From 17beaef6249d69d2a85880686d6271663f010d00 Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Fri, 5 Jul 2019 17:21:31 +0200 Subject: [PATCH] Update Sphinx RST files for lib/ Running sphinx 1.8.5 updates all files (one known update: periods are no longer escaped) --- doc/source/lib/galaxy.actions.rst | 12 +- doc/source/lib/galaxy.auth.providers.rst | 20 +- doc/source/lib/galaxy.auth.rst | 8 +- doc/source/lib/galaxy.authnz.rst | 20 +- doc/source/lib/galaxy.containers.rst | 20 +- .../lib/galaxy.datatypes.converters.rst | 140 +- .../lib/galaxy.datatypes.dataproviders.rst | 40 +- .../galaxy.datatypes.display_applications.rst | 16 +- doc/source/lib/galaxy.datatypes.rst | 162 ++- doc/source/lib/galaxy.datatypes.util.rst | 12 +- doc/source/lib/galaxy.dependencies.rst | 4 +- doc/source/lib/galaxy.eggs.rst | 4 +- doc/source/lib/galaxy.exceptions.rst | 8 +- doc/source/lib/galaxy.forms.rst | 8 +- doc/source/lib/galaxy.job_execution.rst | 28 + .../lib/galaxy.job_metrics.collectl.rst | 44 + .../lib/galaxy.job_metrics.instrumenters.rst | 76 + doc/source/lib/galaxy.job_metrics.rst | 28 + doc/source/lib/galaxy.jobs.actions.rst | 8 +- doc/source/lib/galaxy.jobs.rst | 54 +- doc/source/lib/galaxy.jobs.rules.rst | 8 + doc/source/lib/galaxy.jobs.runners.rst | 56 +- .../galaxy.jobs.runners.state_handlers.rst | 8 +- .../lib/galaxy.jobs.runners.util.cli.job.rst | 20 +- .../lib/galaxy.jobs.runners.util.cli.rst | 8 +- .../galaxy.jobs.runners.util.cli.shell.rst | 12 +- .../lib/galaxy.jobs.runners.util.condor.rst | 4 +- .../galaxy.jobs.runners.util.job_script.rst | 4 +- doc/source/lib/galaxy.jobs.runners.util.rst | 28 +- doc/source/lib/galaxy.jobs.splitters.rst | 12 +- doc/source/lib/galaxy.managers.rst | 138 +- doc/source/lib/galaxy.metadata.rst | 16 +- .../lib/galaxy.model.dataset_collections.rst | 67 + ...galaxy.model.dataset_collections.types.rst | 28 + doc/source/lib/galaxy.model.migrate.rst | 15 +- .../lib/galaxy.model.migrate.versions.rst | 1252 +++++++++++++++++ doc/source/lib/galaxy.model.orm.rst | 20 +- doc/source/lib/galaxy.model.rst | 66 +- doc/source/lib/galaxy.model.store.rst | 28 + ...galaxy.model.tool_shed_install.migrate.rst | 8 +- .../lib/galaxy.model.tool_shed_install.rst | 8 +- doc/source/lib/galaxy.objectstore.rst | 32 +- doc/source/lib/galaxy.openid.rst | 28 + doc/source/lib/galaxy.quota.rst | 4 +- doc/source/lib/galaxy.rst | 30 +- doc/source/lib/galaxy.security.rst | 20 +- doc/source/lib/galaxy.tool_util.cwl.rst | 60 + ...axy.tool_util.deps.container_resolvers.rst | 28 + .../lib/galaxy.tool_util.deps.mulled.rst | 60 + .../lib/galaxy.tool_util.deps.resolvers.rst | 84 ++ doc/source/lib/galaxy.tool_util.deps.rst | 133 ++ doc/source/lib/galaxy.tool_util.locations.rst | 36 + doc/source/lib/galaxy.tool_util.parser.rst | 92 ++ doc/source/lib/galaxy.tool_util.rst | 54 + doc/source/lib/galaxy.tools.actions.rst | 32 +- doc/source/lib/galaxy.tools.data.rst | 4 +- doc/source/lib/galaxy.tools.data_manager.rst | 8 +- .../galaxy.tools.error_reports.plugins.rst | 38 +- doc/source/lib/galaxy.tools.error_reports.rst | 4 +- doc/source/lib/galaxy.tools.expressions.rst | 36 + doc/source/lib/galaxy.tools.filters.rst | 4 +- doc/source/lib/galaxy.tools.imp_exp.rst | 12 +- doc/source/lib/galaxy.tools.linters.rst | 48 +- doc/source/lib/galaxy.tools.parameters.rst | 56 +- doc/source/lib/galaxy.tools.rst | 85 +- doc/source/lib/galaxy.tools.search.rst | 4 +- .../lib/galaxy.tools.toolbox.filters.rst | 4 +- .../lib/galaxy.tools.toolbox.lineages.rst | 12 +- doc/source/lib/galaxy.tools.toolbox.rst | 28 +- .../lib/galaxy.tools.util.galaxyops.rst | 4 +- doc/source/lib/galaxy.tools.util.rst | 8 +- .../lib/galaxy.tools.verify.asserts.rst | 28 +- doc/source/lib/galaxy.tools.verify.rst | 16 +- doc/source/lib/galaxy.tours.rst | 4 +- doc/source/lib/galaxy.util.logging.rst | 8 +- doc/source/lib/galaxy.util.pastescript.rst | 12 +- doc/source/lib/galaxy.util.path.rst | 12 +- doc/source/lib/galaxy.util.rst | 224 +-- ....visualization.data_providers.phyloviz.rst | 20 +- .../galaxy.visualization.data_providers.rst | 20 +- .../lib/galaxy.visualization.genome.rst | 4 +- .../lib/galaxy.visualization.plugins.rst | 28 +- doc/source/lib/galaxy.visualization.rst | 8 +- .../lib/galaxy.visualization.tracks.rst | 4 +- doc/source/lib/galaxy.web.base.rst | 8 +- .../lib/galaxy.web.framework.helpers.rst | 12 +- .../lib/galaxy.web.framework.middleware.rst | 48 +- doc/source/lib/galaxy.web.framework.rst | 16 +- doc/source/lib/galaxy.web.proxy.rst | 4 +- doc/source/lib/galaxy.web.rst | 22 +- doc/source/lib/galaxy.web_stack.rst | 36 + doc/source/lib/galaxy.webapps.galaxy.api.rst | 192 +-- .../lib/galaxy.webapps.galaxy.controllers.rst | 104 +- doc/source/lib/galaxy.webapps.galaxy.rst | 12 +- .../galaxy.webapps.reports.controllers.rst | 40 +- .../lib/galaxy.webapps.reports.framework.rst | 8 +- doc/source/lib/galaxy.webapps.reports.rst | 16 +- doc/source/lib/galaxy.webapps.rst | 12 +- .../lib/galaxy.webapps.tool_shed.api.rst | 36 +- .../galaxy.webapps.tool_shed.controllers.rst | 32 +- ...webapps.tool_shed.framework.middleware.rst | 8 +- .../galaxy.webapps.tool_shed.framework.rst | 4 +- ...galaxy.webapps.tool_shed.model.migrate.rst | 8 +- .../lib/galaxy.webapps.tool_shed.model.rst | 8 +- doc/source/lib/galaxy.webapps.tool_shed.rst | 16 +- .../lib/galaxy.webapps.tool_shed.search.rst | 12 +- .../lib/galaxy.webapps.tool_shed.security.rst | 4 +- .../lib/galaxy.webapps.tool_shed.util.rst | 16 +- doc/source/lib/galaxy.webhooks.rst | 4 +- doc/source/lib/galaxy.work.rst | 8 +- doc/source/lib/galaxy.workflow.resources.rst | 4 +- doc/source/lib/galaxy.workflow.rst | 32 +- doc/source/lib/galaxy.workflow.schedulers.rst | 8 +- doc/source/lib/galaxy_ext.expressions.rst | 20 + doc/source/lib/galaxy_ext.metadata.rst | 8 +- doc/source/lib/galaxy_ext.rst | 1 + doc/source/lib/tool_shed.capsule.rst | 8 +- .../lib/tool_shed.dependencies.repository.rst | 8 +- doc/source/lib/tool_shed.dependencies.rst | 8 +- .../lib/tool_shed.dependencies.tool.rst | 8 +- .../tool_shed.galaxy_install.datatypes.rst | 8 +- .../lib/tool_shed.galaxy_install.grids.rst | 8 +- .../lib/tool_shed.galaxy_install.metadata.rst | 8 +- .../lib/tool_shed.galaxy_install.migrate.rst | 12 +- ...galaxy_install.repository_dependencies.rst | 8 +- doc/source/lib/tool_shed.galaxy_install.rst | 28 +- ...alaxy_install.tool_dependencies.recipe.rst | 28 +- ..._shed.galaxy_install.tool_dependencies.rst | 8 +- .../lib/tool_shed.galaxy_install.tools.rst | 12 +- ...shed.galaxy_install.utility_containers.rst | 4 +- doc/source/lib/tool_shed.grids.rst | 24 +- doc/source/lib/tool_shed.managers.rst | 12 +- doc/source/lib/tool_shed.metadata.rst | 12 +- doc/source/lib/tool_shed.repository_types.rst | 28 +- doc/source/lib/tool_shed.rst | 8 +- doc/source/lib/tool_shed.tools.rst | 16 +- doc/source/lib/tool_shed.util.rst | 80 +- .../lib/tool_shed.utility_containers.rst | 8 +- 138 files changed, 3696 insertions(+), 1361 deletions(-) create mode 100644 doc/source/lib/galaxy.job_execution.rst create mode 100644 doc/source/lib/galaxy.job_metrics.collectl.rst create mode 100644 doc/source/lib/galaxy.job_metrics.instrumenters.rst create mode 100644 doc/source/lib/galaxy.job_metrics.rst create mode 100644 doc/source/lib/galaxy.jobs.rules.rst create mode 100644 doc/source/lib/galaxy.model.dataset_collections.rst create mode 100644 doc/source/lib/galaxy.model.dataset_collections.types.rst create mode 100644 doc/source/lib/galaxy.model.migrate.versions.rst create mode 100644 doc/source/lib/galaxy.model.store.rst create mode 100644 doc/source/lib/galaxy.openid.rst create mode 100644 doc/source/lib/galaxy.tool_util.cwl.rst create mode 100644 doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst create mode 100644 doc/source/lib/galaxy.tool_util.deps.mulled.rst create mode 100644 doc/source/lib/galaxy.tool_util.deps.resolvers.rst create mode 100644 doc/source/lib/galaxy.tool_util.deps.rst create mode 100644 doc/source/lib/galaxy.tool_util.locations.rst create mode 100644 doc/source/lib/galaxy.tool_util.parser.rst create mode 100644 doc/source/lib/galaxy.tool_util.rst create mode 100644 doc/source/lib/galaxy.tools.expressions.rst create mode 100644 doc/source/lib/galaxy.web_stack.rst create mode 100644 doc/source/lib/galaxy_ext.expressions.rst diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index dc400ceef5f..6bef88c7bc6 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -1,5 +1,5 @@ -galaxy\.actions package -======================= +galaxy.actions package +====================== .. automodule:: galaxy.actions :members: @@ -9,16 +9,16 @@ galaxy\.actions package Submodules ---------- -galaxy\.actions\.admin module ------------------------------ +galaxy.actions.admin module +--------------------------- .. automodule:: galaxy.actions.admin :members: :undoc-members: :show-inheritance: -galaxy\.actions\.library module -------------------------------- +galaxy.actions.library module +----------------------------- .. automodule:: galaxy.actions.library :members: diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index 7ead6289940..2a5a44ea5bf 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -1,5 +1,5 @@ -galaxy\.auth\.providers package -=============================== +galaxy.auth.providers package +============================= .. automodule:: galaxy.auth.providers :members: @@ -9,32 +9,32 @@ galaxy\.auth\.providers package Submodules ---------- -galaxy\.auth\.providers\.alwaysreject module --------------------------------------------- +galaxy.auth.providers.alwaysreject module +----------------------------------------- .. automodule:: galaxy.auth.providers.alwaysreject :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.ldap\_ad module ----------------------------------------- +galaxy.auth.providers.ldap\_ad module +------------------------------------- .. automodule:: galaxy.auth.providers.ldap_ad :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.localdb module ---------------------------------------- +galaxy.auth.providers.localdb module +------------------------------------ .. automodule:: galaxy.auth.providers.localdb :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.pam\_auth module ------------------------------------------ +galaxy.auth.providers.pam\_auth module +-------------------------------------- .. automodule:: galaxy.auth.providers.pam_auth :members: diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst index 9ccf366fb84..ac0af26959e 100644 --- a/doc/source/lib/galaxy.auth.rst +++ b/doc/source/lib/galaxy.auth.rst @@ -1,5 +1,5 @@ -galaxy\.auth package -==================== +galaxy.auth package +=================== .. automodule:: galaxy.auth :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.auth\.util module -------------------------- +galaxy.auth.util module +----------------------- .. automodule:: galaxy.auth.util :members: diff --git a/doc/source/lib/galaxy.authnz.rst b/doc/source/lib/galaxy.authnz.rst index 0cf9364b89b..156c62d7961 100644 --- a/doc/source/lib/galaxy.authnz.rst +++ b/doc/source/lib/galaxy.authnz.rst @@ -1,5 +1,5 @@ -galaxy\.authnz package -====================== +galaxy.authnz package +===================== .. automodule:: galaxy.authnz :members: @@ -9,16 +9,24 @@ galaxy\.authnz package Submodules ---------- -galaxy\.authnz\.managers module -------------------------------- +galaxy.authnz.custos\_authnz module +----------------------------------- + +.. automodule:: galaxy.authnz.custos_authnz + :members: + :undoc-members: + :show-inheritance: + +galaxy.authnz.managers module +----------------------------- .. automodule:: galaxy.authnz.managers :members: :undoc-members: :show-inheritance: -galaxy\.authnz\.psa\_authnz module ----------------------------------- +galaxy.authnz.psa\_authnz module +-------------------------------- .. automodule:: galaxy.authnz.psa_authnz :members: diff --git a/doc/source/lib/galaxy.containers.rst b/doc/source/lib/galaxy.containers.rst index 79af3f5e408..8d61cd41340 100644 --- a/doc/source/lib/galaxy.containers.rst +++ b/doc/source/lib/galaxy.containers.rst @@ -1,5 +1,5 @@ -galaxy\.containers package -========================== +galaxy.containers package +========================= .. automodule:: galaxy.containers :members: @@ -9,32 +9,32 @@ galaxy\.containers package Submodules ---------- -galaxy\.containers\.docker module ---------------------------------- +galaxy.containers.docker module +------------------------------- .. automodule:: galaxy.containers.docker :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_decorators module ---------------------------------------------- +galaxy.containers.docker\_decorators module +------------------------------------------- .. automodule:: galaxy.containers.docker_decorators :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_model module ----------------------------------------- +galaxy.containers.docker\_model module +-------------------------------------- .. automodule:: galaxy.containers.docker_model :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_swarm module ----------------------------------------- +galaxy.containers.docker\_swarm module +-------------------------------------- .. automodule:: galaxy.containers.docker_swarm :members: diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 6fd2583c819..17b7134c037 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.converters package -===================================== +galaxy.datatypes.converters package +=================================== .. automodule:: galaxy.datatypes.converters :members: @@ -9,256 +9,264 @@ galaxy\.datatypes\.converters package Submodules ---------- -galaxy\.datatypes\.converters\.bed\_to\_gff\_converter module -------------------------------------------------------------- +galaxy.datatypes.converters.bed\_to\_gff\_converter module +---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bed_to_gff_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.bedgraph\_to\_array\_tree\_converter module --------------------------------------------------------------------------- +galaxy.datatypes.converters.bedgraph\_to\_array\_tree\_converter module +----------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.bgzip module -------------------------------------------- +galaxy.datatypes.converters.bgzip module +---------------------------------------- .. automodule:: galaxy.datatypes.converters.bgzip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.cram\_to\_bam module ---------------------------------------------------- +galaxy.datatypes.converters.cram\_to\_bam module +------------------------------------------------ .. automodule:: galaxy.datatypes.converters.cram_to_bam :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fasta\_to\_len module ----------------------------------------------------- +galaxy.datatypes.converters.fasta\_to\_len module +------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_len :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fasta\_to\_tabular\_converter module -------------------------------------------------------------------- +galaxy.datatypes.converters.fasta\_to\_tabular\_converter module +---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastq\_to\_fqtoc module ------------------------------------------------------- +galaxy.datatypes.converters.fastq\_to\_fqtoc module +--------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastqsolexa\_to\_fasta\_converter module ------------------------------------------------------------------------ +galaxy.datatypes.converters.fastqsolexa\_to\_fasta\_converter module +-------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastqsolexa\_to\_qual\_converter module ----------------------------------------------------------------------- +galaxy.datatypes.converters.fastqsolexa\_to\_qual\_converter module +------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.gff\_to\_bed\_converter module -------------------------------------------------------------- +galaxy.datatypes.converters.gff\_to\_bed\_converter module +---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_bed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.gff\_to\_interval\_index\_converter module -------------------------------------------------------------------------- +galaxy.datatypes.converters.gff\_to\_interval\_index\_converter module +---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_bed\_converter module ------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_bed\_converter module +--------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_bedstrict\_converter module ------------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_bedstrict\_converter module +--------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_coverage module ------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_coverage module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_coverage :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_fli module -------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_fli module +---------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_fli :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_interval\_index\_converter module ------------------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_interval\_index\_converter module +--------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_tabix\_converter module --------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_tabix\_converter module +----------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.lped\_to\_fped\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.lped\_to\_fped\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_fped_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.lped\_to\_pbed\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.lped\_to\_pbed\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.maf\_to\_fasta\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.maf\_to\_fasta\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.maf\_to\_interval\_converter module ------------------------------------------------------------------- +galaxy.datatypes.converters.maf\_to\_interval\_converter module +--------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.maf_to_interval_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.pbed\_ldreduced\_converter module ----------------------------------------------------------------- +galaxy.datatypes.converters.pbed\_ldreduced\_converter module +------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.pbed\_to\_lped\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.pbed\_to\_lped\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.picard\_interval\_list\_to\_bed6\_converter module ---------------------------------------------------------------------------------- +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: -galaxy\.datatypes\.converters\.pileup\_to\_interval\_index\_converter module ----------------------------------------------------------------------------- +galaxy.datatypes.converters.pileup\_to\_interval\_index\_converter module +------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.ref\_to\_seq\_taxonomy\_converter module ------------------------------------------------------------------------ +galaxy.datatypes.converters.ref\_to\_seq\_taxonomy\_converter module +-------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.ref_to_seq_taxonomy_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.sam\_to\_bam module --------------------------------------------------- +galaxy.datatypes.converters.sam\_to\_bam module +----------------------------------------------- .. automodule:: galaxy.datatypes.converters.sam_to_bam :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.tabular\_to\_dbnsfp module ---------------------------------------------------------- +galaxy.datatypes.converters.tabular\_csv module +----------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.tabular_csv + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.converters.tabular\_to\_dbnsfp module +------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.tabular_to_dbnsfp :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.vcf\_to\_interval\_index\_converter module -------------------------------------------------------------------------- +galaxy.datatypes.converters.vcf\_to\_interval\_index\_converter module +---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.vcf\_to\_vcf\_bgzip module ---------------------------------------------------------- +galaxy.datatypes.converters.vcf\_to\_vcf\_bgzip module +------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.wiggle\_to\_array\_tree\_converter module ------------------------------------------------------------------------- +galaxy.datatypes.converters.wiggle\_to\_array\_tree\_converter module +--------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.wiggle\_to\_simple\_converter module -------------------------------------------------------------------- +galaxy.datatypes.converters.wiggle\_to\_simple\_converter module +---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter :members: diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst index 960b5c0c304..cd85ef190df 100644 --- a/doc/source/lib/galaxy.datatypes.dataproviders.rst +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.dataproviders package -======================================== +galaxy.datatypes.dataproviders package +====================================== .. automodule:: galaxy.datatypes.dataproviders :members: @@ -9,72 +9,72 @@ galaxy\.datatypes\.dataproviders package Submodules ---------- -galaxy\.datatypes\.dataproviders\.base module ---------------------------------------------- +galaxy.datatypes.dataproviders.base module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.base :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.chunk module ----------------------------------------------- +galaxy.datatypes.dataproviders.chunk module +------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.chunk :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.column module ------------------------------------------------ +galaxy.datatypes.dataproviders.column module +-------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.column :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.dataset module ------------------------------------------------- +galaxy.datatypes.dataproviders.dataset module +--------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.dataset :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.decorators module ---------------------------------------------------- +galaxy.datatypes.dataproviders.decorators module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.decorators :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.exceptions module ---------------------------------------------------- +galaxy.datatypes.dataproviders.exceptions module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.exceptions :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.external module -------------------------------------------------- +galaxy.datatypes.dataproviders.external module +---------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.external :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.hierarchy module --------------------------------------------------- +galaxy.datatypes.dataproviders.hierarchy module +----------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.hierarchy :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.line module ---------------------------------------------- +galaxy.datatypes.dataproviders.line module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.line :members: diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index e536e1ec0b6..acbf8fd2f9c 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.display\_applications package -================================================ +galaxy.datatypes.display\_applications package +============================================== .. automodule:: galaxy.datatypes.display_applications :members: @@ -9,24 +9,24 @@ galaxy\.datatypes\.display\_applications package Submodules ---------- -galaxy\.datatypes\.display\_applications\.application module ------------------------------------------------------------- +galaxy.datatypes.display\_applications.application module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.application :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.display\_applications\.parameters module ------------------------------------------------------------ +galaxy.datatypes.display\_applications.parameters module +-------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.parameters :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.display\_applications\.util module ------------------------------------------------------ +galaxy.datatypes.display\_applications.util module +-------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.util :members: diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index 94d35a51e72..b34c4e24783 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes package -========================= +galaxy.datatypes package +======================== .. automodule:: galaxy.datatypes :members: @@ -19,272 +19,296 @@ Subpackages Submodules ---------- -galaxy\.datatypes\.annotation module ------------------------------------- +galaxy.datatypes.annotation module +---------------------------------- .. automodule:: galaxy.datatypes.annotation :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.anvio module -------------------------------- +galaxy.datatypes.anvio module +----------------------------- .. automodule:: galaxy.datatypes.anvio :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.assembly module ----------------------------------- +galaxy.datatypes.assembly module +-------------------------------- .. automodule:: galaxy.datatypes.assembly :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.binary module --------------------------------- +galaxy.datatypes.binary module +------------------------------ .. automodule:: galaxy.datatypes.binary :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.blast module -------------------------------- +galaxy.datatypes.blast module +----------------------------- .. automodule:: galaxy.datatypes.blast :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.checkers module ----------------------------------- +galaxy.datatypes.checkers module +-------------------------------- .. automodule:: galaxy.datatypes.checkers :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.chrominfo module ------------------------------------ +galaxy.datatypes.chrominfo module +--------------------------------- .. automodule:: galaxy.datatypes.chrominfo :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.constructive\_solid\_geometry module -------------------------------------------------------- +galaxy.datatypes.constructive\_solid\_geometry module +----------------------------------------------------- .. automodule:: galaxy.datatypes.constructive_solid_geometry :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.coverage module ----------------------------------- +galaxy.datatypes.coverage module +-------------------------------- .. automodule:: galaxy.datatypes.coverage :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.data module ------------------------------- +galaxy.datatypes.data module +---------------------------- .. automodule:: galaxy.datatypes.data :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.genetics module ----------------------------------- +galaxy.datatypes.genetics module +-------------------------------- .. automodule:: galaxy.datatypes.genetics :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.graph module -------------------------------- +galaxy.datatypes.gis module +--------------------------- + +.. automodule:: galaxy.datatypes.gis + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.graph module +----------------------------- .. automodule:: galaxy.datatypes.graph :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.images module --------------------------------- +galaxy.datatypes.images module +------------------------------ .. automodule:: galaxy.datatypes.images :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.interval module ----------------------------------- +galaxy.datatypes.interval module +-------------------------------- .. automodule:: galaxy.datatypes.interval :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.isa module ------------------------------ +galaxy.datatypes.isa module +--------------------------- .. automodule:: galaxy.datatypes.isa :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.metadata module ----------------------------------- +galaxy.datatypes.metadata module +-------------------------------- .. automodule:: galaxy.datatypes.metadata :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.molecules module +galaxy.datatypes.microarrays module ----------------------------------- +.. automodule:: galaxy.datatypes.microarrays + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.molecules module +--------------------------------- + .. automodule:: galaxy.datatypes.molecules :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.mothur module --------------------------------- +galaxy.datatypes.mothur module +------------------------------ .. automodule:: galaxy.datatypes.mothur :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.msa module ------------------------------ +galaxy.datatypes.msa module +--------------------------- .. automodule:: galaxy.datatypes.msa :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.neo4j module -------------------------------- +galaxy.datatypes.neo4j module +----------------------------- .. automodule:: galaxy.datatypes.neo4j :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.ngsindex module ----------------------------------- +galaxy.datatypes.ngsindex module +-------------------------------- .. automodule:: galaxy.datatypes.ngsindex :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.phylip module --------------------------------- +galaxy.datatypes.phylip module +------------------------------ .. automodule:: galaxy.datatypes.phylip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.plant\_tribes module ---------------------------------------- +galaxy.datatypes.plant\_tribes module +------------------------------------- .. automodule:: galaxy.datatypes.plant_tribes :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.proteomics module ------------------------------------- +galaxy.datatypes.proteomics module +---------------------------------- .. automodule:: galaxy.datatypes.proteomics :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.qualityscore module --------------------------------------- +galaxy.datatypes.qualityscore module +------------------------------------ .. automodule:: galaxy.datatypes.qualityscore :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.registry module ----------------------------------- +galaxy.datatypes.registry module +-------------------------------- .. automodule:: galaxy.datatypes.registry :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.sequence module ----------------------------------- +galaxy.datatypes.sequence module +-------------------------------- .. automodule:: galaxy.datatypes.sequence :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.sniff module -------------------------------- +galaxy.datatypes.sniff module +----------------------------- .. automodule:: galaxy.datatypes.sniff :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.tabular module ---------------------------------- +galaxy.datatypes.spaln module +----------------------------- + +.. automodule:: galaxy.datatypes.spaln + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tabular module +------------------------------- .. automodule:: galaxy.datatypes.tabular :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.text module ------------------------------- +galaxy.datatypes.text module +---------------------------- .. automodule:: galaxy.datatypes.text :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.tracks module --------------------------------- +galaxy.datatypes.tracks module +------------------------------ .. automodule:: galaxy.datatypes.tracks :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.triples module ---------------------------------- +galaxy.datatypes.triples module +------------------------------- .. automodule:: galaxy.datatypes.triples :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.upload\_util module --------------------------------------- +galaxy.datatypes.upload\_util module +------------------------------------ .. automodule:: galaxy.datatypes.upload_util :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.xml module ------------------------------ +galaxy.datatypes.xml module +--------------------------- .. automodule:: galaxy.datatypes.xml :members: diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 12c35b4fa78..8ac6f2c599d 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.util package -=============================== +galaxy.datatypes.util package +============================= .. automodule:: galaxy.datatypes.util :members: @@ -9,16 +9,16 @@ galaxy\.datatypes\.util package Submodules ---------- -galaxy\.datatypes\.util\.generic\_util module ---------------------------------------------- +galaxy.datatypes.util.generic\_util module +------------------------------------------ .. automodule:: galaxy.datatypes.util.generic_util :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.util\.gff\_util module ------------------------------------------ +galaxy.datatypes.util.gff\_util module +-------------------------------------- .. automodule:: galaxy.datatypes.util.gff_util :members: diff --git a/doc/source/lib/galaxy.dependencies.rst b/doc/source/lib/galaxy.dependencies.rst index 4d1dd03016a..16ce685cbc1 100644 --- a/doc/source/lib/galaxy.dependencies.rst +++ b/doc/source/lib/galaxy.dependencies.rst @@ -1,5 +1,5 @@ -galaxy\.dependencies package -============================ +galaxy.dependencies package +=========================== .. automodule:: galaxy.dependencies :members: diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index f5f8f207e3a..6331aa38fdd 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -1,5 +1,5 @@ -galaxy\.eggs package -==================== +galaxy.eggs package +=================== .. automodule:: galaxy.eggs :members: diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index 2e52a13009d..8f118c6aa45 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -1,5 +1,5 @@ -galaxy\.exceptions package -========================== +galaxy.exceptions package +========================= .. automodule:: galaxy.exceptions :members: @@ -9,8 +9,8 @@ galaxy\.exceptions package Submodules ---------- -galaxy\.exceptions\.error\_codes module ---------------------------------------- +galaxy.exceptions.error\_codes module +------------------------------------- .. automodule:: galaxy.exceptions.error_codes :members: diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst index ef27c97400e..088d52bcb9c 100644 --- a/doc/source/lib/galaxy.forms.rst +++ b/doc/source/lib/galaxy.forms.rst @@ -1,5 +1,5 @@ -galaxy\.forms package -===================== +galaxy.forms package +==================== .. automodule:: galaxy.forms :members: @@ -9,8 +9,8 @@ galaxy\.forms package Submodules ---------- -galaxy\.forms\.forms module ---------------------------- +galaxy.forms.forms module +------------------------- .. automodule:: galaxy.forms.forms :members: diff --git a/doc/source/lib/galaxy.job_execution.rst b/doc/source/lib/galaxy.job_execution.rst new file mode 100644 index 00000000000..58ab804eaf1 --- /dev/null +++ b/doc/source/lib/galaxy.job_execution.rst @@ -0,0 +1,28 @@ +galaxy.job\_execution package +============================= + +.. automodule:: galaxy.job_execution + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_execution.datasets module +------------------------------------- + +.. automodule:: galaxy.job_execution.datasets + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_execution.output\_collect module +-------------------------------------------- + +.. automodule:: galaxy.job_execution.output_collect + :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 new file mode 100644 index 00000000000..74c5ee89df1 --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.collectl.rst @@ -0,0 +1,44 @@ +galaxy.job\_metrics.collectl package +==================================== + +.. automodule:: galaxy.job_metrics.collectl + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_metrics.collectl.cli module +--------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.cli + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.processes module +--------------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.processes + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.stats module +----------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.stats + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.subsystems module +---------------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.subsystems + :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 new file mode 100644 index 00000000000..232ba437a5a --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.instrumenters.rst @@ -0,0 +1,76 @@ +galaxy.job\_metrics.instrumenters package +========================================= + +.. automodule:: galaxy.job_metrics.instrumenters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_metrics.instrumenters.cgroup module +----------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.cgroup + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.collectl module +------------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.collectl + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.core module +--------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.core + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.cpuinfo module +------------------------------------------------ + +.. automodule:: galaxy.job_metrics.instrumenters.cpuinfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.env module +-------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.env + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.hostname module +------------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.hostname + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.meminfo module +------------------------------------------------ + +.. automodule:: galaxy.job_metrics.instrumenters.meminfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.uname module +---------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.uname + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.job_metrics.rst b/doc/source/lib/galaxy.job_metrics.rst new file mode 100644 index 00000000000..9419d2aebd1 --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.rst @@ -0,0 +1,28 @@ +galaxy.job\_metrics package +=========================== + +.. automodule:: galaxy.job_metrics + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.job_metrics.collectl + galaxy.job_metrics.instrumenters + +Submodules +---------- + +galaxy.job\_metrics.formatting module +------------------------------------- + +.. automodule:: galaxy.job_metrics.formatting + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst index f0c64ad3699..7ec9a937d81 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.actions package -============================= +galaxy.jobs.actions package +=========================== .. automodule:: galaxy.jobs.actions :members: @@ -9,8 +9,8 @@ galaxy\.jobs\.actions package Submodules ---------- -galaxy\.jobs\.actions\.post module ----------------------------------- +galaxy.jobs.actions.post module +------------------------------- .. automodule:: galaxy.jobs.actions.post :members: diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index b70b8f2df86..900a19d1680 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -1,5 +1,5 @@ -galaxy\.jobs package -==================== +galaxy.jobs package +=================== .. automodule:: galaxy.jobs :members: @@ -12,87 +12,71 @@ Subpackages .. toctree:: galaxy.jobs.actions - galaxy.jobs.metrics + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters Submodules ---------- -galaxy\.jobs\.command\_factory module -------------------------------------- +galaxy.jobs.command\_factory module +----------------------------------- .. automodule:: galaxy.jobs.command_factory :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.datasets module ------------------------------ - -.. automodule:: galaxy.jobs.datasets - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.dynamic\_tool\_destination module ------------------------------------------------ +galaxy.jobs.dynamic\_tool\_destination module +--------------------------------------------- .. automodule:: galaxy.jobs.dynamic_tool_destination :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.handler module ----------------------------- +galaxy.jobs.handler module +-------------------------- .. automodule:: galaxy.jobs.handler :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.manager module ----------------------------- +galaxy.jobs.manager module +-------------------------- .. automodule:: galaxy.jobs.manager :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.mapper module ---------------------------- +galaxy.jobs.mapper module +------------------------- .. automodule:: galaxy.jobs.mapper :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.output\_checker module ------------------------------------- - -.. automodule:: galaxy.jobs.output_checker - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.rule\_helper module ---------------------------------- +galaxy.jobs.rule\_helper module +------------------------------- .. automodule:: galaxy.jobs.rule_helper :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.stock\_rules module ---------------------------------- +galaxy.jobs.stock\_rules module +------------------------------- .. automodule:: galaxy.jobs.stock_rules :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.transfer\_manager module --------------------------------------- +galaxy.jobs.transfer\_manager module +------------------------------------ .. automodule:: galaxy.jobs.transfer_manager :members: diff --git a/doc/source/lib/galaxy.jobs.rules.rst b/doc/source/lib/galaxy.jobs.rules.rst new file mode 100644 index 00000000000..29f0510c5a9 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.rules.rst @@ -0,0 +1,8 @@ +galaxy.jobs.rules package +========================= + +.. automodule:: galaxy.jobs.rules + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index cc47f56014c..937787d586c 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners package -============================= +galaxy.jobs.runners package +=========================== .. automodule:: galaxy.jobs.runners :members: @@ -17,104 +17,104 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.chronos module -------------------------------------- +galaxy.jobs.runners.chronos module +---------------------------------- .. automodule:: galaxy.jobs.runners.chronos :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.cli module ---------------------------------- +galaxy.jobs.runners.cli module +------------------------------ .. automodule:: galaxy.jobs.runners.cli :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.condor module ------------------------------------- +galaxy.jobs.runners.condor module +--------------------------------- .. automodule:: galaxy.jobs.runners.condor :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.drmaa module ------------------------------------ +galaxy.jobs.runners.drmaa module +-------------------------------- .. automodule:: galaxy.jobs.runners.drmaa :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.godocker module --------------------------------------- +galaxy.jobs.runners.godocker module +----------------------------------- .. automodule:: galaxy.jobs.runners.godocker :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.kubernetes module ----------------------------------------- +galaxy.jobs.runners.kubernetes module +------------------------------------- .. automodule:: galaxy.jobs.runners.kubernetes :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.local module ------------------------------------ +galaxy.jobs.runners.local module +-------------------------------- .. automodule:: galaxy.jobs.runners.local :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.pbs module ---------------------------------- +galaxy.jobs.runners.pbs module +------------------------------ .. automodule:: galaxy.jobs.runners.pbs :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.pulsar module ------------------------------------- +galaxy.jobs.runners.pulsar module +--------------------------------- .. automodule:: galaxy.jobs.runners.pulsar :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.slurm module ------------------------------------ +galaxy.jobs.runners.slurm module +-------------------------------- .. automodule:: galaxy.jobs.runners.slurm :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.state\_handler\_factory module ------------------------------------------------------ +galaxy.jobs.runners.state\_handler\_factory module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handler_factory :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.tasks module ------------------------------------ +galaxy.jobs.runners.tasks module +-------------------------------- .. automodule:: galaxy.jobs.runners.tasks :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.univa module ------------------------------------ +galaxy.jobs.runners.univa module +-------------------------------- .. automodule:: galaxy.jobs.runners.univa :members: diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst index be55fd3c029..1e71d735662 100644 --- a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.state\_handlers package -============================================== +galaxy.jobs.runners.state\_handlers package +=========================================== .. automodule:: galaxy.jobs.runners.state_handlers :members: @@ -9,8 +9,8 @@ galaxy\.jobs\.runners\.state\_handlers package Submodules ---------- -galaxy\.jobs\.runners\.state\_handlers\.resubmit module -------------------------------------------------------- +galaxy.jobs.runners.state\_handlers.resubmit module +--------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handlers.resubmit :members: 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 cb401ca9704..11813c7a0d1 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli\.job package -============================================= +galaxy.jobs.runners.util.cli.job package +======================================== .. automodule:: galaxy.jobs.runners.util.cli.job :members: @@ -9,32 +9,32 @@ galaxy\.jobs\.runners\.util\.cli\.job package Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.job\.lsf module -------------------------------------------------- +galaxy.jobs.runners.util.cli.job.lsf module +------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.lsf :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.slurm module ---------------------------------------------------- +galaxy.jobs.runners.util.cli.job.slurm module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.slurm\_torque module ------------------------------------------------------------ +galaxy.jobs.runners.util.cli.job.slurm\_torque module +----------------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.torque module ----------------------------------------------------- +galaxy.jobs.runners.util.cli.job.torque module +---------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.torque :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst index 16294903ae9..dadd626718b 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli package -======================================== +galaxy.jobs.runners.util.cli package +==================================== .. automodule:: galaxy.jobs.runners.util.cli :members: @@ -17,8 +17,8 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.factory module ------------------------------------------------- +galaxy.jobs.runners.util.cli.factory module +------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.factory :members: 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 db42713ebd0..42e5c7ffe73 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli\.shell package -=============================================== +galaxy.jobs.runners.util.cli.shell package +========================================== .. automodule:: galaxy.jobs.runners.util.cli.shell :members: @@ -9,16 +9,16 @@ galaxy\.jobs\.runners\.util\.cli\.shell package Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.shell\.local module ------------------------------------------------------ +galaxy.jobs.runners.util.cli.shell.local module +----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.local :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.shell\.rsh module ---------------------------------------------------- +galaxy.jobs.runners.util.cli.shell.rsh module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.rsh :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst index b1b5fa9f1d4..823ea51ac3e 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.condor.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.condor package -=========================================== +galaxy.jobs.runners.util.condor package +======================================= .. automodule:: galaxy.jobs.runners.util.condor :members: 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 562df4ae6b8..28119d40f7d 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.job\_script package -================================================ +galaxy.jobs.runners.util.job\_script package +============================================ .. automodule:: galaxy.jobs.runners.util.job_script :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst index 85487d46d30..ad9a2d1c85d 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util package -=================================== +galaxy.jobs.runners.util package +================================ .. automodule:: galaxy.jobs.runners.util :members: @@ -18,32 +18,40 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.util\.env module ---------------------------------------- +galaxy.jobs.runners.util.env module +----------------------------------- .. automodule:: galaxy.jobs.runners.util.env :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.external module --------------------------------------------- +galaxy.jobs.runners.util.external module +---------------------------------------- .. automodule:: galaxy.jobs.runners.util.external :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.kill module ----------------------------------------- +galaxy.jobs.runners.util.kill module +------------------------------------ .. automodule:: galaxy.jobs.runners.util.kill :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.sudo module ----------------------------------------- +galaxy.jobs.runners.util.pykube\_util module +-------------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.pykube_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.sudo module +------------------------------------ .. automodule:: galaxy.jobs.runners.util.sudo :members: diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst index 545d1e121fe..d8af934e1be 100644 --- a/doc/source/lib/galaxy.jobs.splitters.rst +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.splitters package -=============================== +galaxy.jobs.splitters package +============================= .. automodule:: galaxy.jobs.splitters :members: @@ -9,16 +9,16 @@ galaxy\.jobs\.splitters package Submodules ---------- -galaxy\.jobs\.splitters\.basic module -------------------------------------- +galaxy.jobs.splitters.basic module +---------------------------------- .. automodule:: galaxy.jobs.splitters.basic :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.splitters\.multi module -------------------------------------- +galaxy.jobs.splitters.multi module +---------------------------------- .. automodule:: galaxy.jobs.splitters.multi :members: diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index a68ec4f53df..829568b9685 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -1,5 +1,5 @@ -galaxy\.managers package -======================== +galaxy.managers package +======================= .. automodule:: galaxy.managers :members: @@ -9,264 +9,264 @@ galaxy\.managers package Submodules ---------- -galaxy\.managers\.annotatable module ------------------------------------- +galaxy.managers.annotatable module +---------------------------------- .. automodule:: galaxy.managers.annotatable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.api\_keys module ----------------------------------- +galaxy.managers.api\_keys module +-------------------------------- .. automodule:: galaxy.managers.api_keys :members: :undoc-members: :show-inheritance: -galaxy\.managers\.base module ------------------------------ +galaxy.managers.base module +--------------------------- .. automodule:: galaxy.managers.base :members: :undoc-members: :show-inheritance: -galaxy\.managers\.citations module ----------------------------------- +galaxy.managers.citations module +-------------------------------- .. automodule:: galaxy.managers.citations :members: :undoc-members: :show-inheritance: -galaxy\.managers\.cloud module ------------------------------- +galaxy.managers.cloud module +---------------------------- .. automodule:: galaxy.managers.cloud :members: :undoc-members: :show-inheritance: -galaxy\.managers\.cloudauthzs module ------------------------------------- +galaxy.managers.cloudauthzs module +---------------------------------- .. automodule:: galaxy.managers.cloudauthzs :members: :undoc-members: :show-inheritance: -galaxy\.managers\.collections module ------------------------------------- +galaxy.managers.collections module +---------------------------------- .. automodule:: galaxy.managers.collections :members: :undoc-members: :show-inheritance: -galaxy\.managers\.collections\_util module ------------------------------------------- +galaxy.managers.collections\_util module +---------------------------------------- .. automodule:: galaxy.managers.collections_util :members: :undoc-members: :show-inheritance: -galaxy\.managers\.configuration module --------------------------------------- +galaxy.managers.configuration module +------------------------------------ .. automodule:: galaxy.managers.configuration :members: :undoc-members: :show-inheritance: -galaxy\.managers\.containers module ------------------------------------ +galaxy.managers.containers module +--------------------------------- .. automodule:: galaxy.managers.containers :members: :undoc-members: :show-inheritance: -galaxy\.managers\.context module --------------------------------- +galaxy.managers.context module +------------------------------ .. automodule:: galaxy.managers.context :members: :undoc-members: :show-inheritance: -galaxy\.managers\.datasets module ---------------------------------- +galaxy.managers.datasets module +------------------------------- .. automodule:: galaxy.managers.datasets :members: :undoc-members: :show-inheritance: -galaxy\.managers\.deletable module ----------------------------------- +galaxy.managers.deletable module +-------------------------------- .. automodule:: galaxy.managers.deletable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.folders module --------------------------------- +galaxy.managers.folders module +------------------------------ .. automodule:: galaxy.managers.folders :members: :undoc-members: :show-inheritance: -galaxy\.managers\.hdas module ------------------------------ +galaxy.managers.hdas module +--------------------------- .. automodule:: galaxy.managers.hdas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.hdcas module ------------------------------- +galaxy.managers.hdcas module +---------------------------- .. automodule:: galaxy.managers.hdcas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.histories module ----------------------------------- +galaxy.managers.histories module +-------------------------------- .. automodule:: galaxy.managers.histories :members: :undoc-members: :show-inheritance: -galaxy\.managers\.history\_contents module ------------------------------------------- +galaxy.managers.history\_contents module +---------------------------------------- .. automodule:: galaxy.managers.history_contents :members: :undoc-members: :show-inheritance: -galaxy\.managers\.jobs module ------------------------------ +galaxy.managers.jobs module +--------------------------- .. automodule:: galaxy.managers.jobs :members: :undoc-members: :show-inheritance: -galaxy\.managers\.lddas module ------------------------------- +galaxy.managers.lddas module +---------------------------- .. automodule:: galaxy.managers.lddas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.libraries module ----------------------------------- +galaxy.managers.libraries module +-------------------------------- .. automodule:: galaxy.managers.libraries :members: :undoc-members: :show-inheritance: -galaxy\.managers\.library\_datasets module ------------------------------------------- +galaxy.managers.library\_datasets module +---------------------------------------- .. automodule:: galaxy.managers.library_datasets :members: :undoc-members: :show-inheritance: -galaxy\.managers\.pages module ------------------------------- +galaxy.managers.pages module +---------------------------- .. automodule:: galaxy.managers.pages :members: :undoc-members: :show-inheritance: -galaxy\.managers\.ratable module --------------------------------- +galaxy.managers.ratable module +------------------------------ .. automodule:: galaxy.managers.ratable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.rbac\_secured module --------------------------------------- +galaxy.managers.rbac\_secured module +------------------------------------ .. automodule:: galaxy.managers.rbac_secured :members: :undoc-members: :show-inheritance: -galaxy\.managers\.roles module ------------------------------- +galaxy.managers.roles module +---------------------------- .. automodule:: galaxy.managers.roles :members: :undoc-members: :show-inheritance: -galaxy\.managers\.secured module --------------------------------- +galaxy.managers.secured module +------------------------------ .. automodule:: galaxy.managers.secured :members: :undoc-members: :show-inheritance: -galaxy\.managers\.sharable module ---------------------------------- +galaxy.managers.sharable module +------------------------------- .. automodule:: galaxy.managers.sharable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.taggable module ---------------------------------- +galaxy.managers.taggable module +------------------------------- .. automodule:: galaxy.managers.taggable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.tags module ------------------------------ +galaxy.managers.tools module +---------------------------- -.. automodule:: galaxy.managers.tags +.. automodule:: galaxy.managers.tools :members: :undoc-members: :show-inheritance: -galaxy\.managers\.users module ------------------------------- +galaxy.managers.users module +---------------------------- .. automodule:: galaxy.managers.users :members: :undoc-members: :show-inheritance: -galaxy\.managers\.visualizations module ---------------------------------------- +galaxy.managers.visualizations module +------------------------------------- .. automodule:: galaxy.managers.visualizations :members: :undoc-members: :show-inheritance: -galaxy\.managers\.workflows module ----------------------------------- +galaxy.managers.workflows module +-------------------------------- .. automodule:: galaxy.managers.workflows :members: diff --git a/doc/source/lib/galaxy.metadata.rst b/doc/source/lib/galaxy.metadata.rst index a6943075f44..43f1a71c0e2 100644 --- a/doc/source/lib/galaxy.metadata.rst +++ b/doc/source/lib/galaxy.metadata.rst @@ -1,8 +1,20 @@ -galaxy\.metadata package -======================== +galaxy.metadata package +======================= .. automodule:: galaxy.metadata :members: :undoc-members: :show-inheritance: +Submodules +---------- + +galaxy.metadata.set\_metadata module +------------------------------------ + +.. automodule:: galaxy.metadata.set_metadata + :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 new file mode 100644 index 00000000000..688cd5e87e7 --- /dev/null +++ b/doc/source/lib/galaxy.model.dataset_collections.rst @@ -0,0 +1,67 @@ +galaxy.model.dataset\_collections package +========================================= + +.. automodule:: galaxy.model.dataset_collections + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.model.dataset_collections.types + +Submodules +---------- + +galaxy.model.dataset\_collections.builder module +------------------------------------------------ + +.. automodule:: galaxy.model.dataset_collections.builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.matching module +------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.matching + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.registry module +------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.structure module +-------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.structure + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.subcollections module +------------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.subcollections + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.type\_description module +---------------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.type_description + :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 new file mode 100644 index 00000000000..e13a8a83e88 --- /dev/null +++ b/doc/source/lib/galaxy.model.dataset_collections.types.rst @@ -0,0 +1,28 @@ +galaxy.model.dataset\_collections.types package +=============================================== + +.. automodule:: galaxy.model.dataset_collections.types + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.dataset\_collections.types.list module +--------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.types.list + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.types.paired module +----------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.types.paired + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 030077897a5..2d56bcc2878 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -1,16 +1,23 @@ -galaxy\.model\.migrate package -============================== +galaxy.model.migrate package +============================ .. automodule:: galaxy.model.migrate :members: :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.model.migrate.versions + Submodules ---------- -galaxy\.model\.migrate\.check module ------------------------------------- +galaxy.model.migrate.check module +--------------------------------- .. automodule:: galaxy.model.migrate.check :members: diff --git a/doc/source/lib/galaxy.model.migrate.versions.rst b/doc/source/lib/galaxy.model.migrate.versions.rst new file mode 100644 index 00000000000..e920777b10f --- /dev/null +++ b/doc/source/lib/galaxy.model.migrate.versions.rst @@ -0,0 +1,1252 @@ +galaxy.model.migrate.versions package +===================================== + +.. automodule:: galaxy.model.migrate.versions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrate.versions.0001\_initial\_tables module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0001_initial_tables + :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: + +galaxy.model.migrate.versions.0003\_security\_and\_libraries module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0003_security_and_libraries + :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: + +galaxy.model.migrate.versions.0005\_cleanup\_datasets\_fix module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0005_cleanup_datasets_fix + :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: + +galaxy.model.migrate.versions.0007\_sharing\_histories module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0007_sharing_histories + :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: + +galaxy.model.migrate.versions.0009\_request\_table module +--------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0009_request_table + :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: + +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: + +galaxy.model.migrate.versions.0012\_user\_address module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0012_user_address + :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: + +galaxy.model.migrate.versions.0014\_pages module +------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0014_pages + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0015\_tagging module +-------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0015_tagging + :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: + +galaxy.model.migrate.versions.0017\_library\_item\_indexes module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0017_library_item_indexes + :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: + +galaxy.model.migrate.versions.0019\_request\_library\_folder module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0019_request_library_folder + :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: + +galaxy.model.migrate.versions.0021\_user\_prefs module +------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0021_user_prefs + :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: + +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: + +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: + +galaxy.model.migrate.versions.0025\_user\_info module +----------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0025_user_info + :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: + +galaxy.model.migrate.versions.0027\_request\_events module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0027_request_events + :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: + +galaxy.model.migrate.versions.0029\_user\_actions module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0029_user_actions + :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: + +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: + +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: + +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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0037\_samples\_library module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0037_samples_library + :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: + +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: + +galaxy.model.migrate.versions.0040\_page\_annotations module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0040_page_annotations + :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: + +galaxy.model.migrate.versions.0042\_workflow\_invocation\_fix module +-------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0042_workflow_invocation_fix + :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: + +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: + +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: + +galaxy.model.migrate.versions.0046\_post\_job\_actions module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0046_post_job_actions + :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: + +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: + +galaxy.model.migrate.versions.0049\_api\_keys\_table module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0049_api_keys_table + :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: + +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: + +galaxy.model.migrate.versions.0052\_sample\_dataset\_table module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0052_sample_dataset_table + :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: + +galaxy.model.migrate.versions.0054\_visualization\_dbkey module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0054_visualization_dbkey + :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: + +galaxy.model.migrate.versions.0056\_workflow\_outputs module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0056_workflow_outputs + :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: + +galaxy.model.migrate.versions.0058\_history\_import\_export module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0058_history_import_export + :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: + +galaxy.model.migrate.versions.0060\_history\_archive\_import module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0060_history_archive_import + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0061\_tasks module +------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0061_tasks + :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: + +galaxy.model.migrate.versions.0063\_sequencer\_table module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0063_sequencer_table + :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: + +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: + +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: + +galaxy.model.migrate.versions.0067\_populate\_sequencer\_table module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0067_populate_sequencer_table + :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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0080\_quota\_tables module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0080_quota_tables + :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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0085\_add\_task\_info module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0085_add_task_info + :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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0095\_hda\_subsets module +------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0095_hda_subsets + :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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0106\_add\_missing\_indexes module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0106_add_missing_indexes + :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: + +galaxy.model.migrate.versions.0108\_add\_extended\_metadata module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0108_add_extended_metadata + :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: + +galaxy.model.migrate.versions.0110\_add\_dataset\_uuid module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0110_add_dataset_uuid + :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: + +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: + +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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0117\_add\_user\_activation module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0117_add_user_activation + :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: + +galaxy.model.migrate.versions.0119\_job\_metrics module +------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0119_job_metrics + :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: + +galaxy.model.migrate.versions.0121\_workflow\_uuids module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0121_workflow_uuids + :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: + +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: + +galaxy.model.migrate.versions.0124\_job\_state\_history module +-------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0124_job_state_history + :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: + +galaxy.model.migrate.versions.0126\_password\_reset module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0126_password_reset + :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: + +galaxy.model.migrate.versions.0128\_session\_timeout module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0128_session_timeout + :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: + +galaxy.model.migrate.versions.0130\_change\_pref\_datatype module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0130_change_pref_datatype + :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: + +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: + +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: + +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: + +galaxy.model.migrate.versions.0135\_add\_library\_tags module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0135_add_library_tags + :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: + +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: + +galaxy.model.migrate.versions.0138\_add\_hda\_version module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0138_add_hda_version + :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: + +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: + +galaxy.model.migrate.versions.0141\_add\_oidc\_tables module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0141_add_oidc_tables + :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: + +galaxy.model.migrate.versions.0143\_add\_cloudauthz\_tables module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0143_add_cloudauthz_tables + :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: + +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: + +galaxy.model.migrate.versions.0146\_workflow\_paths module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0146_workflow_paths + :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: + +galaxy.model.migrate.versions.0148\_add\_checksum\_table module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0148_add_checksum_table + :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: + +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: + +galaxy.model.migrate.versions.0151\_add\_worker\_process module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0151_add_worker_process + :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: + +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: + +galaxy.model.migrate.versions.0154\_created\_from\_basename module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0154_created_from_basename + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.util module +----------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 14a7389711f..c42fe0be8a6 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -1,5 +1,5 @@ -galaxy\.model\.orm package -========================== +galaxy.model.orm package +======================== .. automodule:: galaxy.model.orm :members: @@ -9,32 +9,32 @@ galaxy\.model\.orm package Submodules ---------- -galaxy\.model\.orm\.engine\_factory module ------------------------------------------- +galaxy.model.orm.engine\_factory module +--------------------------------------- .. automodule:: galaxy.model.orm.engine_factory :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.logging\_connection\_proxy module ------------------------------------------------------ +galaxy.model.orm.logging\_connection\_proxy module +-------------------------------------------------- .. automodule:: galaxy.model.orm.logging_connection_proxy :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.now module ------------------------------- +galaxy.model.orm.now module +--------------------------- .. automodule:: galaxy.model.orm.now :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.scripts module ----------------------------------- +galaxy.model.orm.scripts module +------------------------------- .. automodule:: galaxy.model.orm.scripts :members: diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index 7345edf3cfb..828f4226020 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -1,5 +1,5 @@ -galaxy\.model package -===================== +galaxy.model package +==================== .. automodule:: galaxy.model :members: @@ -11,63 +11,97 @@ Subpackages .. toctree:: + galaxy.model.dataset_collections galaxy.model.migrate galaxy.model.orm + galaxy.model.store galaxy.model.tool_shed_install Submodules ---------- -galaxy\.model\.base module --------------------------- +galaxy.model.base module +------------------------ .. automodule:: galaxy.model.base :members: :undoc-members: :show-inheritance: -galaxy\.model\.custom\_types module ------------------------------------ +galaxy.model.custom\_types module +--------------------------------- .. automodule:: galaxy.model.custom_types :members: :undoc-members: :show-inheritance: -galaxy\.model\.item\_attrs module ---------------------------------- +galaxy.model.database\_heartbeat module +--------------------------------------- + +.. automodule:: galaxy.model.database_heartbeat + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.item\_attrs module +------------------------------- .. automodule:: galaxy.model.item_attrs :members: :undoc-members: :show-inheritance: -galaxy\.model\.mapping module ------------------------------ +galaxy.model.mapping module +--------------------------- .. automodule:: galaxy.model.mapping :members: :undoc-members: :show-inheritance: -galaxy\.model\.metadata module ------------------------------- +galaxy.model.metadata module +---------------------------- .. automodule:: galaxy.model.metadata :members: :undoc-members: :show-inheritance: -galaxy\.model\.search module ----------------------------- +galaxy.model.none\_like module +------------------------------ + +.. automodule:: galaxy.model.none_like + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.search module +-------------------------- .. automodule:: galaxy.model.search :members: :undoc-members: :show-inheritance: -galaxy\.model\.util module --------------------------- +galaxy.model.security module +---------------------------- + +.. automodule:: galaxy.model.security + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tags module +------------------------ + +.. automodule:: galaxy.model.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.util module +------------------------ .. automodule:: galaxy.model.util :members: diff --git a/doc/source/lib/galaxy.model.store.rst b/doc/source/lib/galaxy.model.store.rst new file mode 100644 index 00000000000..1ab8db02595 --- /dev/null +++ b/doc/source/lib/galaxy.model.store.rst @@ -0,0 +1,28 @@ +galaxy.model.store package +========================== + +.. automodule:: galaxy.model.store + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.store.build\_objects module +---------------------------------------- + +.. automodule:: galaxy.model.store.build_objects + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.store.discover module +---------------------------------- + +.. automodule:: galaxy.model.store.discover + :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 b437c0167ff..fdd56b65033 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -1,5 +1,5 @@ -galaxy\.model\.tool\_shed\_install\.migrate package -=================================================== +galaxy.model.tool\_shed\_install.migrate package +================================================ .. automodule:: galaxy.model.tool_shed_install.migrate :members: @@ -9,8 +9,8 @@ galaxy\.model\.tool\_shed\_install\.migrate package Submodules ---------- -galaxy\.model\.tool\_shed\_install\.migrate\.check module ---------------------------------------------------------- +galaxy.model.tool\_shed\_install.migrate.check module +----------------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.migrate.check :members: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index 5346e7b2db8..d074ead1e89 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -1,5 +1,5 @@ -galaxy\.model\.tool\_shed\_install package -========================================== +galaxy.model.tool\_shed\_install package +======================================== .. automodule:: galaxy.model.tool_shed_install :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.model\.tool\_shed\_install\.mapping module --------------------------------------------------- +galaxy.model.tool\_shed\_install.mapping module +----------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.mapping :members: diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 7367d42410c..62acaf29546 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -1,5 +1,5 @@ -galaxy\.objectstore package -=========================== +galaxy.objectstore package +========================== .. automodule:: galaxy.objectstore :members: @@ -9,56 +9,56 @@ galaxy\.objectstore package Submodules ---------- -galaxy\.objectstore\.azure\_blob module ---------------------------------------- +galaxy.objectstore.azure\_blob module +------------------------------------- .. automodule:: galaxy.objectstore.azure_blob :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.cloud module ---------------------------------- +galaxy.objectstore.cloud module +------------------------------- .. automodule:: galaxy.objectstore.cloud :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.pithos module ----------------------------------- +galaxy.objectstore.pithos module +-------------------------------- .. automodule:: galaxy.objectstore.pithos :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.pulsar module ----------------------------------- +galaxy.objectstore.pulsar module +-------------------------------- .. automodule:: galaxy.objectstore.pulsar :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.rods module --------------------------------- +galaxy.objectstore.rods module +------------------------------ .. automodule:: galaxy.objectstore.rods :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.s3 module ------------------------------- +galaxy.objectstore.s3 module +---------------------------- .. automodule:: galaxy.objectstore.s3 :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.s3\_multipart\_upload module -------------------------------------------------- +galaxy.objectstore.s3\_multipart\_upload module +----------------------------------------------- .. automodule:: galaxy.objectstore.s3_multipart_upload :members: diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst new file mode 100644 index 00000000000..90031e56aad --- /dev/null +++ b/doc/source/lib/galaxy.openid.rst @@ -0,0 +1,28 @@ +galaxy.openid package +===================== + +.. automodule:: galaxy.openid + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.openid.openid\_manager module +------------------------------------ + +.. automodule:: galaxy.openid.openid_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.openid.providers module +------------------------------ + +.. automodule:: galaxy.openid.providers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.quota.rst b/doc/source/lib/galaxy.quota.rst index f04cf0b2872..36802033ce1 100644 --- a/doc/source/lib/galaxy.quota.rst +++ b/doc/source/lib/galaxy.quota.rst @@ -1,5 +1,5 @@ -galaxy\.quota package -===================== +galaxy.quota package +==================== .. automodule:: galaxy.quota :members: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index b1160511c4b..321bfcfcd7c 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -15,24 +15,28 @@ Subpackages galaxy.auth galaxy.authnz galaxy.containers - galaxy.dataset_collections 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.tool_util galaxy.tools galaxy.tours galaxy.util galaxy.visualization galaxy.web + galaxy.web_stack galaxy.webapps galaxy.webhooks galaxy.work @@ -41,48 +45,48 @@ Subpackages Submodules ---------- -galaxy\.app module ------------------- +galaxy.app module +----------------- .. automodule:: galaxy.app :members: :undoc-members: :show-inheritance: -galaxy\.config module ---------------------- +galaxy.config module +-------------------- .. automodule:: galaxy.config :members: :undoc-members: :show-inheritance: -galaxy\.main module -------------------- +galaxy.main module +------------------ .. automodule:: galaxy.main :members: :undoc-members: :show-inheritance: -galaxy\.queue\_worker module ----------------------------- +galaxy.queue\_worker module +--------------------------- .. automodule:: galaxy.queue_worker :members: :undoc-members: :show-inheritance: -galaxy\.queues module ---------------------- +galaxy.queues module +-------------------- .. automodule:: galaxy.queues :members: :undoc-members: :show-inheritance: -galaxy\.version module ----------------------- +galaxy.version module +--------------------- .. automodule:: galaxy.version :members: diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index b5c5757506f..351ecf61547 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -1,5 +1,5 @@ -galaxy\.security package -======================== +galaxy.security package +======================= .. automodule:: galaxy.security :members: @@ -9,16 +9,24 @@ galaxy\.security package Submodules ---------- -galaxy\.security\.passwords module ----------------------------------- +galaxy.security.idencoding module +--------------------------------- + +.. automodule:: galaxy.security.idencoding + :members: + :undoc-members: + :show-inheritance: + +galaxy.security.passwords module +-------------------------------- .. automodule:: galaxy.security.passwords :members: :undoc-members: :show-inheritance: -galaxy\.security\.validate\_user\_input module ----------------------------------------------- +galaxy.security.validate\_user\_input module +-------------------------------------------- .. automodule:: galaxy.security.validate_user_input :members: diff --git a/doc/source/lib/galaxy.tool_util.cwl.rst b/doc/source/lib/galaxy.tool_util.cwl.rst new file mode 100644 index 00000000000..5049af0a7af --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.cwl.rst @@ -0,0 +1,60 @@ +galaxy.tool\_util.cwl package +============================= + +.. automodule:: galaxy.tool_util.cwl + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.cwl.cwltool\_deps module +------------------------------------------ + +.. automodule:: galaxy.tool_util.cwl.cwltool_deps + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.parser module +----------------------------------- + +.. automodule:: galaxy.tool_util.cwl.parser + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.representation module +------------------------------------------- + +.. automodule:: galaxy.tool_util.cwl.representation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.runtime\_actions module +--------------------------------------------- + +.. automodule:: galaxy.tool_util.cwl.runtime_actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.schema module +----------------------------------- + +.. automodule:: galaxy.tool_util.cwl.schema + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.util module +--------------------------------- + +.. automodule:: galaxy.tool_util.cwl.util + :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 new file mode 100644 index 00000000000..3866cb37a3b --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst @@ -0,0 +1,28 @@ +galaxy.tool\_util.deps.container\_resolvers package +=================================================== + +.. automodule:: galaxy.tool_util.deps.container_resolvers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.deps.container\_resolvers.explicit module +----------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.container_resolvers.explicit + :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: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.mulled.rst b/doc/source/lib/galaxy.tool_util.deps.mulled.rst new file mode 100644 index 00000000000..2b1aff39940 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.mulled.rst @@ -0,0 +1,60 @@ +galaxy.tool\_util.deps.mulled package +===================================== + +.. automodule:: galaxy.tool_util.deps.mulled + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.deps.mulled.mulled\_build module +-------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build + :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: + +galaxy.tool\_util.deps.mulled.mulled\_build\_files module +--------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_files + :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: + +galaxy.tool\_util.deps.mulled.mulled\_search module +--------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_search + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.util module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.util + :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 new file mode 100644 index 00000000000..06be31af971 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.resolvers.rst @@ -0,0 +1,84 @@ +galaxy.tool\_util.deps.resolvers package +======================================== + +.. automodule:: galaxy.tool_util.deps.resolvers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +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: + +galaxy.tool\_util.deps.resolvers.conda module +--------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.conda + :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: + +galaxy.tool\_util.deps.resolvers.homebrew module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.resolvers.homebrew + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.lmod module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.lmod + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.modules module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.modules + :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: + +galaxy.tool\_util.deps.resolvers.tool\_shed\_packages module +------------------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.resolvers.tool_shed_packages + :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: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.rst b/doc/source/lib/galaxy.tool_util.deps.rst new file mode 100644 index 00000000000..9a1aaf79da2 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.rst @@ -0,0 +1,133 @@ +galaxy.tool\_util.deps package +============================== + +.. automodule:: galaxy.tool_util.deps + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_util.deps.container_resolvers + galaxy.tool_util.deps.mulled + galaxy.tool_util.deps.resolvers + +Submodules +---------- + +galaxy.tool\_util.deps.brew\_exts module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.brew_exts + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.brew\_util module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.brew_util + :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: + +galaxy.tool\_util.deps.conda\_util module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.conda_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.container\_classes module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.container_classes + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.containers module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.containers + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.dependencies module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.dependencies + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.docker\_util module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.docker_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.dockerfiles module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.dockerfiles + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.installable module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.installable + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.requirements module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.requirements + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.singularity\_util module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.singularity_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.views module +----------------------------------- + +.. automodule:: galaxy.tool_util.deps.views + :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 new file mode 100644 index 00000000000..12de3f42acf --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.locations.rst @@ -0,0 +1,36 @@ +galaxy.tool\_util.locations package +=================================== + +.. automodule:: galaxy.tool_util.locations + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.locations.dockstore module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.locations.dockstore + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.locations.file module +--------------------------------------- + +.. automodule:: galaxy.tool_util.locations.file + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.locations.http module +--------------------------------------- + +.. automodule:: galaxy.tool_util.locations.http + :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 new file mode 100644 index 00000000000..66a201433be --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.parser.rst @@ -0,0 +1,92 @@ +galaxy.tool\_util.parser package +================================ + +.. automodule:: galaxy.tool_util.parser + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.parser.cwl module +----------------------------------- + +.. automodule:: galaxy.tool_util.parser.cwl + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.error\_level module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.error_level + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.factory module +--------------------------------------- + +.. automodule:: galaxy.tool_util.parser.factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.interface module +----------------------------------------- + +.. automodule:: galaxy.tool_util.parser.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.output\_actions module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.output_actions + :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: + +galaxy.tool\_util.parser.output\_objects module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.output_objects + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.util module +------------------------------------ + +.. automodule:: galaxy.tool_util.parser.util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.xml module +----------------------------------- + +.. automodule:: galaxy.tool_util.parser.xml + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.yaml module +------------------------------------ + +.. automodule:: galaxy.tool_util.parser.yaml + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst new file mode 100644 index 00000000000..1d006d7c914 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.rst @@ -0,0 +1,54 @@ +galaxy.tool\_util package +========================= + +.. automodule:: galaxy.tool_util + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_util.cwl + galaxy.tool_util.deps + galaxy.tool_util.locations + galaxy.tool_util.parser + +Submodules +---------- + +galaxy.tool\_util.fetcher module +-------------------------------- + +.. automodule:: galaxy.tool_util.fetcher + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.loader module +------------------------------- + +.. automodule:: galaxy.tool_util.loader + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.output\_checker module +---------------------------------------- + +.. automodule:: galaxy.tool_util.output_checker + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.provided\_metadata module +------------------------------------------- + +.. automodule:: galaxy.tool_util.provided_metadata + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 4a706194a7e..1ef158180cd 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.actions package -============================== +galaxy.tools.actions package +============================ .. automodule:: galaxy.tools.actions :members: @@ -9,56 +9,56 @@ galaxy\.tools\.actions package Submodules ---------- -galaxy\.tools\.actions\.data\_manager module --------------------------------------------- +galaxy.tools.actions.data\_manager module +----------------------------------------- .. automodule:: galaxy.tools.actions.data_manager :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.data\_source module -------------------------------------------- +galaxy.tools.actions.data\_source module +---------------------------------------- .. automodule:: galaxy.tools.actions.data_source :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.history\_imp\_exp module ------------------------------------------------- +galaxy.tools.actions.history\_imp\_exp module +--------------------------------------------- .. automodule:: galaxy.tools.actions.history_imp_exp :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.metadata module ---------------------------------------- +galaxy.tools.actions.metadata module +------------------------------------ .. automodule:: galaxy.tools.actions.metadata :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.model\_operations module ------------------------------------------------- +galaxy.tools.actions.model\_operations module +--------------------------------------------- .. automodule:: galaxy.tools.actions.model_operations :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.upload module -------------------------------------- +galaxy.tools.actions.upload module +---------------------------------- .. automodule:: galaxy.tools.actions.upload :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.upload\_common module ---------------------------------------------- +galaxy.tools.actions.upload\_common module +------------------------------------------ .. automodule:: galaxy.tools.actions.upload_common :members: diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst index 6c2c91c2e65..4435ba549f8 100644 --- a/doc/source/lib/galaxy.tools.data.rst +++ b/doc/source/lib/galaxy.tools.data.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.data package -=========================== +galaxy.tools.data package +========================= .. automodule:: galaxy.tools.data :members: diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst index c80f07b3db3..53e9b630fb9 100644 --- a/doc/source/lib/galaxy.tools.data_manager.rst +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.data\_manager package -==================================== +galaxy.tools.data\_manager package +================================== .. automodule:: galaxy.tools.data_manager :members: @@ -9,8 +9,8 @@ galaxy\.tools\.data\_manager package Submodules ---------- -galaxy\.tools\.data\_manager\.manager module --------------------------------------------- +galaxy.tools.data\_manager.manager module +----------------------------------------- .. automodule:: galaxy.tools.data_manager.manager :members: diff --git a/doc/source/lib/galaxy.tools.error_reports.plugins.rst b/doc/source/lib/galaxy.tools.error_reports.plugins.rst index 5f6c51b9612..3491c92977c 100644 --- a/doc/source/lib/galaxy.tools.error_reports.plugins.rst +++ b/doc/source/lib/galaxy.tools.error_reports.plugins.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.error\_reports\.plugins package -============================================== +galaxy.tools.error\_reports.plugins package +=========================================== .. automodule:: galaxy.tools.error_reports.plugins :members: @@ -9,48 +9,56 @@ galaxy\.tools\.error\_reports\.plugins package Submodules ---------- -galaxy\.tools\.error\_reports\.plugins\.biostars module -------------------------------------------------------- +galaxy.tools.error\_reports.plugins.base\_git module +---------------------------------------------------- -.. automodule:: galaxy.tools.error_reports.plugins.biostars +.. automodule:: galaxy.tools.error_reports.plugins.base_git :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.email module ----------------------------------------------------- +galaxy.tools.error\_reports.plugins.email module +------------------------------------------------ .. automodule:: galaxy.tools.error_reports.plugins.email :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.github module ------------------------------------------------------ +galaxy.tools.error\_reports.plugins.github module +------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.github :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.influxdb module -------------------------------------------------------- +galaxy.tools.error\_reports.plugins.gitlab module +------------------------------------------------- + +.. automodule:: galaxy.tools.error_reports.plugins.gitlab + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.error\_reports.plugins.influxdb module +--------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.influxdb :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.json module ---------------------------------------------------- +galaxy.tools.error\_reports.plugins.json module +----------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.json :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.sentry module ------------------------------------------------------ +galaxy.tools.error\_reports.plugins.sentry module +------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.sentry :members: diff --git a/doc/source/lib/galaxy.tools.error_reports.rst b/doc/source/lib/galaxy.tools.error_reports.rst index 8e4012b832a..7cf8be64e4c 100644 --- a/doc/source/lib/galaxy.tools.error_reports.rst +++ b/doc/source/lib/galaxy.tools.error_reports.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.error\_reports package -===================================== +galaxy.tools.error\_reports package +=================================== .. automodule:: galaxy.tools.error_reports :members: diff --git a/doc/source/lib/galaxy.tools.expressions.rst b/doc/source/lib/galaxy.tools.expressions.rst new file mode 100644 index 00000000000..6c952368f2e --- /dev/null +++ b/doc/source/lib/galaxy.tools.expressions.rst @@ -0,0 +1,36 @@ +galaxy.tools.expressions package +================================ + +.. automodule:: galaxy.tools.expressions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tools.expressions.evaluation module +------------------------------------------ + +.. automodule:: galaxy.tools.expressions.evaluation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.expressions.script module +-------------------------------------- + +.. automodule:: galaxy.tools.expressions.script + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.expressions.util module +------------------------------------ + +.. automodule:: galaxy.tools.expressions.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst index aa10e47d4fe..bbea7ec45e4 100644 --- a/doc/source/lib/galaxy.tools.filters.rst +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.filters package -============================== +galaxy.tools.filters package +============================ .. automodule:: galaxy.tools.filters :members: diff --git a/doc/source/lib/galaxy.tools.imp_exp.rst b/doc/source/lib/galaxy.tools.imp_exp.rst index c0dc717f6cf..6cefd450f76 100644 --- a/doc/source/lib/galaxy.tools.imp_exp.rst +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.imp\_exp package -=============================== +galaxy.tools.imp\_exp package +============================= .. automodule:: galaxy.tools.imp_exp :members: @@ -9,16 +9,16 @@ galaxy\.tools\.imp\_exp package Submodules ---------- -galaxy\.tools\.imp\_exp\.export\_history module ------------------------------------------------ +galaxy.tools.imp\_exp.export\_history module +-------------------------------------------- .. automodule:: galaxy.tools.imp_exp.export_history :members: :undoc-members: :show-inheritance: -galaxy\.tools\.imp\_exp\.unpack\_tar\_gz\_archive module --------------------------------------------------------- +galaxy.tools.imp\_exp.unpack\_tar\_gz\_archive module +----------------------------------------------------- .. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive :members: diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst index 2012642a7cb..f79ce27f18b 100644 --- a/doc/source/lib/galaxy.tools.linters.rst +++ b/doc/source/lib/galaxy.tools.linters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.linters package -============================== +galaxy.tools.linters package +============================ .. automodule:: galaxy.tools.linters :members: @@ -9,72 +9,80 @@ galaxy\.tools\.linters package Submodules ---------- -galaxy\.tools\.linters\.citations module ----------------------------------------- +galaxy.tools.linters.citations module +------------------------------------- .. automodule:: galaxy.tools.linters.citations :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.command module --------------------------------------- +galaxy.tools.linters.command module +----------------------------------- .. automodule:: galaxy.tools.linters.command :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.general module --------------------------------------- +galaxy.tools.linters.cwl module +------------------------------- + +.. automodule:: galaxy.tools.linters.cwl + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.linters.general module +----------------------------------- .. automodule:: galaxy.tools.linters.general :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.help module ------------------------------------ +galaxy.tools.linters.help module +-------------------------------- .. automodule:: galaxy.tools.linters.help :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.inputs module -------------------------------------- +galaxy.tools.linters.inputs module +---------------------------------- .. automodule:: galaxy.tools.linters.inputs :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.outputs module --------------------------------------- +galaxy.tools.linters.outputs module +----------------------------------- .. automodule:: galaxy.tools.linters.outputs :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.stdio module ------------------------------------- +galaxy.tools.linters.stdio module +--------------------------------- .. automodule:: galaxy.tools.linters.stdio :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.tests module ------------------------------------- +galaxy.tools.linters.tests module +--------------------------------- .. automodule:: galaxy.tools.linters.tests :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.xml\_order module ------------------------------------------ +galaxy.tools.linters.xml\_order module +-------------------------------------- .. automodule:: galaxy.tools.linters.xml_order :members: diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 6a8136986d8..568fb0c2c5f 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.parameters package -================================= +galaxy.tools.parameters package +=============================== .. automodule:: galaxy.tools.parameters :members: @@ -9,96 +9,88 @@ galaxy\.tools\.parameters package Submodules ---------- -galaxy\.tools\.parameters\.basic module ---------------------------------------- +galaxy.tools.parameters.basic module +------------------------------------ .. automodule:: galaxy.tools.parameters.basic :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.dataset\_matcher module --------------------------------------------------- +galaxy.tools.parameters.dataset\_matcher module +----------------------------------------------- .. automodule:: galaxy.tools.parameters.dataset_matcher :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.dynamic\_options module --------------------------------------------------- +galaxy.tools.parameters.dynamic\_options module +----------------------------------------------- .. automodule:: galaxy.tools.parameters.dynamic_options :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.grouping module ------------------------------------------- +galaxy.tools.parameters.grouping module +--------------------------------------- .. automodule:: galaxy.tools.parameters.grouping :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.history\_query module ------------------------------------------------- +galaxy.tools.parameters.history\_query module +--------------------------------------------- .. automodule:: galaxy.tools.parameters.history_query :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.input\_translation module ----------------------------------------------------- +galaxy.tools.parameters.input\_translation module +------------------------------------------------- .. automodule:: galaxy.tools.parameters.input_translation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.meta module --------------------------------------- +galaxy.tools.parameters.meta module +----------------------------------- .. automodule:: galaxy.tools.parameters.meta :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.output\_collect module -------------------------------------------------- - -.. automodule:: galaxy.tools.parameters.output_collect - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parameters\.sanitize module ------------------------------------------- +galaxy.tools.parameters.sanitize module +--------------------------------------- .. automodule:: galaxy.tools.parameters.sanitize :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.validation module --------------------------------------------- +galaxy.tools.parameters.validation module +----------------------------------------- .. automodule:: galaxy.tools.parameters.validation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.wrapped module ------------------------------------------ +galaxy.tools.parameters.wrapped module +-------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.wrapped\_json module ------------------------------------------------ +galaxy.tools.parameters.wrapped\_json module +-------------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped_json :members: diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 1c6441f5780..2a8aa83ea90 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -1,5 +1,5 @@ -galaxy\.tools package -===================== +galaxy.tools package +==================== .. automodule:: galaxy.tools :members: @@ -12,17 +12,14 @@ Subpackages .. toctree:: galaxy.tools.actions - galaxy.tools.cwl galaxy.tools.data galaxy.tools.data_manager - galaxy.tools.deps galaxy.tools.error_reports + galaxy.tools.expressions galaxy.tools.filters galaxy.tools.imp_exp galaxy.tools.linters - galaxy.tools.locations galaxy.tools.parameters - galaxy.tools.parser galaxy.tools.search galaxy.tools.toolbox galaxy.tools.util @@ -31,128 +28,104 @@ Subpackages Submodules ---------- -galaxy\.tools\.cache module ---------------------------- +galaxy.tools.cache module +------------------------- .. automodule:: galaxy.tools.cache :members: :undoc-members: :show-inheritance: -galaxy\.tools\.data\_fetch module ---------------------------------- +galaxy.tools.data\_fetch module +------------------------------- .. automodule:: galaxy.tools.data_fetch :members: :undoc-members: :show-inheritance: -galaxy\.tools\.errors module ----------------------------- +galaxy.tools.errors module +-------------------------- .. automodule:: galaxy.tools.errors :members: :undoc-members: :show-inheritance: -galaxy\.tools\.evaluation module --------------------------------- +galaxy.tools.evaluation module +------------------------------ .. automodule:: galaxy.tools.evaluation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.exception\_handling module ------------------------------------------ +galaxy.tools.exception\_handling module +--------------------------------------- .. automodule:: galaxy.tools.exception_handling :members: :undoc-members: :show-inheritance: -galaxy\.tools\.execute module ------------------------------ +galaxy.tools.execute module +--------------------------- .. automodule:: galaxy.tools.execute :members: :undoc-members: :show-inheritance: -galaxy\.tools\.fetcher module ------------------------------ - -.. automodule:: galaxy.tools.fetcher - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.lint module --------------------------- +galaxy.tools.lint module +------------------------ .. automodule:: galaxy.tools.lint :members: :undoc-members: :show-inheritance: -galaxy\.tools\.lint\_util module --------------------------------- +galaxy.tools.lint\_util module +------------------------------ .. automodule:: galaxy.tools.lint_util :members: :undoc-members: :show-inheritance: -galaxy\.tools\.loader module ----------------------------- - -.. automodule:: galaxy.tools.loader - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.loader\_directory module ---------------------------------------- +galaxy.tools.loader\_directory module +------------------------------------- .. automodule:: galaxy.tools.loader_directory :members: :undoc-members: :show-inheritance: -galaxy\.tools\.provided\_metadata module ----------------------------------------- - -.. automodule:: galaxy.tools.provided_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.repositories module ----------------------------------- +galaxy.tools.repositories module +-------------------------------- .. automodule:: galaxy.tools.repositories :members: :undoc-members: :show-inheritance: -galaxy\.tools\.special\_tools module ------------------------------------- +galaxy.tools.special\_tools module +---------------------------------- .. automodule:: galaxy.tools.special_tools :members: :undoc-members: :show-inheritance: -galaxy\.tools\.test module --------------------------- +galaxy.tools.test module +------------------------ .. automodule:: galaxy.tools.test :members: :undoc-members: :show-inheritance: -galaxy\.tools\.wrappers module ------------------------------- +galaxy.tools.wrappers module +---------------------------- .. automodule:: galaxy.tools.wrappers :members: diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst index 8f67c61620f..edbb5bf3c79 100644 --- a/doc/source/lib/galaxy.tools.search.rst +++ b/doc/source/lib/galaxy.tools.search.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.search package -============================= +galaxy.tools.search package +=========================== .. automodule:: galaxy.tools.search :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst index a04372a8eb1..a5a81d279fb 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox\.filters package -======================================= +galaxy.tools.toolbox.filters package +==================================== .. automodule:: galaxy.tools.toolbox.filters :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst index 1f7794bff3d..e2628fd8bc4 100644 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox\.lineages package -======================================== +galaxy.tools.toolbox.lineages package +===================================== .. automodule:: galaxy.tools.toolbox.lineages :members: @@ -9,16 +9,16 @@ galaxy\.tools\.toolbox\.lineages package Submodules ---------- -galaxy\.tools\.toolbox\.lineages\.factory module ------------------------------------------------- +galaxy.tools.toolbox.lineages.factory module +-------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.factory :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.lineages\.interface module --------------------------------------------------- +galaxy.tools.toolbox.lineages.interface module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.interface :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst index 6ff0362872e..9631687f40f 100644 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox package -============================== +galaxy.tools.toolbox package +============================ .. automodule:: galaxy.tools.toolbox :members: @@ -17,48 +17,48 @@ Subpackages Submodules ---------- -galaxy\.tools\.toolbox\.base module ------------------------------------ +galaxy.tools.toolbox.base module +-------------------------------- .. automodule:: galaxy.tools.toolbox.base :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.integrated\_panel module ------------------------------------------------- +galaxy.tools.toolbox.integrated\_panel module +--------------------------------------------- .. automodule:: galaxy.tools.toolbox.integrated_panel :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.panel module ------------------------------------- +galaxy.tools.toolbox.panel module +--------------------------------- .. automodule:: galaxy.tools.toolbox.panel :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.parser module -------------------------------------- +galaxy.tools.toolbox.parser module +---------------------------------- .. automodule:: galaxy.tools.toolbox.parser :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.tags module ------------------------------------ +galaxy.tools.toolbox.tags module +-------------------------------- .. automodule:: galaxy.tools.toolbox.tags :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.watcher module --------------------------------------- +galaxy.tools.toolbox.watcher module +----------------------------------- .. automodule:: galaxy.tools.toolbox.watcher :members: diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst index c4f03d0cc4c..4ea949a2fac 100644 --- a/doc/source/lib/galaxy.tools.util.galaxyops.rst +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.util\.galaxyops package -====================================== +galaxy.tools.util.galaxyops package +=================================== .. automodule:: galaxy.tools.util.galaxyops :members: diff --git a/doc/source/lib/galaxy.tools.util.rst b/doc/source/lib/galaxy.tools.util.rst index d0e040291c7..588817928fa 100644 --- a/doc/source/lib/galaxy.tools.util.rst +++ b/doc/source/lib/galaxy.tools.util.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.util package -=========================== +galaxy.tools.util package +========================= .. automodule:: galaxy.tools.util :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.tools\.util\.maf\_utilities module ------------------------------------------- +galaxy.tools.util.maf\_utilities module +--------------------------------------- .. automodule:: galaxy.tools.util.maf_utilities :members: diff --git a/doc/source/lib/galaxy.tools.verify.asserts.rst b/doc/source/lib/galaxy.tools.verify.asserts.rst index 97d35d8da2e..66b69426efb 100644 --- a/doc/source/lib/galaxy.tools.verify.asserts.rst +++ b/doc/source/lib/galaxy.tools.verify.asserts.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.verify\.asserts package -====================================== +galaxy.tools.verify.asserts package +=================================== .. automodule:: galaxy.tools.verify.asserts :members: @@ -9,32 +9,40 @@ galaxy\.tools\.verify\.asserts package Submodules ---------- -galaxy\.tools\.verify\.asserts\.hdf5 module -------------------------------------------- +galaxy.tools.verify.asserts.archive module +------------------------------------------ + +.. automodule:: galaxy.tools.verify.asserts.archive + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.verify.asserts.hdf5 module +--------------------------------------- .. automodule:: galaxy.tools.verify.asserts.hdf5 :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.tabular module ----------------------------------------------- +galaxy.tools.verify.asserts.tabular module +------------------------------------------ .. automodule:: galaxy.tools.verify.asserts.tabular :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.text module -------------------------------------------- +galaxy.tools.verify.asserts.text module +--------------------------------------- .. automodule:: galaxy.tools.verify.asserts.text :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.xml module ------------------------------------------- +galaxy.tools.verify.asserts.xml module +-------------------------------------- .. automodule:: galaxy.tools.verify.asserts.xml :members: diff --git a/doc/source/lib/galaxy.tools.verify.rst b/doc/source/lib/galaxy.tools.verify.rst index 11325b39a71..4daf18a03de 100644 --- a/doc/source/lib/galaxy.tools.verify.rst +++ b/doc/source/lib/galaxy.tools.verify.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.verify package -============================= +galaxy.tools.verify package +=========================== .. automodule:: galaxy.tools.verify :members: @@ -16,24 +16,24 @@ Subpackages Submodules ---------- -galaxy\.tools\.verify\.interactor module ----------------------------------------- +galaxy.tools.verify.interactor module +------------------------------------- .. automodule:: galaxy.tools.verify.interactor :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.script module ------------------------------------- +galaxy.tools.verify.script module +--------------------------------- .. automodule:: galaxy.tools.verify.script :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.test\_data module ----------------------------------------- +galaxy.tools.verify.test\_data module +------------------------------------- .. automodule:: galaxy.tools.verify.test_data :members: diff --git a/doc/source/lib/galaxy.tours.rst b/doc/source/lib/galaxy.tours.rst index f83cb65d652..9729a10a6fe 100644 --- a/doc/source/lib/galaxy.tours.rst +++ b/doc/source/lib/galaxy.tours.rst @@ -1,5 +1,5 @@ -galaxy\.tours package -===================== +galaxy.tours package +==================== .. automodule:: galaxy.tours :members: diff --git a/doc/source/lib/galaxy.util.logging.rst b/doc/source/lib/galaxy.util.logging.rst index 1bc9f1ab01f..84e18059461 100644 --- a/doc/source/lib/galaxy.util.logging.rst +++ b/doc/source/lib/galaxy.util.logging.rst @@ -1,5 +1,5 @@ -galaxy\.util\.logging package -============================= +galaxy.util.logging package +=========================== .. automodule:: galaxy.util.logging :members: @@ -9,8 +9,8 @@ galaxy\.util\.logging package Submodules ---------- -galaxy\.util\.logging\.fluent\_log module ------------------------------------------ +galaxy.util.logging.fluent\_log module +-------------------------------------- .. automodule:: galaxy.util.logging.fluent_log :members: diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst index 92f5eb055b5..0a861eb5a4f 100644 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -1,5 +1,5 @@ -galaxy\.util\.pastescript package -================================= +galaxy.util.pastescript package +=============================== .. automodule:: galaxy.util.pastescript :members: @@ -9,16 +9,16 @@ galaxy\.util\.pastescript package Submodules ---------- -galaxy\.util\.pastescript\.loadwsgi module ------------------------------------------- +galaxy.util.pastescript.loadwsgi module +--------------------------------------- .. automodule:: galaxy.util.pastescript.loadwsgi :members: :undoc-members: :show-inheritance: -galaxy\.util\.pastescript\.serve module ---------------------------------------- +galaxy.util.pastescript.serve module +------------------------------------ .. automodule:: galaxy.util.pastescript.serve :members: diff --git a/doc/source/lib/galaxy.util.path.rst b/doc/source/lib/galaxy.util.path.rst index 2476ed017ef..c74056d2d89 100644 --- a/doc/source/lib/galaxy.util.path.rst +++ b/doc/source/lib/galaxy.util.path.rst @@ -1,5 +1,5 @@ -galaxy\.util\.path package -========================== +galaxy.util.path package +======================== .. automodule:: galaxy.util.path :members: @@ -9,16 +9,16 @@ galaxy\.util\.path package Submodules ---------- -galaxy\.util\.path\.ntpath module ---------------------------------- +galaxy.util.path.ntpath module +------------------------------ .. automodule:: galaxy.util.path.ntpath :members: :undoc-members: :show-inheritance: -galaxy\.util\.path\.posixpath module ------------------------------------- +galaxy.util.path.posixpath module +--------------------------------- .. automodule:: galaxy.util.path.posixpath :members: diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 9da8e2db529..792c0dfabb9 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -1,5 +1,5 @@ -galaxy\.util package -==================== +galaxy.util package +=================== .. automodule:: galaxy.util :members: @@ -18,352 +18,360 @@ Subpackages Submodules ---------- -galaxy\.util\.aliaspickler module ---------------------------------- +galaxy.util.aliaspickler module +------------------------------- .. automodule:: galaxy.util.aliaspickler :members: :undoc-members: :show-inheritance: -galaxy\.util\.biostar module ----------------------------- - -.. automodule:: galaxy.util.biostar - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.bunch module --------------------------- +galaxy.util.bunch module +------------------------ .. automodule:: galaxy.util.bunch :members: :undoc-members: :show-inheritance: -galaxy\.util\.checkers module ------------------------------ +galaxy.util.bytesize module +--------------------------- + +.. automodule:: galaxy.util.bytesize + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.checkers module +--------------------------- .. automodule:: galaxy.util.checkers :members: :undoc-members: :show-inheritance: -galaxy\.util\.compression\_utils module ---------------------------------------- +galaxy.util.compression\_utils module +------------------------------------- .. automodule:: galaxy.util.compression_utils :members: :undoc-members: :show-inheritance: -galaxy\.util\.create\_history\_template module ----------------------------------------------- - -.. automodule:: galaxy.util.create_history_template - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.dbkeys module ---------------------------- +galaxy.util.dbkeys module +------------------------- .. automodule:: galaxy.util.dbkeys :members: :undoc-members: :show-inheritance: -galaxy\.util\.dictifiable module --------------------------------- +galaxy.util.dictifiable module +------------------------------ .. automodule:: galaxy.util.dictifiable :members: :undoc-members: :show-inheritance: -galaxy\.util\.expressions module --------------------------------- +galaxy.util.expressions module +------------------------------ .. automodule:: galaxy.util.expressions :members: :undoc-members: :show-inheritance: -galaxy\.util\.facts module --------------------------- +galaxy.util.facts module +------------------------ .. automodule:: galaxy.util.facts :members: :undoc-members: :show-inheritance: -galaxy\.util\.filelock module ------------------------------ +galaxy.util.filelock module +--------------------------- .. automodule:: galaxy.util.filelock :members: :undoc-members: :show-inheritance: -galaxy\.util\.hash\_util module -------------------------------- +galaxy.util.form\_builder module +-------------------------------- + +.. automodule:: galaxy.util.form_builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.getargspec module +----------------------------- + +.. automodule:: galaxy.util.getargspec + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.hash\_util module +----------------------------- .. automodule:: galaxy.util.hash_util :members: :undoc-members: :show-inheritance: -galaxy\.util\.heartbeat module ------------------------------- +galaxy.util.heartbeat module +---------------------------- .. automodule:: galaxy.util.heartbeat :members: :undoc-members: :show-inheritance: -galaxy\.util\.image\_util module --------------------------------- +galaxy.util.image\_util module +------------------------------ .. automodule:: galaxy.util.image_util :members: :undoc-members: :show-inheritance: -galaxy\.util\.inflection module -------------------------------- +galaxy.util.inflection module +----------------------------- .. automodule:: galaxy.util.inflection :members: :undoc-members: :show-inheritance: -galaxy\.util\.json module -------------------------- +galaxy.util.json module +----------------------- .. automodule:: galaxy.util.json :members: :undoc-members: :show-inheritance: -galaxy\.util\.jstree module ---------------------------- +galaxy.util.jstree module +------------------------- .. automodule:: galaxy.util.jstree :members: :undoc-members: :show-inheritance: -galaxy\.util\.lazy\_process module ----------------------------------- +galaxy.util.lazy\_process module +-------------------------------- .. automodule:: galaxy.util.lazy_process :members: :undoc-members: :show-inheritance: -galaxy\.util\.monitors module ------------------------------ +galaxy.util.monitors module +--------------------------- .. automodule:: galaxy.util.monitors :members: :undoc-members: :show-inheritance: -galaxy\.util\.none\_like module -------------------------------- - -.. automodule:: galaxy.util.none_like - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.object\_wrapper module ------------------------------------- +galaxy.util.object\_wrapper module +---------------------------------- .. automodule:: galaxy.util.object_wrapper :members: :undoc-members: :show-inheritance: -galaxy\.util\.odict module --------------------------- +galaxy.util.odict module +------------------------ .. automodule:: galaxy.util.odict :members: :undoc-members: :show-inheritance: -galaxy\.util\.oset module -------------------------- +galaxy.util.oset module +----------------------- .. automodule:: galaxy.util.oset :members: :undoc-members: :show-inheritance: -galaxy\.util\.permutations module ---------------------------------- +galaxy.util.permutations module +------------------------------- .. automodule:: galaxy.util.permutations :members: :undoc-members: :show-inheritance: -galaxy\.util\.plugin\_config module ------------------------------------ +galaxy.util.plugin\_config module +--------------------------------- .. automodule:: galaxy.util.plugin_config :members: :undoc-members: :show-inheritance: -galaxy\.util\.properties module -------------------------------- +galaxy.util.properties module +----------------------------- .. automodule:: galaxy.util.properties :members: :undoc-members: :show-inheritance: -galaxy\.util\.renamed\_temporary\_file module ---------------------------------------------- +galaxy.util.renamed\_temporary\_file module +------------------------------------------- .. automodule:: galaxy.util.renamed_temporary_file :members: :undoc-members: :show-inheritance: -galaxy\.util\.rules\_dsl module -------------------------------- +galaxy.util.rules\_dsl module +----------------------------- .. automodule:: galaxy.util.rules_dsl :members: :undoc-members: :show-inheritance: -galaxy\.util\.sanitize\_html module ------------------------------------ +galaxy.util.sanitize\_html module +--------------------------------- .. automodule:: galaxy.util.sanitize_html :members: :undoc-members: :show-inheritance: -galaxy\.util\.script module ---------------------------- +galaxy.util.script module +------------------------- .. automodule:: galaxy.util.script :members: :undoc-members: :show-inheritance: -galaxy\.util\.simplegraph module --------------------------------- +galaxy.util.simplegraph module +------------------------------ .. automodule:: galaxy.util.simplegraph :members: :undoc-members: :show-inheritance: -galaxy\.util\.sleeper module ----------------------------- +galaxy.util.sleeper module +-------------------------- .. automodule:: galaxy.util.sleeper :members: :undoc-members: :show-inheritance: -galaxy\.util\.sockets module ----------------------------- +galaxy.util.sockets module +-------------------------- .. automodule:: galaxy.util.sockets :members: :undoc-members: :show-inheritance: -galaxy\.util\.specs module --------------------------- +galaxy.util.specs module +------------------------ .. automodule:: galaxy.util.specs :members: :undoc-members: :show-inheritance: -galaxy\.util\.sqlite module ---------------------------- +galaxy.util.sqlite module +------------------------- .. automodule:: galaxy.util.sqlite :members: :undoc-members: :show-inheritance: -galaxy\.util\.streamball module -------------------------------- +galaxy.util.streamball module +----------------------------- .. automodule:: galaxy.util.streamball :members: :undoc-members: :show-inheritance: -galaxy\.util\.submodules module -------------------------------- +galaxy.util.submodules module +----------------------------- .. automodule:: galaxy.util.submodules :members: :undoc-members: :show-inheritance: -galaxy\.util\.template module ------------------------------ +galaxy.util.template module +--------------------------- .. automodule:: galaxy.util.template :members: :undoc-members: :show-inheritance: -galaxy\.util\.tool\_version module ----------------------------------- +galaxy.util.tool\_version module +-------------------------------- .. automodule:: galaxy.util.tool_version :members: :undoc-members: :show-inheritance: -galaxy\.util\.topsort module ----------------------------- +galaxy.util.topsort module +-------------------------- .. automodule:: galaxy.util.topsort :members: :undoc-members: :show-inheritance: -galaxy\.util\.ucsc module -------------------------- +galaxy.util.ucsc module +----------------------- .. automodule:: galaxy.util.ucsc :members: :undoc-members: :show-inheritance: -galaxy\.util\.validation module -------------------------------- +galaxy.util.validation module +----------------------------- .. automodule:: galaxy.util.validation :members: :undoc-members: :show-inheritance: -galaxy\.util\.watcher module ----------------------------- +galaxy.util.watcher module +-------------------------- .. automodule:: galaxy.util.watcher :members: :undoc-members: :show-inheritance: -galaxy\.util\.xml\_macros module --------------------------------- +galaxy.util.web\_compat module +------------------------------ + +.. automodule:: galaxy.util.web_compat + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.xml\_macros module +------------------------------ .. automodule:: galaxy.util.xml_macros :members: diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst index ee55c5577f0..1866488ed19 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.data\_providers\.phyloviz package -======================================================== +galaxy.visualization.data\_providers.phyloviz package +===================================================== .. automodule:: galaxy.visualization.data_providers.phyloviz :members: @@ -9,32 +9,32 @@ galaxy\.visualization\.data\_providers\.phyloviz package Submodules ---------- -galaxy\.visualization\.data\_providers\.phyloviz\.baseparser module -------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.baseparser module +--------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.newickparser module ---------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.newickparser module +----------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.nexusparser module --------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.nexusparser module +---------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.phyloxmlparser module ------------------------------------------------------------------------ +galaxy.visualization.data\_providers.phyloviz.phyloxmlparser module +------------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser :members: diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index 7502835ba31..326f6c75321 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.data\_providers package -============================================== +galaxy.visualization.data\_providers package +============================================ .. automodule:: galaxy.visualization.data_providers :members: @@ -16,32 +16,32 @@ Subpackages Submodules ---------- -galaxy\.visualization\.data\_providers\.basic module ----------------------------------------------------- +galaxy.visualization.data\_providers.basic module +------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.basic :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.cigar module ----------------------------------------------------- +galaxy.visualization.data\_providers.cigar module +------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.cigar :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.genome module ------------------------------------------------------ +galaxy.visualization.data\_providers.genome module +-------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.genome :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.registry module -------------------------------------------------------- +galaxy.visualization.data\_providers.registry module +---------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.registry :members: diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index f32e8d9c115..9097529321c 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.genome package -===================================== +galaxy.visualization.genome package +=================================== .. automodule:: galaxy.visualization.genome :members: diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst index 78ddcd27c36..019f744d8b4 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.plugins package -====================================== +galaxy.visualization.plugins package +==================================== .. automodule:: galaxy.visualization.plugins :members: @@ -9,48 +9,48 @@ galaxy\.visualization\.plugins package Submodules ---------- -galaxy\.visualization\.plugins\.config\_parser module ------------------------------------------------------ +galaxy.visualization.plugins.config\_parser module +-------------------------------------------------- .. automodule:: galaxy.visualization.plugins.config_parser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.interactive\_environments module ----------------------------------------------------------------- +galaxy.visualization.plugins.interactive\_environments module +------------------------------------------------------------- .. automodule:: galaxy.visualization.plugins.interactive_environments :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.plugin module ---------------------------------------------- +galaxy.visualization.plugins.plugin module +------------------------------------------ .. automodule:: galaxy.visualization.plugins.plugin :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.registry module ------------------------------------------------ +galaxy.visualization.plugins.registry module +-------------------------------------------- .. automodule:: galaxy.visualization.plugins.registry :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.resource\_parser module -------------------------------------------------------- +galaxy.visualization.plugins.resource\_parser module +---------------------------------------------------- .. automodule:: galaxy.visualization.plugins.resource_parser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.utils module --------------------------------------------- +galaxy.visualization.plugins.utils module +----------------------------------------- .. automodule:: galaxy.visualization.plugins.utils :members: diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index 862305917c7..1f334499e29 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -1,5 +1,5 @@ -galaxy\.visualization package -============================= +galaxy.visualization package +============================ .. automodule:: galaxy.visualization :members: @@ -19,8 +19,8 @@ Subpackages Submodules ---------- -galaxy\.visualization\.genomes module -------------------------------------- +galaxy.visualization.genomes module +----------------------------------- .. automodule:: galaxy.visualization.genomes :members: diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 370ed638ff0..2d279399ef6 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.tracks package -===================================== +galaxy.visualization.tracks package +=================================== .. automodule:: galaxy.visualization.tracks :members: diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index f1a799c04a7..f81bd29947a 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -1,5 +1,5 @@ -galaxy\.web\.base package -========================= +galaxy.web.base package +======================= .. automodule:: galaxy.web.base :members: @@ -9,8 +9,8 @@ galaxy\.web\.base package Submodules ---------- -galaxy\.web\.base\.controller module ------------------------------------- +galaxy.web.base.controller module +--------------------------------- .. automodule:: galaxy.web.base.controller :members: diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst index 420afef6be1..e0024343c0c 100644 --- a/doc/source/lib/galaxy.web.framework.helpers.rst +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework\.helpers package -======================================= +galaxy.web.framework.helpers package +==================================== .. automodule:: galaxy.web.framework.helpers :members: @@ -9,16 +9,16 @@ galaxy\.web\.framework\.helpers package Submodules ---------- -galaxy\.web\.framework\.helpers\.grids module ---------------------------------------------- +galaxy.web.framework.helpers.grids module +----------------------------------------- .. automodule:: galaxy.web.framework.helpers.grids :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.helpers\.tags module --------------------------------------------- +galaxy.web.framework.helpers.tags module +---------------------------------------- .. automodule:: galaxy.web.framework.helpers.tags :members: diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index f320560dbae..675615531da 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework\.middleware package -========================================== +galaxy.web.framework.middleware package +======================================= .. automodule:: galaxy.web.framework.middleware :members: @@ -9,88 +9,88 @@ galaxy\.web\.framework\.middleware package Submodules ---------- -galaxy\.web\.framework\.middleware\.batch module ------------------------------------------------- +galaxy.web.framework.middleware.batch module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.batch :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.error module ------------------------------------------------- +galaxy.web.framework.middleware.error module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.error :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.profile module --------------------------------------------------- +galaxy.web.framework.middleware.profile module +---------------------------------------------- .. automodule:: galaxy.web.framework.middleware.profile :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.remoteuser module ------------------------------------------------------ +galaxy.web.framework.middleware.remoteuser module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.request\_id module ------------------------------------------------------- +galaxy.web.framework.middleware.request\_id module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.request_id :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.sentry module -------------------------------------------------- +galaxy.web.framework.middleware.sentry module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sentry :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.sqldebug module ---------------------------------------------------- +galaxy.web.framework.middleware.sqldebug module +----------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sqldebug :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.static module -------------------------------------------------- +galaxy.web.framework.middleware.static module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.static :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.statsd module -------------------------------------------------- +galaxy.web.framework.middleware.statsd module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.statsd :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.translogger module ------------------------------------------------------- +galaxy.web.framework.middleware.translogger module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.translogger :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.xforwardedhost module ---------------------------------------------------------- +galaxy.web.framework.middleware.xforwardedhost module +----------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.xforwardedhost :members: diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index 6aba7ac3035..a7dc4812d56 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework package -============================== +galaxy.web.framework package +============================ .. automodule:: galaxy.web.framework :members: @@ -17,24 +17,24 @@ Subpackages Submodules ---------- -galaxy\.web\.framework\.base module ------------------------------------ +galaxy.web.framework.base module +-------------------------------- .. automodule:: galaxy.web.framework.base :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.decorators module ------------------------------------------ +galaxy.web.framework.decorators module +-------------------------------------- .. automodule:: galaxy.web.framework.decorators :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.webapp module -------------------------------------- +galaxy.web.framework.webapp module +---------------------------------- .. automodule:: galaxy.web.framework.webapp :members: diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst index 04e2eb4b105..d69630ba177 100644 --- a/doc/source/lib/galaxy.web.proxy.rst +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -1,5 +1,5 @@ -galaxy\.web\.proxy package -========================== +galaxy.web.proxy package +======================== .. automodule:: galaxy.web.proxy :members: diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index 846708b7f88..dc3fd75cfd6 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -1,5 +1,5 @@ -galaxy\.web package -=================== +galaxy.web package +================== .. automodule:: galaxy.web :members: @@ -14,38 +14,36 @@ Subpackages galaxy.web.base galaxy.web.framework galaxy.web.proxy - galaxy.web.security - galaxy.web.stack Submodules ---------- -galaxy\.web\.buildapp module ----------------------------- +galaxy.web.buildapp module +-------------------------- .. automodule:: galaxy.web.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.web\.form\_builder module ---------------------------------- +galaxy.web.form\_builder module +------------------------------- .. automodule:: galaxy.web.form_builder :members: :undoc-members: :show-inheritance: -galaxy\.web\.formatting module ------------------------------- +galaxy.web.formatting module +---------------------------- .. automodule:: galaxy.web.formatting :members: :undoc-members: :show-inheritance: -galaxy\.web\.params module --------------------------- +galaxy.web.params module +------------------------ .. automodule:: galaxy.web.params :members: diff --git a/doc/source/lib/galaxy.web_stack.rst b/doc/source/lib/galaxy.web_stack.rst new file mode 100644 index 00000000000..26d7b0e02d6 --- /dev/null +++ b/doc/source/lib/galaxy.web_stack.rst @@ -0,0 +1,36 @@ +galaxy.web\_stack package +========================= + +.. automodule:: galaxy.web_stack + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.web\_stack.handlers module +--------------------------------- + +.. automodule:: galaxy.web_stack.handlers + :members: + :undoc-members: + :show-inheritance: + +galaxy.web\_stack.message module +-------------------------------- + +.. automodule:: galaxy.web_stack.message + :members: + :undoc-members: + :show-inheritance: + +galaxy.web\_stack.transport module +---------------------------------- + +.. automodule:: galaxy.web_stack.transport + :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 2f91b43359a..fffbce8dbf1 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy\.api package -==================================== +galaxy.webapps.galaxy.api package +================================= .. automodule:: galaxy.webapps.galaxy.api :members: @@ -9,360 +9,368 @@ galaxy\.webapps\.galaxy\.api package Submodules ---------- -galaxy\.webapps\.galaxy\.api\.annotations module ------------------------------------------------- +galaxy.webapps.galaxy.api.annotations module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.authenticate module -------------------------------------------------- +galaxy.webapps.galaxy.api.authenticate module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.cloud module ------------------------------------------- +galaxy.webapps.galaxy.api.cloud module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloud :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.cloudauthz module ------------------------------------------------ +galaxy.webapps.galaxy.api.cloudauthz module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloudauthz :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.configuration module --------------------------------------------------- +galaxy.webapps.galaxy.api.configuration module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.dataset\_collections module ---------------------------------------------------------- +galaxy.webapps.galaxy.api.dataset\_collections module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.datasets module ---------------------------------------------- +galaxy.webapps.galaxy.api.datasets module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.datatypes module ----------------------------------------------- +galaxy.webapps.galaxy.api.datatypes module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.datatypes :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.display\_applications module ----------------------------------------------------------- +galaxy.webapps.galaxy.api.display\_applications module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.display_applications :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.extended\_metadata module -------------------------------------------------------- +galaxy.webapps.galaxy.api.dynamic\_tools module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.dynamic_tools + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.api.extended\_metadata module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.folder\_contents module ------------------------------------------------------ +galaxy.webapps.galaxy.api.folder\_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folder_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.folders module --------------------------------------------- +galaxy.webapps.galaxy.api.folders module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folders :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.forms module ------------------------------------------- +galaxy.webapps.galaxy.api.forms module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.forms :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.genomes module --------------------------------------------- +galaxy.webapps.galaxy.api.genomes module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.group\_roles module -------------------------------------------------- +galaxy.webapps.galaxy.api.group\_roles module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.group\_users module -------------------------------------------------- +galaxy.webapps.galaxy.api.group\_users module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.groups module -------------------------------------------- +galaxy.webapps.galaxy.api.groups module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.histories module ----------------------------------------------- +galaxy.webapps.galaxy.api.histories module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.histories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.history\_contents module ------------------------------------------------------- +galaxy.webapps.galaxy.api.history\_contents module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.history_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.item\_tags module ------------------------------------------------ +galaxy.webapps.galaxy.api.item\_tags module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.item_tags :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.job\_files module ------------------------------------------------ +galaxy.webapps.galaxy.api.job\_files module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.job_files :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.jobs module ------------------------------------------ +galaxy.webapps.galaxy.api.jobs module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.jobs :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.libraries module ----------------------------------------------- +galaxy.webapps.galaxy.api.libraries module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.libraries :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.library\_contents module ------------------------------------------------------- +galaxy.webapps.galaxy.api.library\_contents module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.library\_datasets module ------------------------------------------------------- +galaxy.webapps.galaxy.api.library\_datasets module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_datasets :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.metrics module --------------------------------------------- +galaxy.webapps.galaxy.api.metrics module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.page\_revisions module ----------------------------------------------------- +galaxy.webapps.galaxy.api.page\_revisions module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.page_revisions :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.pages module ------------------------------------------- +galaxy.webapps.galaxy.api.pages module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.pages :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.plugins module --------------------------------------------- +galaxy.webapps.galaxy.api.plugins module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.plugins :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.provenance module ------------------------------------------------ +galaxy.webapps.galaxy.api.provenance module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.provenance :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.quotas module -------------------------------------------- +galaxy.webapps.galaxy.api.quotas module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.remote\_files module --------------------------------------------------- +galaxy.webapps.galaxy.api.remote\_files module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.roles module ------------------------------------------- +galaxy.webapps.galaxy.api.roles module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.roles :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.search module -------------------------------------------- +galaxy.webapps.galaxy.api.search module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.search :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_data module ------------------------------------------------ +galaxy.webapps.galaxy.api.tool\_data module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_data :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_dependencies module -------------------------------------------------------- +galaxy.webapps.galaxy.api.tool\_dependencies module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_dependencies :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_shed\_repositories module -------------------------------------------------------------- +galaxy.webapps.galaxy.api.tool\_shed\_repositories module +--------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tools module ------------------------------------------- +galaxy.webapps.galaxy.api.tools module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.toolshed module ---------------------------------------------- +galaxy.webapps.galaxy.api.toolshed module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.toolshed :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tours module ------------------------------------------- +galaxy.webapps.galaxy.api.tours module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tours :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.uploads module --------------------------------------------- +galaxy.webapps.galaxy.api.uploads module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.uploads :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.users module ------------------------------------------- +galaxy.webapps.galaxy.api.users module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.visualizations module ---------------------------------------------------- +galaxy.webapps.galaxy.api.visualizations module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.webhooks module ---------------------------------------------- +galaxy.webapps.galaxy.api.webhooks module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.webhooks :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.workflows module ----------------------------------------------- +galaxy.webapps.galaxy.api.workflows module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.workflows :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index a30a246f2d9..880ae45d9ba 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy\.controllers package -============================================ +galaxy.webapps.galaxy.controllers package +========================================= .. automodule:: galaxy.webapps.galaxy.controllers :members: @@ -9,160 +9,168 @@ galaxy\.webapps\.galaxy\.controllers package Submodules ---------- -galaxy\.webapps\.galaxy\.controllers\.admin module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.admin module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.admin\_toolshed module ------------------------------------------------------------- +galaxy.webapps.galaxy.controllers.admin\_toolshed module +-------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.async module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.async module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.async :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.authnz module ---------------------------------------------------- +galaxy.webapps.galaxy.controllers.authnz module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.authnz :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.biostar module ----------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.controllers.biostar - :members: - :undoc-members: - :show-inheritance: - -galaxy\.webapps\.galaxy\.controllers\.data\_manager module ----------------------------------------------------------- +galaxy.webapps.galaxy.controllers.data\_manager module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.data_manager :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.dataset module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.dataset module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.dataset :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.error module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.error module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.error :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.forms module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.forms module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.forms :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.history module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.history module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.history :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.interactive\_environments module ----------------------------------------------------------------------- +galaxy.webapps.galaxy.controllers.interactive\_environments module +------------------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.interactive_environments :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.library module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.library module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.page module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.openid module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.openid + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.controllers.page module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.page :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.root module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.root module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.root :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.tag module ------------------------------------------------- +galaxy.webapps.galaxy.controllers.shed\_tool\_static module +----------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.shed_tool_static + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.controllers.tag module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tag :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.tool\_runner module ---------------------------------------------------------- +galaxy.webapps.galaxy.controllers.tool\_runner module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tool_runner :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.user module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.user module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.user :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.userskeys module ------------------------------------------------------- +galaxy.webapps.galaxy.controllers.userskeys module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.userskeys :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.visualization module ----------------------------------------------------------- +galaxy.webapps.galaxy.controllers.visualization module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.visualization :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.workflow module ------------------------------------------------------ +galaxy.webapps.galaxy.controllers.workflow module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.workflow :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index e9a3b53c3b2..f5e0f2027ef 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy package -=============================== +galaxy.webapps.galaxy package +============================= .. automodule:: galaxy.webapps.galaxy :members: @@ -17,16 +17,16 @@ Subpackages Submodules ---------- -galaxy\.webapps\.galaxy\.buildapp module ----------------------------------------- +galaxy.webapps.galaxy.buildapp module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.config\_watchers module ------------------------------------------------- +galaxy.webapps.galaxy.config\_watchers module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.config_watchers :members: diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index 8b969287dc6..b6039634602 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports\.controllers package -============================================= +galaxy.webapps.reports.controllers package +========================================== .. automodule:: galaxy.webapps.reports.controllers :members: @@ -9,72 +9,72 @@ galaxy\.webapps\.reports\.controllers package Submodules ---------- -galaxy\.webapps\.reports\.controllers\.history module ------------------------------------------------------ +galaxy.webapps.reports.controllers.history module +------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.history :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.home module --------------------------------------------------- +galaxy.webapps.reports.controllers.home module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.home :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.jobs module --------------------------------------------------- +galaxy.webapps.reports.controllers.jobs module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.jobs :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.query module ---------------------------------------------------- +galaxy.webapps.reports.controllers.query module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.query :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.root module --------------------------------------------------- +galaxy.webapps.reports.controllers.root module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.root :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.system module ----------------------------------------------------- +galaxy.webapps.reports.controllers.system module +------------------------------------------------ .. automodule:: galaxy.webapps.reports.controllers.system :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.tools module ---------------------------------------------------- +galaxy.webapps.reports.controllers.tools module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.users module ---------------------------------------------------- +galaxy.webapps.reports.controllers.users module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.workflows module -------------------------------------------------------- +galaxy.webapps.reports.controllers.workflows module +--------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.workflows :members: diff --git a/doc/source/lib/galaxy.webapps.reports.framework.rst b/doc/source/lib/galaxy.webapps.reports.framework.rst index 0b5a37f2e89..0d4cec5661f 100644 --- a/doc/source/lib/galaxy.webapps.reports.framework.rst +++ b/doc/source/lib/galaxy.webapps.reports.framework.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports\.framework package -=========================================== +galaxy.webapps.reports.framework package +======================================== .. automodule:: galaxy.webapps.reports.framework :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.reports\.framework package Submodules ---------- -galaxy\.webapps\.reports\.framework\.grids module -------------------------------------------------- +galaxy.webapps.reports.framework.grids module +--------------------------------------------- .. automodule:: galaxy.webapps.reports.framework.grids :members: diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index 4e74f62ff70..84dcee28911 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports package -================================ +galaxy.webapps.reports package +============================== .. automodule:: galaxy.webapps.reports :members: @@ -17,24 +17,24 @@ Subpackages Submodules ---------- -galaxy\.webapps\.reports\.app module ------------------------------------- +galaxy.webapps.reports.app module +--------------------------------- .. automodule:: galaxy.webapps.reports.app :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.buildapp module ------------------------------------------ +galaxy.webapps.reports.buildapp module +-------------------------------------- .. automodule:: galaxy.webapps.reports.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.config module ---------------------------------------- +galaxy.webapps.reports.config module +------------------------------------ .. automodule:: galaxy.webapps.reports.config :members: diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 59ecc84180d..0ca4f9f0d3a 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -1,5 +1,5 @@ -galaxy\.webapps package -======================= +galaxy.webapps package +====================== .. automodule:: galaxy.webapps :members: @@ -18,16 +18,16 @@ Subpackages Submodules ---------- -galaxy\.webapps\.config\_manage module --------------------------------------- +galaxy.webapps.config\_manage module +------------------------------------ .. automodule:: galaxy.webapps.config_manage :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.util module ----------------------------- +galaxy.webapps.util module +-------------------------- .. automodule:: galaxy.webapps.util :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index 528a3eacdc1..10918ec1adf 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.api package -======================================== +galaxy.webapps.tool\_shed.api package +===================================== .. automodule:: galaxy.webapps.tool_shed.api :members: @@ -9,64 +9,64 @@ galaxy\.webapps\.tool\_shed\.api package Submodules ---------- -galaxy\.webapps\.tool\_shed\.api\.authenticate module ------------------------------------------------------ +galaxy.webapps.tool\_shed.api.authenticate module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.authenticate :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.categories module ---------------------------------------------------- +galaxy.webapps.tool\_shed.api.categories module +----------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.categories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.configuration module ------------------------------------------------------- +galaxy.webapps.tool\_shed.api.configuration module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.configuration :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.groups module ------------------------------------------------ +galaxy.webapps.tool\_shed.api.groups module +------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.repositories module ------------------------------------------------------ +galaxy.webapps.tool\_shed.api.repositories module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repositories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.repository\_revisions module --------------------------------------------------------------- +galaxy.webapps.tool\_shed.api.repository\_revisions module +---------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repository_revisions :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.tools module ----------------------------------------------- +galaxy.webapps.tool\_shed.api.tools module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.users module ----------------------------------------------- +galaxy.webapps.tool\_shed.api.users module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.users :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst index 877e0aff95c..04a6f48e325 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.controllers package -================================================ +galaxy.webapps.tool\_shed.controllers package +============================================= .. automodule:: galaxy.webapps.tool_shed.controllers :members: @@ -9,56 +9,56 @@ galaxy\.webapps\.tool\_shed\.controllers package Submodules ---------- -galaxy\.webapps\.tool\_shed\.controllers\.admin module ------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.admin module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.admin :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.groups module -------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.groups module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.hg module ---------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.hg module +----------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.hg :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.repository module ------------------------------------------------------------ +galaxy.webapps.tool\_shed.controllers.repository module +------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.repository\_review module -------------------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.repository\_review module +--------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository_review :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.upload module -------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.upload module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.upload :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.user module ------------------------------------------------------ +galaxy.webapps.tool\_shed.controllers.user module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.user :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst index 4073f7d8f48..0272f31b493 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.framework\.middleware package -========================================================== +galaxy.webapps.tool\_shed.framework.middleware package +====================================================== .. automodule:: galaxy.webapps.tool_shed.framework.middleware :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.tool\_shed\.framework\.middleware package Submodules ---------- -galaxy\.webapps\.tool\_shed\.framework\.middleware\.remoteuser module ---------------------------------------------------------------------- +galaxy.webapps.tool\_shed.framework.middleware.remoteuser module +---------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst index 94949aafb2a..316a36615a8 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.framework package -============================================== +galaxy.webapps.tool\_shed.framework package +=========================================== .. automodule:: galaxy.webapps.tool_shed.framework :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst index 425b4c1583a..3faeb2ab908 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.model\.migrate package -=================================================== +galaxy.webapps.tool\_shed.model.migrate package +=============================================== .. automodule:: galaxy.webapps.tool_shed.model.migrate :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.tool\_shed\.model\.migrate package Submodules ---------- -galaxy\.webapps\.tool\_shed\.model\.migrate\.check module ---------------------------------------------------------- +galaxy.webapps.tool\_shed.model.migrate.check module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.migrate.check :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.rst index 9b15ee2704a..f530aa8d272 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.model package -========================================== +galaxy.webapps.tool\_shed.model package +======================================= .. automodule:: galaxy.webapps.tool_shed.model :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.webapps\.tool\_shed\.model\.mapping module --------------------------------------------------- +galaxy.webapps.tool\_shed.model.mapping module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.mapping :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst index 2b69f949ec6..75bae1a95a2 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed package -=================================== +galaxy.webapps.tool\_shed package +================================= .. automodule:: galaxy.webapps.tool_shed :members: @@ -22,24 +22,24 @@ Subpackages Submodules ---------- -galaxy\.webapps\.tool\_shed\.app module ---------------------------------------- +galaxy.webapps.tool\_shed.app module +------------------------------------ .. automodule:: galaxy.webapps.tool_shed.app :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.buildapp module --------------------------------------------- +galaxy.webapps.tool\_shed.buildapp module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.config module ------------------------------------------- +galaxy.webapps.tool\_shed.config module +--------------------------------------- .. automodule:: galaxy.webapps.tool_shed.config :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst index e7a919f32be..0577e985c4a 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.search.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.search package -=========================================== +galaxy.webapps.tool\_shed.search package +======================================== .. automodule:: galaxy.webapps.tool_shed.search :members: @@ -9,16 +9,16 @@ galaxy\.webapps\.tool\_shed\.search package Submodules ---------- -galaxy\.webapps\.tool\_shed\.search\.repo\_search module --------------------------------------------------------- +galaxy.webapps.tool\_shed.search.repo\_search module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.repo_search :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.search\.tool\_search module --------------------------------------------------------- +galaxy.webapps.tool\_shed.search.tool\_search module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.tool_search :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.security.rst b/doc/source/lib/galaxy.webapps.tool_shed.security.rst index f12f0747fba..a8923945985 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.security.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.security package -============================================= +galaxy.webapps.tool\_shed.security package +========================================== .. automodule:: galaxy.webapps.tool_shed.security :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.util.rst b/doc/source/lib/galaxy.webapps.tool_shed.util.rst index 8081fe26591..7400a9864c3 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.util package -========================================= +galaxy.webapps.tool\_shed.util package +====================================== .. automodule:: galaxy.webapps.tool_shed.util :members: @@ -9,24 +9,24 @@ galaxy\.webapps\.tool\_shed\.util package Submodules ---------- -galaxy\.webapps\.tool\_shed\.util\.hgweb\_config module -------------------------------------------------------- +galaxy.webapps.tool\_shed.util.hgweb\_config module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.hgweb_config :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.util\.ratings\_util module -------------------------------------------------------- +galaxy.webapps.tool\_shed.util.ratings\_util module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.ratings_util :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.util\.shed\_statistics module ----------------------------------------------------------- +galaxy.webapps.tool\_shed.util.shed\_statistics module +------------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.util.shed_statistics :members: diff --git a/doc/source/lib/galaxy.webhooks.rst b/doc/source/lib/galaxy.webhooks.rst index fb714f1d80a..866964ebc4c 100644 --- a/doc/source/lib/galaxy.webhooks.rst +++ b/doc/source/lib/galaxy.webhooks.rst @@ -1,5 +1,5 @@ -galaxy\.webhooks package -======================== +galaxy.webhooks package +======================= .. automodule:: galaxy.webhooks :members: diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst index a10a6da6d9b..415a5b881c8 100644 --- a/doc/source/lib/galaxy.work.rst +++ b/doc/source/lib/galaxy.work.rst @@ -1,5 +1,5 @@ -galaxy\.work package -==================== +galaxy.work package +=================== .. automodule:: galaxy.work :members: @@ -9,8 +9,8 @@ galaxy\.work package Submodules ---------- -galaxy\.work\.context module ----------------------------- +galaxy.work.context module +-------------------------- .. automodule:: galaxy.work.context :members: diff --git a/doc/source/lib/galaxy.workflow.resources.rst b/doc/source/lib/galaxy.workflow.resources.rst index 4a5ab70fb6c..30773bc1ce9 100644 --- a/doc/source/lib/galaxy.workflow.resources.rst +++ b/doc/source/lib/galaxy.workflow.resources.rst @@ -1,5 +1,5 @@ -galaxy\.workflow\.resources package -=================================== +galaxy.workflow.resources package +================================= .. automodule:: galaxy.workflow.resources :members: diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 31ba5fdf1be..b4c6c95299c 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -1,5 +1,5 @@ -galaxy\.workflow package -======================== +galaxy.workflow package +======================= .. automodule:: galaxy.workflow :members: @@ -17,56 +17,56 @@ Subpackages Submodules ---------- -galaxy\.workflow\.extract module --------------------------------- +galaxy.workflow.extract module +------------------------------ .. automodule:: galaxy.workflow.extract :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.modules module --------------------------------- +galaxy.workflow.modules module +------------------------------ .. automodule:: galaxy.workflow.modules :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.render module -------------------------------- +galaxy.workflow.render module +----------------------------- .. automodule:: galaxy.workflow.render :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.run module ----------------------------- +galaxy.workflow.run module +-------------------------- .. automodule:: galaxy.workflow.run :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.run\_request module -------------------------------------- +galaxy.workflow.run\_request module +----------------------------------- .. automodule:: galaxy.workflow.run_request :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.scheduling\_manager module --------------------------------------------- +galaxy.workflow.scheduling\_manager module +------------------------------------------ .. automodule:: galaxy.workflow.scheduling_manager :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.steps module ------------------------------- +galaxy.workflow.steps module +---------------------------- .. automodule:: galaxy.workflow.steps :members: diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst index 8232320f3a5..43801194aa8 100644 --- a/doc/source/lib/galaxy.workflow.schedulers.rst +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -1,5 +1,5 @@ -galaxy\.workflow\.schedulers package -==================================== +galaxy.workflow.schedulers package +================================== .. automodule:: galaxy.workflow.schedulers :members: @@ -9,8 +9,8 @@ galaxy\.workflow\.schedulers package Submodules ---------- -galaxy\.workflow\.schedulers\.core module ------------------------------------------ +galaxy.workflow.schedulers.core module +-------------------------------------- .. automodule:: galaxy.workflow.schedulers.core :members: diff --git a/doc/source/lib/galaxy_ext.expressions.rst b/doc/source/lib/galaxy_ext.expressions.rst new file mode 100644 index 00000000000..8ddd34f7020 --- /dev/null +++ b/doc/source/lib/galaxy_ext.expressions.rst @@ -0,0 +1,20 @@ +galaxy\_ext.expressions package +=============================== + +.. automodule:: galaxy_ext.expressions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy\_ext.expressions.handle\_job module +------------------------------------------ + +.. automodule:: galaxy_ext.expressions.handle_job + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst index 0beb59a7750..f02145f9106 100644 --- a/doc/source/lib/galaxy_ext.metadata.rst +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -1,5 +1,5 @@ -galaxy\_ext\.metadata package -============================= +galaxy\_ext.metadata package +============================ .. automodule:: galaxy_ext.metadata :members: @@ -9,8 +9,8 @@ galaxy\_ext\.metadata package Submodules ---------- -galaxy\_ext\.metadata\.set\_metadata module -------------------------------------------- +galaxy\_ext.metadata.set\_metadata module +----------------------------------------- .. automodule:: galaxy_ext.metadata.set_metadata :members: diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index b6fc32b517d..824dc1eaf63 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -11,5 +11,6 @@ Subpackages .. toctree:: + galaxy_ext.expressions galaxy_ext.metadata diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst index ef81ac2ad3a..620229be4ca 100644 --- a/doc/source/lib/tool_shed.capsule.rst +++ b/doc/source/lib/tool_shed.capsule.rst @@ -1,5 +1,5 @@ -tool\_shed\.capsule package -=========================== +tool\_shed.capsule package +========================== .. automodule:: tool_shed.capsule :members: @@ -9,8 +9,8 @@ tool\_shed\.capsule package Submodules ---------- -tool\_shed\.capsule\.capsule\_manager module --------------------------------------------- +tool\_shed.capsule.capsule\_manager module +------------------------------------------ .. automodule:: tool_shed.capsule.capsule_manager :members: diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst index 723d86b61d6..a0fec837ad4 100644 --- a/doc/source/lib/tool_shed.dependencies.repository.rst +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies\.repository package -============================================ +tool\_shed.dependencies.repository package +========================================== .. automodule:: tool_shed.dependencies.repository :members: @@ -9,8 +9,8 @@ tool\_shed\.dependencies\.repository package Submodules ---------- -tool\_shed\.dependencies\.repository\.relation\_builder module --------------------------------------------------------------- +tool\_shed.dependencies.repository.relation\_builder module +----------------------------------------------------------- .. automodule:: tool_shed.dependencies.repository.relation_builder :members: diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst index c273abec922..d78fa5a2b7b 100644 --- a/doc/source/lib/tool_shed.dependencies.rst +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies package -================================ +tool\_shed.dependencies package +=============================== .. automodule:: tool_shed.dependencies :members: @@ -17,8 +17,8 @@ Subpackages Submodules ---------- -tool\_shed\.dependencies\.attribute\_handlers module ----------------------------------------------------- +tool\_shed.dependencies.attribute\_handlers module +-------------------------------------------------- .. automodule:: tool_shed.dependencies.attribute_handlers :members: diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst index a86bbcf02f2..024726c14b2 100644 --- a/doc/source/lib/tool_shed.dependencies.tool.rst +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies\.tool package -====================================== +tool\_shed.dependencies.tool package +==================================== .. automodule:: tool_shed.dependencies.tool :members: @@ -9,8 +9,8 @@ tool\_shed\.dependencies\.tool package Submodules ---------- -tool\_shed\.dependencies\.tool\.tag\_attribute\_handler module --------------------------------------------------------------- +tool\_shed.dependencies.tool.tag\_attribute\_handler module +----------------------------------------------------------- .. automodule:: tool_shed.dependencies.tool.tag_attribute_handler :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst index 55842225535..b5a24ff3508 100644 --- a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst +++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.datatypes package -============================================== +tool\_shed.galaxy\_install.datatypes package +============================================ .. automodule:: tool_shed.galaxy_install.datatypes :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.datatypes package Submodules ---------- -tool\_shed\.galaxy\_install\.datatypes\.custom\_datatype\_manager module ------------------------------------------------------------------------- +tool\_shed.galaxy\_install.datatypes.custom\_datatype\_manager module +--------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst index c1f626a6926..04e2fc38e54 100644 --- a/doc/source/lib/tool_shed.galaxy_install.grids.rst +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.grids package -========================================== +tool\_shed.galaxy\_install.grids package +======================================== .. automodule:: tool_shed.galaxy_install.grids :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.grids package Submodules ---------- -tool\_shed\.galaxy\_install\.grids\.admin\_toolshed\_grids module ------------------------------------------------------------------ +tool\_shed.galaxy\_install.grids.admin\_toolshed\_grids module +-------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst index 6e21b8d2d95..a32894a3a7c 100644 --- a/doc/source/lib/tool_shed.galaxy_install.metadata.rst +++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.metadata package -============================================= +tool\_shed.galaxy\_install.metadata package +=========================================== .. automodule:: tool_shed.galaxy_install.metadata :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.metadata package Submodules ---------- -tool\_shed\.galaxy\_install\.metadata\.installed\_repository\_metadata\_manager module --------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.metadata.installed\_repository\_metadata\_manager module +----------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.rst index 2a09d1b9d07..12d29998abc 100644 --- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.migrate package -============================================ +tool\_shed.galaxy\_install.migrate package +========================================== .. automodule:: tool_shed.galaxy_install.migrate :members: @@ -9,16 +9,16 @@ tool\_shed\.galaxy\_install\.migrate package Submodules ---------- -tool\_shed\.galaxy\_install\.migrate\.check module --------------------------------------------------- +tool\_shed.galaxy\_install.migrate.check module +----------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.check :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.migrate\.common module ---------------------------------------------------- +tool\_shed.galaxy\_install.migrate.common module +------------------------------------------------ .. automodule:: tool_shed.galaxy_install.migrate.common :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst index bfd9f0ad840..e2e52b611bc 100644 --- a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.repository\_dependencies package -============================================================= +tool\_shed.galaxy\_install.repository\_dependencies package +=========================================================== .. automodule:: tool_shed.galaxy_install.repository_dependencies :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.repository\_dependencies package Submodules ---------- -tool\_shed\.galaxy\_install\.repository\_dependencies\.repository\_dependency\_manager module ---------------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.repository\_dependencies.repository\_dependency\_manager module +------------------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index 0ce8f3729e9..4813a78c80d 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install package -=================================== +tool\_shed.galaxy\_install package +================================== .. automodule:: tool_shed.galaxy_install :members: @@ -23,48 +23,48 @@ Subpackages Submodules ---------- -tool\_shed\.galaxy\_install\.dependency\_display module -------------------------------------------------------- +tool\_shed.galaxy\_install.dependency\_display module +----------------------------------------------------- .. automodule:: tool_shed.galaxy_install.dependency_display :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.install\_manager module ----------------------------------------------------- +tool\_shed.galaxy\_install.install\_manager module +-------------------------------------------------- .. automodule:: tool_shed.galaxy_install.install_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.installed\_repository\_manager module ------------------------------------------------------------------- +tool\_shed.galaxy\_install.installed\_repository\_manager module +---------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.installed_repository_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.repair\_repository\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.repair\_repository\_manager module +------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.repair_repository_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_migration\_manager module ------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_migration\_manager module +---------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_migration_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.update\_repository\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.update\_repository\_manager module +------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.update_repository_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst index 56869254e93..a91e9694191 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe package -=============================================================== +tool\_shed.galaxy\_install.tool\_dependencies.recipe package +============================================================ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe :members: @@ -9,48 +9,48 @@ tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe package Submodules ---------- -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.asynchronous\_reader module ------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader module +-------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.env\_file\_builder module ----------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module +------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.install\_environment module ------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module +-------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.recipe\_manager module -------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module +--------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.step\_handler module ------------------------------------------------------------------------------ +tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module +------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.step_handler :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.tag\_handler module ----------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module +------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst index a5064984b24..63efd9498f4 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tool\_dependencies package -======================================================= +tool\_shed.galaxy\_install.tool\_dependencies package +===================================================== .. automodule:: tool_shed.galaxy_install.tool_dependencies :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -tool\_shed\.galaxy\_install\.tool\_dependencies\.env\_manager module --------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst index f62f9de8286..811e11122be 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tools.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tools package -========================================== +tool\_shed.galaxy\_install.tools package +======================================== .. automodule:: tool_shed.galaxy_install.tools :members: @@ -9,16 +9,16 @@ tool\_shed\.galaxy\_install\.tools package Submodules ---------- -tool\_shed\.galaxy\_install\.tools\.data\_manager module --------------------------------------------------------- +tool\_shed.galaxy\_install.tools.data\_manager module +----------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.data_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tools\.tool\_panel\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.tools.tool\_panel\_manager module +------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager :members: 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 20c6f6a504f..768dac7ce96 100644 --- a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.utility\_containers package -======================================================== +tool\_shed.galaxy\_install.utility\_containers package +====================================================== .. automodule:: tool_shed.galaxy_install.utility_containers :members: diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst index 4654eb7e4cd..59ec7e90ad8 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -1,5 +1,5 @@ -tool\_shed\.grids package -========================= +tool\_shed.grids package +======================== .. automodule:: tool_shed.grids :members: @@ -9,40 +9,40 @@ tool\_shed\.grids package Submodules ---------- -tool\_shed\.grids\.admin\_grids module --------------------------------------- +tool\_shed.grids.admin\_grids module +------------------------------------ .. automodule:: tool_shed.grids.admin_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_grid\_filter\_manager module ------------------------------------------------------------ +tool\_shed.grids.repository\_grid\_filter\_manager module +--------------------------------------------------------- .. automodule:: tool_shed.grids.repository_grid_filter_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_grids module -------------------------------------------- +tool\_shed.grids.repository\_grids module +----------------------------------------- .. automodule:: tool_shed.grids.repository_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_review\_grids module ---------------------------------------------------- +tool\_shed.grids.repository\_review\_grids module +------------------------------------------------- .. automodule:: tool_shed.grids.repository_review_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.util module ------------------------------- +tool\_shed.grids.util module +---------------------------- .. automodule:: tool_shed.grids.util :members: diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst index dabbd71ea24..5c7928cf6e1 100644 --- a/doc/source/lib/tool_shed.managers.rst +++ b/doc/source/lib/tool_shed.managers.rst @@ -1,5 +1,5 @@ -tool\_shed\.managers package -============================ +tool\_shed.managers package +=========================== .. automodule:: tool_shed.managers :members: @@ -9,16 +9,16 @@ tool\_shed\.managers package Submodules ---------- -tool\_shed\.managers\.groups module ------------------------------------ +tool\_shed.managers.groups module +--------------------------------- .. automodule:: tool_shed.managers.groups :members: :undoc-members: :show-inheritance: -tool\_shed\.managers\.repositories module ------------------------------------------ +tool\_shed.managers.repositories module +--------------------------------------- .. automodule:: tool_shed.managers.repositories :members: diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst index 26eda3d0718..8f0215125f6 100644 --- a/doc/source/lib/tool_shed.metadata.rst +++ b/doc/source/lib/tool_shed.metadata.rst @@ -1,5 +1,5 @@ -tool\_shed\.metadata package -============================ +tool\_shed.metadata package +=========================== .. automodule:: tool_shed.metadata :members: @@ -9,16 +9,16 @@ tool\_shed\.metadata package Submodules ---------- -tool\_shed\.metadata\.metadata\_generator module ------------------------------------------------- +tool\_shed.metadata.metadata\_generator module +---------------------------------------------- .. automodule:: tool_shed.metadata.metadata_generator :members: :undoc-members: :show-inheritance: -tool\_shed\.metadata\.repository\_metadata\_manager module ----------------------------------------------------------- +tool\_shed.metadata.repository\_metadata\_manager module +-------------------------------------------------------- .. automodule:: tool_shed.metadata.repository_metadata_manager :members: diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst index 67a6ba69bf3..55d6b2743bc 100644 --- a/doc/source/lib/tool_shed.repository_types.rst +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -1,5 +1,5 @@ -tool\_shed\.repository\_types package -===================================== +tool\_shed.repository\_types package +==================================== .. automodule:: tool_shed.repository_types :members: @@ -9,48 +9,48 @@ tool\_shed\.repository\_types package Submodules ---------- -tool\_shed\.repository\_types\.metadata module ----------------------------------------------- +tool\_shed.repository\_types.metadata module +-------------------------------------------- .. automodule:: tool_shed.repository_types.metadata :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.registry module ----------------------------------------------- +tool\_shed.repository\_types.registry module +-------------------------------------------- .. automodule:: tool_shed.repository_types.registry :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.repository\_suite\_definition module -------------------------------------------------------------------- +tool\_shed.repository\_types.repository\_suite\_definition module +----------------------------------------------------------------- .. automodule:: tool_shed.repository_types.repository_suite_definition :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.tool\_dependency\_definition module ------------------------------------------------------------------- +tool\_shed.repository\_types.tool\_dependency\_definition module +---------------------------------------------------------------- .. automodule:: tool_shed.repository_types.tool_dependency_definition :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.unrestricted module --------------------------------------------------- +tool\_shed.repository\_types.unrestricted module +------------------------------------------------ .. automodule:: tool_shed.repository_types.unrestricted :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.util module ------------------------------------------- +tool\_shed.repository\_types.util module +---------------------------------------- .. automodule:: tool_shed.repository_types.util :members: diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index e357746748c..3a3a78ab5b0 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -25,16 +25,16 @@ Subpackages Submodules ---------- -tool\_shed\.repository\_registry module ---------------------------------------- +tool\_shed.repository\_registry module +-------------------------------------- .. automodule:: tool_shed.repository_registry :members: :undoc-members: :show-inheritance: -tool\_shed\.tool\_shed\_registry module ---------------------------------------- +tool\_shed.tool\_shed\_registry module +-------------------------------------- .. automodule:: tool_shed.tool_shed_registry :members: diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst index 8d4b23e6172..79b0a68851f 100644 --- a/doc/source/lib/tool_shed.tools.rst +++ b/doc/source/lib/tool_shed.tools.rst @@ -1,5 +1,5 @@ -tool\_shed\.tools package -========================= +tool\_shed.tools package +======================== .. automodule:: tool_shed.tools :members: @@ -9,24 +9,24 @@ tool\_shed\.tools package Submodules ---------- -tool\_shed\.tools\.data\_table\_manager module ----------------------------------------------- +tool\_shed.tools.data\_table\_manager module +-------------------------------------------- .. automodule:: tool_shed.tools.data_table_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.tools\.tool\_validator module ------------------------------------------ +tool\_shed.tools.tool\_validator module +--------------------------------------- .. automodule:: tool_shed.tools.tool_validator :members: :undoc-members: :show-inheritance: -tool\_shed\.tools\.tool\_version\_manager module ------------------------------------------------- +tool\_shed.tools.tool\_version\_manager module +---------------------------------------------- .. automodule:: tool_shed.tools.tool_version_manager :members: diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index 4e5e36e3bca..cda03e77ecc 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -1,5 +1,5 @@ -tool\_shed\.util package -======================== +tool\_shed.util package +======================= .. automodule:: tool_shed.util :members: @@ -9,152 +9,152 @@ tool\_shed\.util package Submodules ---------- -tool\_shed\.util\.admin\_util module ------------------------------------- +tool\_shed.util.admin\_util module +---------------------------------- .. automodule:: tool_shed.util.admin_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.basic\_util module ------------------------------------- +tool\_shed.util.basic\_util module +---------------------------------- .. automodule:: tool_shed.util.basic_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.commit\_util module -------------------------------------- +tool\_shed.util.commit\_util module +----------------------------------- .. automodule:: tool_shed.util.commit_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.common\_util module -------------------------------------- +tool\_shed.util.common\_util module +----------------------------------- .. automodule:: tool_shed.util.common_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.container\_util module ----------------------------------------- +tool\_shed.util.container\_util module +-------------------------------------- .. automodule:: tool_shed.util.container_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.encoding\_util module ---------------------------------------- +tool\_shed.util.encoding\_util module +------------------------------------- .. automodule:: tool_shed.util.encoding_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.hg\_util module ---------------------------------- +tool\_shed.util.hg\_util module +------------------------------- .. automodule:: tool_shed.util.hg_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.metadata\_util module ---------------------------------------- +tool\_shed.util.metadata\_util module +------------------------------------- .. automodule:: tool_shed.util.metadata_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.readme\_util module -------------------------------------- +tool\_shed.util.readme\_util module +----------------------------------- .. automodule:: tool_shed.util.readme_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.repository\_content\_util module --------------------------------------------------- +tool\_shed.util.repository\_content\_util module +------------------------------------------------ .. automodule:: tool_shed.util.repository_content_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.repository\_util module ------------------------------------------ +tool\_shed.util.repository\_util module +--------------------------------------- .. automodule:: tool_shed.util.repository_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.review\_util module -------------------------------------- +tool\_shed.util.review\_util module +----------------------------------- .. automodule:: tool_shed.util.review_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.search\_util module -------------------------------------- +tool\_shed.util.search\_util module +----------------------------------- .. automodule:: tool_shed.util.search_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.shed\_util\_common module -------------------------------------------- +tool\_shed.util.shed\_util\_common module +----------------------------------------- .. automodule:: tool_shed.util.shed_util_common :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.tool\_dependency\_util module ------------------------------------------------ +tool\_shed.util.tool\_dependency\_util module +--------------------------------------------- .. automodule:: tool_shed.util.tool_dependency_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.tool\_util module ------------------------------------ +tool\_shed.util.tool\_util module +--------------------------------- .. automodule:: tool_shed.util.tool_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.web\_util module ----------------------------------- +tool\_shed.util.web\_util module +-------------------------------- .. automodule:: tool_shed.util.web_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.workflow\_util module ---------------------------------------- +tool\_shed.util.workflow\_util module +------------------------------------- .. automodule:: tool_shed.util.workflow_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.xml\_util module ----------------------------------- +tool\_shed.util.xml\_util module +-------------------------------- .. automodule:: tool_shed.util.xml_util :members: diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst index 4dd4ca953b8..f34ec9cf8f5 100644 --- a/doc/source/lib/tool_shed.utility_containers.rst +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -1,5 +1,5 @@ -tool\_shed\.utility\_containers package -======================================= +tool\_shed.utility\_containers package +====================================== .. automodule:: tool_shed.utility_containers :members: @@ -9,8 +9,8 @@ tool\_shed\.utility\_containers package Submodules ---------- -tool\_shed\.utility\_containers\.utility\_container\_manager module -------------------------------------------------------------------- +tool\_shed.utility\_containers.utility\_container\_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.utility_containers.utility_container_manager :members: