -------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0460_upload_to_repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0470\_tool\_dependency\_repository\_type module -------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0470_tool_dependency_repository_type - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0480\_tool\_dependency\_xml\_verification module --------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0480_tool_dependency_xml_verification - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0530\_repository\_admin\_feature module ------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_0530_repository_admin_feature - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0540\_get\_all\_metadata\_from\_api module --------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0540_get_all_metadata_from_api - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_0550\_metadata\_updated\_dependencies module ----------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_0550_metadata_updated_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1000\_install\_basic\_repository module ------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1000_install_basic_repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1010\_install\_repository\_with\_tool\_dependencies module ------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1020\_install\_repository\_with\_repository\_dependencies module ------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1030\_install\_repository\_with\_dependency\_revisions module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1040\_install\_repository\_basic\_circular\_dependencies module ------------------------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1050\_circular\_dependencies\_4\_levels module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1050_circular_dependencies_4_levels - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1070\_invalid\_tool module ----------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1070_invalid_tool - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1080\_advanced\_circular\_dependency\_installation module ------------------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1080_advanced_circular_dependency_installation - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1090\_repository\_dependency\_handling module ------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1090_repository_dependency_handling - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1100\_install\_updated\_repository\_dependencies module ---------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1100_install_updated_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1120\_install\_repository\_with\_complex\_dependencies module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1130\_install\_repository\_with\_invalid\_repository\_dependency module -------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1140\_simple\_repository\_dependency\_multiple\_owners module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1150\_datatype\_converters module ------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1150_datatype_converters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1160\_tool\_help\_images module ---------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1160_tool_help_images - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1170\_prior\_installation\_required module --------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1170_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1180\_circular\_prior\_installation\_required module ------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1180_circular_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1190\_complex\_prior\_installation\_required module ------------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1190_complex_prior_installation_required - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1200\_uninstall\_and\_reinstall\_basic\_repository module ------------------------------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1210\_uninstall\_reinstall\_repository\_with\_tool\_dependencies module -------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1220\_uninstall\_reinstall\_repository\_with\_repository\_dependencies module -------------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1230\_uninstall\_reinstall\_repository\_with\_dependency\_revisions module ----------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1300\_reset\_all\_metadata module ------------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1300_reset_all_metadata - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1410\_update\_manager module ------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1410_update_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1420\_tool\_dependency\_environment\_inheritance module ---------------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1430\_repair\_installed\_repository module --------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1430_repair_installed_repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1440\_missing\_env\_sh\_files module --------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1440_missing_env_sh_files - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1450\_installing\_datatypes\_sniffers module ----------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1450_installing_datatypes_sniffers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1460\_data\_managers module ------------------------------------------------------------ .. automodule:: tool_shed.test.functional.test_1460_data_managers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.test.functional.test\_1470\_updating\_installed\_repositories module ------------------------------------------------------------------------------- .. automodule:: tool_shed.test.functional.test_1470_updating_installed_repositories - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.test.rst b/doc/source/lib/tool_shed.test.rst index b6326781c82..9fe5aeb2b23 100644 --- a/doc/source/lib/tool_shed.test.rst +++ b/doc/source/lib/tool_shed.test.rst @@ -2,17 +2,18 @@ tool\_shed.test package ======================= .. automodule:: tool_shed.test - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.test.base - tool_shed.test.functional + tool_shed.test.base + tool_shed.test.functional Submodules ---------- @@ -21,8 +22,6 @@ tool\_shed.test.functional\_tests module ---------------------------------------- .. automodule:: tool_shed.test.functional_tests - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst index 79b0a68851f..08dfff42902 100644 --- a/doc/source/lib/tool_shed.tools.rst +++ b/doc/source/lib/tool_shed.tools.rst @@ -2,9 +2,9 @@ tool\_shed.tools package ======================== .. automodule:: tool_shed.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,24 +13,22 @@ tool\_shed.tools.data\_table\_manager module -------------------------------------------- .. automodule:: tool_shed.tools.data_table_manager - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.tools.tool\_validator module --------------------------------------- .. automodule:: tool_shed.tools.tool_validator - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.tools.tool\_version\_manager module ---------------------------------------------- .. automodule:: tool_shed.tools.tool_version_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index 38b9508f45c..1c641b8ec62 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -2,9 +2,9 @@ tool\_shed.util package ======================= .. automodule:: tool_shed.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,160 +13,158 @@ tool\_shed.util.admin\_util module ---------------------------------- .. automodule:: tool_shed.util.admin_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.basic\_util module ---------------------------------- .. automodule:: tool_shed.util.basic_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.commit\_util module ----------------------------------- .. automodule:: tool_shed.util.commit_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.common\_util module ----------------------------------- .. automodule:: tool_shed.util.common_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.container\_util module -------------------------------------- .. automodule:: tool_shed.util.container_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.encoding\_util module ------------------------------------- .. automodule:: tool_shed.util.encoding_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.hg\_util module ------------------------------- .. automodule:: tool_shed.util.hg_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.hgweb\_config module ------------------------------------ .. automodule:: tool_shed.util.hgweb_config - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.metadata\_util module ------------------------------------- .. automodule:: tool_shed.util.metadata_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.readme\_util module ----------------------------------- .. automodule:: tool_shed.util.readme_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.repository\_content\_util module ------------------------------------------------ .. automodule:: tool_shed.util.repository_content_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.repository\_util module --------------------------------------- .. automodule:: tool_shed.util.repository_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.review\_util module ----------------------------------- .. automodule:: tool_shed.util.review_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.search\_util module ----------------------------------- .. automodule:: tool_shed.util.search_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.shed\_index module ---------------------------------- .. automodule:: tool_shed.util.shed_index - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.shed\_util\_common module ----------------------------------------- .. automodule:: tool_shed.util.shed_util_common - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.tool\_dependency\_util module --------------------------------------------- .. automodule:: tool_shed.util.tool_dependency_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.tool\_util module --------------------------------- .. automodule:: tool_shed.util.tool_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.web\_util module -------------------------------- .. automodule:: tool_shed.util.web_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.util.xml\_util module -------------------------------- .. automodule:: tool_shed.util.xml_util - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst index f34ec9cf8f5..2677a3ca86d 100644 --- a/doc/source/lib/tool_shed.utility_containers.rst +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -2,9 +2,9 @@ tool\_shed.utility\_containers package ====================================== .. automodule:: tool_shed.utility_containers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ tool\_shed.utility\_containers.utility\_container\_manager module ----------------------------------------------------------------- .. automodule:: tool_shed.utility_containers.utility_container_manager - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.api.rst b/doc/source/lib/tool_shed.webapp.api.rst index e994dde56f7..c4681c4a74c 100644 --- a/doc/source/lib/tool_shed.webapp.api.rst +++ b/doc/source/lib/tool_shed.webapp.api.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.api package ============================= .. automodule:: tool_shed.webapp.api - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,64 +13,62 @@ tool\_shed.webapp.api.authenticate module ----------------------------------------- .. automodule:: tool_shed.webapp.api.authenticate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.categories module --------------------------------------- .. automodule:: tool_shed.webapp.api.categories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.configuration module ------------------------------------------ .. automodule:: tool_shed.webapp.api.configuration - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.groups module ----------------------------------- .. automodule:: tool_shed.webapp.api.groups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.repositories module ----------------------------------------- .. automodule:: tool_shed.webapp.api.repositories - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.repository\_revisions module -------------------------------------------------- .. automodule:: tool_shed.webapp.api.repository_revisions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.tools module ---------------------------------- .. automodule:: tool_shed.webapp.api.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.api.users module ---------------------------------- .. automodule:: tool_shed.webapp.api.users - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.controllers.rst b/doc/source/lib/tool_shed.webapp.controllers.rst index 682f885b40a..19c90bfb793 100644 --- a/doc/source/lib/tool_shed.webapp.controllers.rst +++ b/doc/source/lib/tool_shed.webapp.controllers.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.controllers package ===================================== .. automodule:: tool_shed.webapp.controllers - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,56 +13,54 @@ tool\_shed.webapp.controllers.admin module ------------------------------------------ .. automodule:: tool_shed.webapp.controllers.admin - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.groups module ------------------------------------------- .. automodule:: tool_shed.webapp.controllers.groups - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.hg module --------------------------------------- .. automodule:: tool_shed.webapp.controllers.hg - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.repository module ----------------------------------------------- .. automodule:: tool_shed.webapp.controllers.repository - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.repository\_review module ------------------------------------------------------- .. automodule:: tool_shed.webapp.controllers.repository_review - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.upload module ------------------------------------------- .. automodule:: tool_shed.webapp.controllers.upload - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.controllers.user module ----------------------------------------- .. automodule:: tool_shed.webapp.controllers.user - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.framework.middleware.rst b/doc/source/lib/tool_shed.webapp.framework.middleware.rst index 0bbccb893cf..9b02ea6fda2 100644 --- a/doc/source/lib/tool_shed.webapp.framework.middleware.rst +++ b/doc/source/lib/tool_shed.webapp.framework.middleware.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.framework.middleware package ============================================== .. automodule:: tool_shed.webapp.framework.middleware - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,8 +13,6 @@ tool\_shed.webapp.framework.middleware.remoteuser module -------------------------------------------------------- .. automodule:: tool_shed.webapp.framework.middleware.remoteuser - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.framework.rst b/doc/source/lib/tool_shed.webapp.framework.rst index 13bc1d048a6..ec00b6b50b7 100644 --- a/doc/source/lib/tool_shed.webapp.framework.rst +++ b/doc/source/lib/tool_shed.webapp.framework.rst @@ -2,14 +2,14 @@ tool\_shed.webapp.framework package =================================== .. automodule:: tool_shed.webapp.framework - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.webapp.framework.middleware - + tool_shed.webapp.framework.middleware diff --git a/doc/source/lib/tool_shed.webapp.model.migrate.rst b/doc/source/lib/tool_shed.webapp.model.migrate.rst index a2ef40e7a68..ae51d45507e 100644 --- a/doc/source/lib/tool_shed.webapp.model.migrate.rst +++ b/doc/source/lib/tool_shed.webapp.model.migrate.rst @@ -2,16 +2,17 @@ tool\_shed.webapp.model.migrate package ======================================= .. automodule:: tool_shed.webapp.model.migrate - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.webapp.model.migrate.versions + tool_shed.webapp.model.migrate.versions Submodules ---------- @@ -20,8 +21,6 @@ tool\_shed.webapp.model.migrate.check module -------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.check - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.model.migrate.versions.rst b/doc/source/lib/tool_shed.webapp.model.migrate.versions.rst index 5161840079d..ac92fea25a5 100644 --- a/doc/source/lib/tool_shed.webapp.model.migrate.versions.rst +++ b/doc/source/lib/tool_shed.webapp.model.migrate.versions.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.model.migrate.versions package ================================================ .. automodule:: tool_shed.webapp.model.migrate.versions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,208 +13,206 @@ tool\_shed.webapp.model.migrate.versions.0001\_initial\_tables module --------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0001_initial_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0002\_add\_tool\_suite\_column module ------------------------------------------------------------------------------ .. automodule:: tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0003\_review\_and\_review\_association\_tables module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0004\_repository\_tables module ------------------------------------------------------------------------ .. automodule:: tool_shed.webapp.model.migrate.versions.0004_repository_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0005\_drop\_tool\_related\_tables module --------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0006\_add\_email\_alerts\_column module -------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0007\_add\_long\_description\_times\_downloaded\_columns module -------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0008\_add\_repository\_metadata\_table module -------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0009\_add\_malicious\_column module ---------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0009_add_malicious_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0010\_add\_new\_repo\_alert\_column module ----------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0011\_add\_tool\_versions\_column module --------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0012\_add\_downloadable\_column module ------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0013\_add\_review\_tables module ------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0013_add_review_tables - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0014\_add\_deprecated\_column module ----------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0015\_add\_api\_keys\_table module --------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0016\_add\_do\_not\_test\_tools\_functionally\_correct\_errors\_columns module ----------------------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0017\_add\_galaxy\_utility\_columns\_to\_repository\_metadata\_table module -------------------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0018\_add\_repository\_metadata\_flag\_columns module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0019\_add\_skip\_tool\_test\_table\_and\_test\_install\_error\_column module --------------------------------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0020\_add\_repository\_type\_column module ----------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0021\_change\_repository\_type\_value module ------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0022\_add\_repository\_admin\_roles module ----------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0023\_add\_repository\_url\_and\_hompeage\_url module ---------------------------------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0024\_password\_reset module --------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0024_password_reset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0025\_session\_timeout module ---------------------------------------------------------------------- .. automodule:: tool_shed.webapp.model.migrate.versions.0025_session_timeout - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.model.migrate.versions.0026\_add\_numeric\_revision\_column module ------------------------------------------------------------------------------------ .. automodule:: tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.model.rst b/doc/source/lib/tool_shed.webapp.model.rst index e6533dc7022..4faabf36432 100644 --- a/doc/source/lib/tool_shed.webapp.model.rst +++ b/doc/source/lib/tool_shed.webapp.model.rst @@ -2,16 +2,17 @@ tool\_shed.webapp.model package =============================== .. automodule:: tool_shed.webapp.model - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.webapp.model.migrate + tool_shed.webapp.model.migrate Submodules ---------- @@ -20,8 +21,6 @@ tool\_shed.webapp.model.mapping module -------------------------------------- .. automodule:: tool_shed.webapp.model.mapping - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.rst b/doc/source/lib/tool_shed.webapp.rst index 5eb4ee6c7de..03e9896effc 100644 --- a/doc/source/lib/tool_shed.webapp.rst +++ b/doc/source/lib/tool_shed.webapp.rst @@ -2,22 +2,23 @@ tool\_shed.webapp package ========================= .. automodule:: tool_shed.webapp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Subpackages ----------- .. toctree:: + :maxdepth: 4 - tool_shed.webapp.api - tool_shed.webapp.controllers - tool_shed.webapp.framework - tool_shed.webapp.model - tool_shed.webapp.search - tool_shed.webapp.security - tool_shed.webapp.util + tool_shed.webapp.api + tool_shed.webapp.controllers + tool_shed.webapp.framework + tool_shed.webapp.model + tool_shed.webapp.search + tool_shed.webapp.security + tool_shed.webapp.util Submodules ---------- @@ -26,24 +27,22 @@ tool\_shed.webapp.app module ---------------------------- .. automodule:: tool_shed.webapp.app - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.buildapp module --------------------------------- .. automodule:: tool_shed.webapp.buildapp - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.config module ------------------------------- .. automodule:: tool_shed.webapp.config - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.search.rst b/doc/source/lib/tool_shed.webapp.search.rst index 412541e77b3..c8a4d012c9c 100644 --- a/doc/source/lib/tool_shed.webapp.search.rst +++ b/doc/source/lib/tool_shed.webapp.search.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.search package ================================ .. automodule:: tool_shed.webapp.search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ tool\_shed.webapp.search.repo\_search module -------------------------------------------- .. automodule:: tool_shed.webapp.search.repo_search - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.search.tool\_search module -------------------------------------------- .. automodule:: tool_shed.webapp.search.tool_search - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.security.rst b/doc/source/lib/tool_shed.webapp.security.rst index 5942b7917dd..46ba40e2b63 100644 --- a/doc/source/lib/tool_shed.webapp.security.rst +++ b/doc/source/lib/tool_shed.webapp.security.rst @@ -2,7 +2,6 @@ tool\_shed.webapp.security package ================================== .. automodule:: tool_shed.webapp.security - :members: - :undoc-members: - :show-inheritance: - + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.util.rst b/doc/source/lib/tool_shed.webapp.util.rst index 4cb3d52874c..9f2494c084d 100644 --- a/doc/source/lib/tool_shed.webapp.util.rst +++ b/doc/source/lib/tool_shed.webapp.util.rst @@ -2,9 +2,9 @@ tool\_shed.webapp.util package ============================== .. automodule:: tool_shed.webapp.util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: Submodules ---------- @@ -13,16 +13,14 @@ tool\_shed.webapp.util.ratings\_util module ------------------------------------------- .. automodule:: tool_shed.webapp.util.ratings_util - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: tool\_shed.webapp.util.shed\_statistics module ---------------------------------------------- .. automodule:: tool_shed.webapp.util.shed_statistics - :members: - :undoc-members: - :show-inheritance: - - + :members: + :undoc-members: + :show-inheritance: