From ee0ce040cebd043bbb76930ac55cf4f5e11dd40c Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 26 Jun 2015 18:05:12 +0100 Subject: [PATCH] Update to sphinx-apidoc v1.3.1 . sphinx-apidoc -M -o doc/source/lib/ lib/ --- doc/source/conf.py | 4 +- doc/source/lib/galaxy.actions.rst | 17 +- doc/source/lib/galaxy.auth.providers.rst | 23 +- doc/source/lib/galaxy.auth.rst | 7 +- doc/source/lib/galaxy.dataset_collections.rst | 101 ++-- .../lib/galaxy.dataset_collections.types.rst | 19 +- .../lib/galaxy.datatypes.converters.rst | 129 +++-- .../lib/galaxy.datatypes.dataproviders.rst | 47 +- .../galaxy.datatypes.display_applications.rst | 23 +- doc/source/lib/galaxy.datatypes.rst | 349 ++++++------ doc/source/lib/galaxy.datatypes.util.rst | 23 +- doc/source/lib/galaxy.eggs.rst | 19 +- doc/source/lib/galaxy.exceptions.rst | 15 +- ...laxy.external_services.result_handlers.rst | 17 +- doc/source/lib/galaxy.external_services.rst | 53 +- doc/source/lib/galaxy.forms.rst | 17 +- doc/source/lib/galaxy.jobs.actions.rst | 15 +- doc/source/lib/galaxy.jobs.deferred.rst | 23 +- .../lib/galaxy.jobs.metrics.collectl.rst | 27 +- .../lib/galaxy.jobs.metrics.instrumenters.rst | 35 +- doc/source/lib/galaxy.jobs.metrics.rst | 27 +- doc/source/lib/galaxy.jobs.rst | 171 +++--- .../lib/galaxy.jobs.runners.lwr_client.rst | 235 ++++---- ...galaxy.jobs.runners.lwr_client.staging.rst | 19 +- ...laxy.jobs.runners.lwr_client.transport.rst | 19 +- doc/source/lib/galaxy.jobs.runners.rst | 171 +++--- .../galaxy.jobs.runners.state_handlers.rst | 17 +- .../lib/galaxy.jobs.runners.util.cli.job.rst | 23 +- .../lib/galaxy.jobs.runners.util.cli.rst | 27 +- .../galaxy.jobs.runners.util.cli.shell.rst | 19 +- .../lib/galaxy.jobs.runners.util.condor.rst | 7 +- .../galaxy.jobs.runners.util.job_script.rst | 7 +- doc/source/lib/galaxy.jobs.runners.util.rst | 59 +- doc/source/lib/galaxy.jobs.splitters.rst | 21 +- doc/source/lib/galaxy.managers.rst | 119 ++-- doc/source/lib/galaxy.model.migrate.rst | 17 +- doc/source/lib/galaxy.model.orm.rst | 27 +- doc/source/lib/galaxy.model.rst | 107 ++-- ...galaxy.model.tool_shed_install.migrate.rst | 17 +- .../lib/galaxy.model.tool_shed_install.rst | 27 +- doc/source/lib/galaxy.objectstore.rst | 27 +- doc/source/lib/galaxy.openid.rst | 15 +- doc/source/lib/galaxy.quota.rst | 7 +- doc/source/lib/galaxy.rst | 105 ++-- doc/source/lib/galaxy.sample_tracking.rst | 29 +- doc/source/lib/galaxy.security.rst | 19 +- doc/source/lib/galaxy.tags.rst | 7 +- doc/source/lib/galaxy.tools.actions.rst | 35 +- doc/source/lib/galaxy.tools.data.rst | 7 +- doc/source/lib/galaxy.tools.data_manager.rst | 15 +- .../lib/galaxy.tools.deps.resolvers.rst | 35 +- doc/source/lib/galaxy.tools.deps.rst | 139 ++--- doc/source/lib/galaxy.tools.filters.rst | 7 +- doc/source/lib/galaxy.tools.imp_exp.rst | 19 +- doc/source/lib/galaxy.tools.linters.rst | 39 +- doc/source/lib/galaxy.tools.parameters.rst | 59 +- doc/source/lib/galaxy.tools.parser.rst | 31 +- doc/source/lib/galaxy.tools.rst | 155 ++--- doc/source/lib/galaxy.tools.search.rst | 7 +- .../lib/galaxy.tools.toolbox.filters.rst | 7 +- .../lib/galaxy.tools.toolbox.lineages.rst | 27 +- doc/source/lib/galaxy.tools.toolbox.rst | 91 +-- .../lib/galaxy.tools.util.galaxyops.rst | 7 +- doc/source/lib/galaxy.tools.util.rst | 27 +- .../lib/galaxy.util.backports.importlib.rst | 7 +- doc/source/lib/galaxy.util.backports.rst | 7 +- doc/source/lib/galaxy.util.log.rst | 15 +- doc/source/lib/galaxy.util.pastescript.rst | 19 +- doc/source/lib/galaxy.util.rst | 539 +++++++++--------- ....visualization.data_providers.phyloviz.rst | 27 +- .../galaxy.visualization.data_providers.rst | 75 +-- .../lib/galaxy.visualization.genome.rst | 7 +- .../lib/galaxy.visualization.plugins.rst | 33 +- doc/source/lib/galaxy.visualization.rst | 27 +- .../lib/galaxy.visualization.tracks.rst | 7 +- .../lib/galaxy.web.base.controllers.rst | 17 +- doc/source/lib/galaxy.web.base.rst | 53 +- .../lib/galaxy.web.framework.helpers.rst | 15 +- .../lib/galaxy.web.framework.middleware.rst | 43 +- doc/source/lib/galaxy.web.framework.rst | 91 +-- doc/source/lib/galaxy.web.proxy.rst | 15 +- doc/source/lib/galaxy.web.rst | 75 +-- doc/source/lib/galaxy.web.security.rst | 7 +- doc/source/lib/galaxy.webapps.galaxy.api.rst | 165 +++--- .../lib/galaxy.webapps.galaxy.controllers.rst | 131 ++--- doc/source/lib/galaxy.webapps.galaxy.rst | 21 +- .../galaxy.webapps.reports.controllers.rst | 39 +- doc/source/lib/galaxy.webapps.reports.rst | 59 +- doc/source/lib/galaxy.webapps.rst | 7 +- .../lib/galaxy.webapps.tool_shed.api.rst | 41 +- .../galaxy.webapps.tool_shed.controllers.rst | 39 +- ...webapps.tool_shed.framework.middleware.rst | 19 +- .../galaxy.webapps.tool_shed.framework.rst | 7 +- ...galaxy.webapps.tool_shed.model.migrate.rst | 17 +- .../lib/galaxy.webapps.tool_shed.model.rst | 27 +- doc/source/lib/galaxy.webapps.tool_shed.rst | 59 +- .../lib/galaxy.webapps.tool_shed.search.rst | 21 +- .../lib/galaxy.webapps.tool_shed.security.rst | 7 +- .../lib/galaxy.webapps.tool_shed.util.rst | 25 +- doc/source/lib/galaxy.work.rst | 17 +- doc/source/lib/galaxy.workflow.rst | 117 ++-- doc/source/lib/galaxy.workflow.schedulers.rst | 15 +- doc/source/lib/galaxy_ext.metadata.rst | 15 +- doc/source/lib/galaxy_ext.rst | 5 +- doc/source/lib/galaxy_utils.rst | 7 +- doc/source/lib/galaxy_utils.sequence.rst | 33 +- doc/source/lib/log_tempfile.rst | 2 +- doc/source/lib/mimeparse.rst | 2 +- doc/source/lib/pkg_resources.rst | 2 +- doc/source/lib/psyco_full.rst | 2 +- doc/source/lib/pulsar.client.rst | 235 ++++---- doc/source/lib/pulsar.client.staging.rst | 19 +- doc/source/lib/pulsar.client.transport.rst | 31 +- doc/source/lib/pulsar.rst | 7 +- doc/source/lib/tool_shed.capsule.rst | 17 +- .../lib/tool_shed.dependencies.repository.rst | 17 +- doc/source/lib/tool_shed.dependencies.rst | 21 +- .../lib/tool_shed.dependencies.tool.rst | 17 +- .../tool_shed.galaxy_install.datatypes.rst | 17 +- .../lib/tool_shed.galaxy_install.grids.rst | 17 +- .../lib/tool_shed.galaxy_install.metadata.rst | 17 +- .../lib/tool_shed.galaxy_install.migrate.rst | 21 +- ...galaxy_install.repository_dependencies.rst | 17 +- doc/source/lib/tool_shed.galaxy_install.rst | 101 ++-- ...alaxy_install.tool_dependencies.recipe.rst | 37 +- ..._shed.galaxy_install.tool_dependencies.rst | 21 +- .../lib/tool_shed.galaxy_install.tools.rst | 21 +- ...shed.galaxy_install.utility_containers.rst | 7 +- doc/source/lib/tool_shed.grids.rst | 33 +- doc/source/lib/tool_shed.managers.rst | 21 +- doc/source/lib/tool_shed.metadata.rst | 21 +- doc/source/lib/tool_shed.repository_types.rst | 37 +- doc/source/lib/tool_shed.rst | 35 +- doc/source/lib/tool_shed.tools.rst | 25 +- doc/source/lib/tool_shed.util.rst | 85 +-- .../lib/tool_shed.utility_containers.rst | 15 +- 136 files changed, 3162 insertions(+), 2745 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index 2b25d7fdce2..9e8ae5b0f70 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -17,8 +17,6 @@ import sys, os, datetime ####### REQUIRED GALAXY INCLUDES sys.path.append(os.path.join(os.getcwd(), '../../lib')) -import galaxy -from galaxy import eggs ####### @@ -103,7 +101,7 @@ pygments_style = 'sphinx' # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -html_theme = 'default' +html_theme = 'classic' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index d022b96ef2b..bd4c48070b6 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -1,11 +1,20 @@ -actions Package -=============== +galaxy.actions package +====================== -:mod:`admin` Module -------------------- +.. automodule:: galaxy.actions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.actions.admin module +--------------------------- .. automodule:: galaxy.actions.admin :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index aff6f57976d..1c5c1945329 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -1,35 +1,36 @@ -providers Package -================= - -:mod:`providers` Package ------------------------- +galaxy.auth.providers package +============================= .. automodule:: galaxy.auth.providers :members: :undoc-members: :show-inheritance: -:mod:`alwaysreject` Module --------------------------- +Submodules +---------- + +galaxy.auth.providers.alwaysreject module +----------------------------------------- .. automodule:: galaxy.auth.providers.alwaysreject :members: :undoc-members: :show-inheritance: -:mod:`ldap_ad` Module ---------------------- +galaxy.auth.providers.ldap_ad module +------------------------------------ .. automodule:: galaxy.auth.providers.ldap_ad :members: :undoc-members: :show-inheritance: -:mod:`localdb` Module ---------------------- +galaxy.auth.providers.localdb module +------------------------------------ .. automodule:: galaxy.auth.providers.localdb :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst index 885330d32ec..eefcbc6f87d 100644 --- a/doc/source/lib/galaxy.auth.rst +++ b/doc/source/lib/galaxy.auth.rst @@ -1,8 +1,5 @@ -auth Package -============ - -:mod:`auth` Package -------------------- +galaxy.auth package +=================== .. automodule:: galaxy.auth :members: diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst index a507225613f..e065d302c50 100644 --- a/doc/source/lib/galaxy.dataset_collections.rst +++ b/doc/source/lib/galaxy.dataset_collections.rst @@ -1,50 +1,7 @@ -dataset_collections Package -=========================== +galaxy.dataset_collections package +================================== -:mod:`builder` Module ---------------------- - -.. automodule:: galaxy.dataset_collections.builder - :members: - :undoc-members: - :show-inheritance: - -:mod:`matching` Module ----------------------- - -.. automodule:: galaxy.dataset_collections.matching - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.dataset_collections.registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`structure` Module ------------------------ - -.. automodule:: galaxy.dataset_collections.structure - :members: - :undoc-members: - :show-inheritance: - -:mod:`subcollections` Module ----------------------------- - -.. automodule:: galaxy.dataset_collections.subcollections - :members: - :undoc-members: - :show-inheritance: - -:mod:`type_description` Module ------------------------------- - -.. automodule:: galaxy.dataset_collections.type_description +.. automodule:: galaxy.dataset_collections :members: :undoc-members: :show-inheritance: @@ -56,3 +13,55 @@ Subpackages galaxy.dataset_collections.types +Submodules +---------- + +galaxy.dataset_collections.builder module +----------------------------------------- + +.. automodule:: galaxy.dataset_collections.builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.matching module +------------------------------------------ + +.. automodule:: galaxy.dataset_collections.matching + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.registry module +------------------------------------------ + +.. automodule:: galaxy.dataset_collections.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.structure module +------------------------------------------- + +.. automodule:: galaxy.dataset_collections.structure + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.subcollections module +------------------------------------------------ + +.. automodule:: galaxy.dataset_collections.subcollections + :members: + :undoc-members: + :show-inheritance: + +galaxy.dataset_collections.type_description module +-------------------------------------------------- + +.. automodule:: galaxy.dataset_collections.type_description + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst index 83352f729b1..639fbf2b5c5 100644 --- a/doc/source/lib/galaxy.dataset_collections.types.rst +++ b/doc/source/lib/galaxy.dataset_collections.types.rst @@ -1,27 +1,28 @@ -types Package -============= - -:mod:`types` Package --------------------- +galaxy.dataset_collections.types package +======================================== .. automodule:: galaxy.dataset_collections.types :members: :undoc-members: :show-inheritance: -:mod:`list` Module ------------------- +Submodules +---------- + +galaxy.dataset_collections.types.list module +-------------------------------------------- .. automodule:: galaxy.dataset_collections.types.list :members: :undoc-members: :show-inheritance: -:mod:`paired` Module --------------------- +galaxy.dataset_collections.types.paired module +---------------------------------------------- .. automodule:: galaxy.dataset_collections.types.paired :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 342ba17312a..7435e980ab5 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -1,235 +1,244 @@ -converters Package -================== +galaxy.datatypes.converters package +=================================== -:mod:`bed_to_gff_converter` Module ----------------------------------- +.. automodule:: galaxy.datatypes.converters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.datatypes.converters.bed_to_gff_converter module +------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bed_to_gff_converter :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`bgzip` Module -------------------- +galaxy.datatypes.converters.bgzip module +---------------------------------------- .. automodule:: galaxy.datatypes.converters.bgzip :members: :undoc-members: :show-inheritance: -:mod:`fasta_to_len` Module --------------------------- +galaxy.datatypes.converters.fasta_to_len module +----------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_len :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`fastq_to_fqtoc` Module ----------------------------- +galaxy.datatypes.converters.fastq_to_fqtoc module +------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`interval_to_coverage` Module ----------------------------------- +galaxy.datatypes.converters.interval_to_coverage module +------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_coverage :members: :undoc-members: :show-inheritance: -:mod:`interval_to_fli` Module ------------------------------ +galaxy.datatypes.converters.interval_to_fli module +-------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_fli :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`pbed_ldreduced_converter` Module --------------------------------------- +galaxy.datatypes.converters.pbed_ldreduced_converter module +----------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`sam_to_bam` Module ------------------------- +galaxy.datatypes.converters.sam_to_bam module +--------------------------------------------- .. automodule:: galaxy.datatypes.converters.sam_to_bam :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`wiggle_to_simple_converter` Module ----------------------------------------- +galaxy.datatypes.converters.wiggle_to_simple_converter module +------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst index a804265f0df..cd85ef190df 100644 --- a/doc/source/lib/galaxy.datatypes.dataproviders.rst +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -1,83 +1,84 @@ -dataproviders Package -===================== - -:mod:`dataproviders` Package ----------------------------- +galaxy.datatypes.dataproviders package +====================================== .. automodule:: galaxy.datatypes.dataproviders :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- +Submodules +---------- + +galaxy.datatypes.dataproviders.base module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.base :members: :undoc-members: :show-inheritance: -:mod:`chunk` Module -------------------- +galaxy.datatypes.dataproviders.chunk module +------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.chunk :members: :undoc-members: :show-inheritance: -:mod:`column` Module --------------------- +galaxy.datatypes.dataproviders.column module +-------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.column :members: :undoc-members: :show-inheritance: -:mod:`dataset` Module ---------------------- +galaxy.datatypes.dataproviders.dataset module +--------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.dataset :members: :undoc-members: :show-inheritance: -:mod:`decorators` Module ------------------------- +galaxy.datatypes.dataproviders.decorators module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.decorators :members: :undoc-members: :show-inheritance: -:mod:`exceptions` Module ------------------------- +galaxy.datatypes.dataproviders.exceptions module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.exceptions :members: :undoc-members: :show-inheritance: -:mod:`external` Module ----------------------- +galaxy.datatypes.dataproviders.external module +---------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.external :members: :undoc-members: :show-inheritance: -:mod:`hierarchy` Module ------------------------ +galaxy.datatypes.dataproviders.hierarchy module +----------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.hierarchy :members: :undoc-members: :show-inheritance: -:mod:`line` Module ------------------- +galaxy.datatypes.dataproviders.line module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.line :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index 11300857cf8..a6f3e5e53a2 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -1,35 +1,36 @@ -display_applications Package -============================ - -:mod:`display_applications` Package ------------------------------------ +galaxy.datatypes.display_applications package +============================================= .. automodule:: galaxy.datatypes.display_applications :members: :undoc-members: :show-inheritance: -:mod:`application` Module -------------------------- +Submodules +---------- + +galaxy.datatypes.display_applications.application module +-------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.application :members: :undoc-members: :show-inheritance: -:mod:`parameters` Module ------------------------- +galaxy.datatypes.display_applications.parameters module +------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.parameters :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +galaxy.datatypes.display_applications.util module +------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index c85f459d43f..e660f27b6e5 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -1,170 +1,7 @@ -datatypes Package -================= +galaxy.datatypes package +======================== -:mod:`assembly` Module ----------------------- - -.. automodule:: galaxy.datatypes.assembly - :members: - :undoc-members: - :show-inheritance: - -:mod:`binary` Module --------------------- - -.. automodule:: galaxy.datatypes.binary - :members: - :undoc-members: - :show-inheritance: - -:mod:`checkers` Module ----------------------- - -.. automodule:: galaxy.datatypes.checkers - :members: - :undoc-members: - :show-inheritance: - -:mod:`chrominfo` Module ------------------------ - -.. automodule:: galaxy.datatypes.chrominfo - :members: - :undoc-members: - :show-inheritance: - -:mod:`coverage` Module ----------------------- - -.. automodule:: galaxy.datatypes.coverage - :members: - :undoc-members: - :show-inheritance: - -:mod:`data` Module ------------------- - -.. automodule:: galaxy.datatypes.data - :members: - :undoc-members: - :show-inheritance: - -:mod:`genetics` Module ----------------------- - -.. automodule:: galaxy.datatypes.genetics - :members: - :undoc-members: - :show-inheritance: - -:mod:`graph` Module -------------------- - -.. automodule:: galaxy.datatypes.graph - :members: - :undoc-members: - :show-inheritance: - -:mod:`images` Module --------------------- - -.. automodule:: galaxy.datatypes.images - :members: - :undoc-members: - :show-inheritance: - -:mod:`interval` Module ----------------------- - -.. automodule:: galaxy.datatypes.interval - :members: - :undoc-members: - :show-inheritance: - -:mod:`metadata` Module ----------------------- - -.. automodule:: galaxy.datatypes.metadata - :members: - :undoc-members: - :show-inheritance: - -:mod:`msa` Module ------------------ - -.. automodule:: galaxy.datatypes.msa - :members: - :undoc-members: - :show-inheritance: - -:mod:`ngsindex` Module ----------------------- - -.. automodule:: galaxy.datatypes.ngsindex - :members: - :undoc-members: - :show-inheritance: - -:mod:`qualityscore` Module --------------------------- - -.. automodule:: galaxy.datatypes.qualityscore - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.datatypes.registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`sequence` Module ----------------------- - -.. automodule:: galaxy.datatypes.sequence - :members: - :undoc-members: - :show-inheritance: - -:mod:`sniff` Module -------------------- - -.. automodule:: galaxy.datatypes.sniff - :members: - :undoc-members: - :show-inheritance: - -:mod:`tabular` Module ---------------------- - -.. automodule:: galaxy.datatypes.tabular - :members: - :undoc-members: - :show-inheritance: - -:mod:`text` Module ------------------- - -.. automodule:: galaxy.datatypes.text - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.datatypes.tracks - :members: - :undoc-members: - :show-inheritance: - -:mod:`xml` Module ------------------ - -.. automodule:: galaxy.datatypes.xml +.. automodule:: galaxy.datatypes :members: :undoc-members: :show-inheritance: @@ -179,3 +16,183 @@ Subpackages galaxy.datatypes.display_applications galaxy.datatypes.util +Submodules +---------- + +galaxy.datatypes.assembly module +-------------------------------- + +.. automodule:: galaxy.datatypes.assembly + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.binary module +------------------------------ + +.. automodule:: galaxy.datatypes.binary + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.checkers module +-------------------------------- + +.. automodule:: galaxy.datatypes.checkers + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.chrominfo module +--------------------------------- + +.. automodule:: galaxy.datatypes.chrominfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.coverage module +-------------------------------- + +.. automodule:: galaxy.datatypes.coverage + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.data module +---------------------------- + +.. automodule:: galaxy.datatypes.data + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.genetics module +-------------------------------- + +.. automodule:: galaxy.datatypes.genetics + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.graph module +----------------------------- + +.. automodule:: galaxy.datatypes.graph + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.images module +------------------------------ + +.. automodule:: galaxy.datatypes.images + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.interval module +-------------------------------- + +.. automodule:: galaxy.datatypes.interval + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.metadata module +-------------------------------- + +.. automodule:: galaxy.datatypes.metadata + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.msa module +--------------------------- + +.. automodule:: galaxy.datatypes.msa + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.ngsindex module +-------------------------------- + +.. automodule:: galaxy.datatypes.ngsindex + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.proteomics module +---------------------------------- + +.. automodule:: galaxy.datatypes.proteomics + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.qualityscore module +------------------------------------ + +.. automodule:: galaxy.datatypes.qualityscore + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.registry module +-------------------------------- + +.. automodule:: galaxy.datatypes.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.sequence module +-------------------------------- + +.. automodule:: galaxy.datatypes.sequence + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.sniff module +----------------------------- + +.. automodule:: galaxy.datatypes.sniff + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tabular module +------------------------------- + +.. automodule:: galaxy.datatypes.tabular + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.text module +---------------------------- + +.. automodule:: galaxy.datatypes.text + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tracks module +------------------------------ + +.. automodule:: galaxy.datatypes.tracks + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.xml module +--------------------------- + +.. automodule:: galaxy.datatypes.xml + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 59705cc70e8..6b9466b202d 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -1,35 +1,36 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.datatypes.util package +============================= .. automodule:: galaxy.datatypes.util :members: :undoc-members: :show-inheritance: -:mod:`generic_util` Module --------------------------- +Submodules +---------- + +galaxy.datatypes.util.generic_util module +----------------------------------------- .. automodule:: galaxy.datatypes.util.generic_util :members: :undoc-members: :show-inheritance: -:mod:`gff_util` Module ----------------------- +galaxy.datatypes.util.gff_util module +------------------------------------- .. automodule:: galaxy.datatypes.util.gff_util :members: :undoc-members: :show-inheritance: -:mod:`image_util` Module ------------------------- +galaxy.datatypes.util.image_util module +--------------------------------------- .. automodule:: galaxy.datatypes.util.image_util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index 948d631b6d7..52a243b3272 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -1,27 +1,28 @@ -eggs Package -============ - -:mod:`eggs` Package -------------------- +galaxy.eggs package +=================== .. automodule:: galaxy.eggs :members: :undoc-members: :show-inheritance: -:mod:`dist` Module ------------------- +Submodules +---------- + +galaxy.eggs.dist module +----------------------- .. automodule:: galaxy.eggs.dist :members: :undoc-members: :show-inheritance: -:mod:`scramble` Module ----------------------- +galaxy.eggs.scramble module +--------------------------- .. automodule:: galaxy.eggs.scramble :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index 8b62b21bf8c..dd83fb808b1 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -1,19 +1,20 @@ -exceptions Package -================== - -:mod:`exceptions` Package -------------------------- +galaxy.exceptions package +========================= .. automodule:: galaxy.exceptions :members: :undoc-members: :show-inheritance: -:mod:`error_codes` Module -------------------------- +Submodules +---------- + +galaxy.exceptions.error_codes module +------------------------------------ .. automodule:: galaxy.exceptions.error_codes :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.external_services.result_handlers.rst b/doc/source/lib/galaxy.external_services.result_handlers.rst index c8946b14b99..749bfb7c25c 100644 --- a/doc/source/lib/galaxy.external_services.result_handlers.rst +++ b/doc/source/lib/galaxy.external_services.result_handlers.rst @@ -1,11 +1,20 @@ -result_handlers Package -======================= +galaxy.external_services.result_handlers package +================================================ -:mod:`basic` Module -------------------- +.. automodule:: galaxy.external_services.result_handlers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.external_services.result_handlers.basic module +----------------------------------------------------- .. automodule:: galaxy.external_services.result_handlers.basic :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.external_services.rst b/doc/source/lib/galaxy.external_services.rst index 955f82eeb7f..b08913dc425 100644 --- a/doc/source/lib/galaxy.external_services.rst +++ b/doc/source/lib/galaxy.external_services.rst @@ -1,26 +1,7 @@ -external_services Package -========================= +galaxy.external_services package +================================ -:mod:`actions` Module ---------------------- - -.. automodule:: galaxy.external_services.actions - :members: - :undoc-members: - :show-inheritance: - -:mod:`parameters` Module ------------------------- - -.. automodule:: galaxy.external_services.parameters - :members: - :undoc-members: - :show-inheritance: - -:mod:`service` Module ---------------------- - -.. automodule:: galaxy.external_services.service +.. automodule:: galaxy.external_services :members: :undoc-members: :show-inheritance: @@ -32,3 +13,31 @@ Subpackages galaxy.external_services.result_handlers +Submodules +---------- + +galaxy.external_services.actions module +--------------------------------------- + +.. automodule:: galaxy.external_services.actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.external_services.parameters module +------------------------------------------ + +.. automodule:: galaxy.external_services.parameters + :members: + :undoc-members: + :show-inheritance: + +galaxy.external_services.service module +--------------------------------------- + +.. automodule:: galaxy.external_services.service + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst index 004bffe09df..088d52bcb9c 100644 --- a/doc/source/lib/galaxy.forms.rst +++ b/doc/source/lib/galaxy.forms.rst @@ -1,11 +1,20 @@ -forms Package -============= +galaxy.forms package +==================== -:mod:`forms` Module -------------------- +.. automodule:: galaxy.forms + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.forms.forms module +------------------------- .. automodule:: galaxy.forms.forms :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst index c3f69a190c9..7ec9a937d81 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -1,19 +1,20 @@ -actions Package -=============== - -:mod:`actions` Package ----------------------- +galaxy.jobs.actions package +=========================== .. automodule:: galaxy.jobs.actions :members: :undoc-members: :show-inheritance: -:mod:`post` Module ------------------- +Submodules +---------- + +galaxy.jobs.actions.post module +------------------------------- .. automodule:: galaxy.jobs.actions.post :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.deferred.rst b/doc/source/lib/galaxy.jobs.deferred.rst index 81709bb1124..371a1721bb7 100644 --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -1,35 +1,36 @@ -deferred Package -================ - -:mod:`deferred` Package ------------------------ +galaxy.jobs.deferred package +============================ .. automodule:: galaxy.jobs.deferred :members: :undoc-members: :show-inheritance: -:mod:`data_transfer` Module ---------------------------- +Submodules +---------- + +galaxy.jobs.deferred.data_transfer module +----------------------------------------- .. automodule:: galaxy.jobs.deferred.data_transfer :members: :undoc-members: :show-inheritance: -:mod:`manual_data_transfer` Module ----------------------------------- +galaxy.jobs.deferred.manual_data_transfer module +------------------------------------------------ .. automodule:: galaxy.jobs.deferred.manual_data_transfer :members: :undoc-members: :show-inheritance: -:mod:`pacific_biosciences_smrt_portal` Module ---------------------------------------------- +galaxy.jobs.deferred.pacific_biosciences_smrt_portal module +----------------------------------------------------------- .. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst index ebd0f3bb2f5..01120a3705a 100644 --- a/doc/source/lib/galaxy.jobs.metrics.collectl.rst +++ b/doc/source/lib/galaxy.jobs.metrics.collectl.rst @@ -1,43 +1,44 @@ -collectl Package -================ - -:mod:`collectl` Package ------------------------ +galaxy.jobs.metrics.collectl package +==================================== .. automodule:: galaxy.jobs.metrics.collectl :members: :undoc-members: :show-inheritance: -:mod:`cli` Module ------------------ +Submodules +---------- + +galaxy.jobs.metrics.collectl.cli module +--------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.cli :members: :undoc-members: :show-inheritance: -:mod:`processes` Module ------------------------ +galaxy.jobs.metrics.collectl.processes module +--------------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.processes :members: :undoc-members: :show-inheritance: -:mod:`stats` Module -------------------- +galaxy.jobs.metrics.collectl.stats module +----------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.stats :members: :undoc-members: :show-inheritance: -:mod:`subsystems` Module ------------------------- +galaxy.jobs.metrics.collectl.subsystems module +---------------------------------------------- .. automodule:: galaxy.jobs.metrics.collectl.subsystems :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst index 94b790d72ce..71b1a865ccb 100644 --- a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst +++ b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst @@ -1,59 +1,60 @@ -instrumenters Package -===================== - -:mod:`instrumenters` Package ----------------------------- +galaxy.jobs.metrics.instrumenters package +========================================= .. automodule:: galaxy.jobs.metrics.instrumenters :members: :undoc-members: :show-inheritance: -:mod:`collectl` Module ----------------------- +Submodules +---------- + +galaxy.jobs.metrics.instrumenters.collectl module +------------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.collectl :members: :undoc-members: :show-inheritance: -:mod:`core` Module ------------------- +galaxy.jobs.metrics.instrumenters.core module +--------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.core :members: :undoc-members: :show-inheritance: -:mod:`cpuinfo` Module ---------------------- +galaxy.jobs.metrics.instrumenters.cpuinfo module +------------------------------------------------ .. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo :members: :undoc-members: :show-inheritance: -:mod:`env` Module ------------------ +galaxy.jobs.metrics.instrumenters.env module +-------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.env :members: :undoc-members: :show-inheritance: -:mod:`meminfo` Module ---------------------- +galaxy.jobs.metrics.instrumenters.meminfo module +------------------------------------------------ .. automodule:: galaxy.jobs.metrics.instrumenters.meminfo :members: :undoc-members: :show-inheritance: -:mod:`uname` Module -------------------- +galaxy.jobs.metrics.instrumenters.uname module +---------------------------------------------- .. automodule:: galaxy.jobs.metrics.instrumenters.uname :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst index a9f3de2d925..b050d0f523f 100644 --- a/doc/source/lib/galaxy.jobs.metrics.rst +++ b/doc/source/lib/galaxy.jobs.metrics.rst @@ -1,22 +1,11 @@ -metrics Package -=============== - -:mod:`metrics` Package ----------------------- +galaxy.jobs.metrics package +=========================== .. automodule:: galaxy.jobs.metrics :members: :undoc-members: :show-inheritance: -:mod:`formatting` Module ------------------------- - -.. automodule:: galaxy.jobs.metrics.formatting - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -25,3 +14,15 @@ Subpackages galaxy.jobs.metrics.collectl galaxy.jobs.metrics.instrumenters +Submodules +---------- + +galaxy.jobs.metrics.formatting module +------------------------------------- + +.. automodule:: galaxy.jobs.metrics.formatting + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index be174b5e8d4..86c56ad5c51 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -1,94 +1,11 @@ -jobs Package -============ - -:mod:`jobs` Package -------------------- +galaxy.jobs package +=================== .. automodule:: galaxy.jobs :members: :undoc-members: :show-inheritance: -:mod:`command_factory` Module ------------------------------ - -.. automodule:: galaxy.jobs.command_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.jobs.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`error_level` Module -------------------------- - -.. automodule:: galaxy.jobs.error_level - :members: - :undoc-members: - :show-inheritance: - -:mod:`handler` Module ---------------------- - -.. automodule:: galaxy.jobs.handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: galaxy.jobs.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`mapper` Module --------------------- - -.. automodule:: galaxy.jobs.mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`output_checker` Module ----------------------------- - -.. automodule:: galaxy.jobs.output_checker - :members: - :undoc-members: - :show-inheritance: - -:mod:`rule_helper` Module -------------------------- - -.. automodule:: galaxy.jobs.rule_helper - :members: - :undoc-members: - :show-inheritance: - -:mod:`stock_rules` Module -------------------------- - -.. automodule:: galaxy.jobs.stock_rules - :members: - :undoc-members: - :show-inheritance: - -:mod:`transfer_manager` Module ------------------------------- - -.. automodule:: galaxy.jobs.transfer_manager - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -101,3 +18,87 @@ Subpackages galaxy.jobs.runners galaxy.jobs.splitters +Submodules +---------- + +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.error_level module +------------------------------ + +.. automodule:: galaxy.jobs.error_level + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.handler module +-------------------------- + +.. automodule:: galaxy.jobs.handler + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.manager module +-------------------------- + +.. automodule:: galaxy.jobs.manager + :members: + :undoc-members: + :show-inheritance: + +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 +------------------------------ + +.. automodule:: galaxy.jobs.rule_helper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.stock_rules module +------------------------------ + +.. automodule:: galaxy.jobs.stock_rules + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.transfer_manager module +----------------------------------- + +.. automodule:: galaxy.jobs.transfer_manager + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst index 74f2efa3f9e..1c0be4e8fac 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.rst @@ -1,126 +1,11 @@ -lwr_client Package -================== - -:mod:`lwr_client` Package -------------------------- +galaxy.jobs.runners.lwr_client package +====================================== .. automodule:: galaxy.jobs.runners.lwr_client :members: :undoc-members: :show-inheritance: -:mod:`action_mapper` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange_factory` Module ------------------------------------ - -.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`client` Module --------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.client - :members: - :undoc-members: - :show-inheritance: - -:mod:`config_util` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.config_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`destination` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.destination - :members: - :undoc-members: - :show-inheritance: - -:mod:`interface` Module ------------------------ - -.. automodule:: galaxy.jobs.runners.lwr_client.interface - :members: - :undoc-members: - :show-inheritance: - -:mod:`job_directory` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.job_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_client` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.object_client - :members: - :undoc-members: - :show-inheritance: - -:mod:`path_mapper` Module -------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`setup_handler` Module ---------------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: galaxy.jobs.runners.lwr_client.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -129,3 +14,119 @@ Subpackages galaxy.jobs.runners.lwr_client.staging galaxy.jobs.runners.lwr_client.transport +Submodules +---------- + +galaxy.jobs.runners.lwr_client.action_mapper module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.amqp_exchange module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.amqp_exchange_factory module +----------------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.client module +-------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.client + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.config_util module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.config_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.decorators module +------------------------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.decorators + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.destination module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.destination + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.interface module +----------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.job_directory module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.job_directory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.manager module +--------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.object_client module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.object_client + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.path_mapper module +------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.setup_handler module +--------------------------------------------------- + +.. automodule:: galaxy.jobs.runners.lwr_client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr_client.util module +------------------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr_client.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst index 62feff29ae9..7ae6a269d3a 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst @@ -1,27 +1,28 @@ -staging Package -=============== - -:mod:`staging` Package ----------------------- +galaxy.jobs.runners.lwr_client.staging package +============================================== .. automodule:: galaxy.jobs.runners.lwr_client.staging :members: :undoc-members: :show-inheritance: -:mod:`down` Module ------------------- +Submodules +---------- + +galaxy.jobs.runners.lwr_client.staging.down module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.staging.down :members: :undoc-members: :show-inheritance: -:mod:`up` Module ----------------- +galaxy.jobs.runners.lwr_client.staging.up module +------------------------------------------------ .. automodule:: galaxy.jobs.runners.lwr_client.staging.up :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst index 427b43e96d1..f884599ba2d 100644 --- a/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst +++ b/doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst @@ -1,27 +1,28 @@ -transport Package -================= - -:mod:`transport` Package ------------------------- +galaxy.jobs.runners.lwr_client.transport package +================================================ .. automodule:: galaxy.jobs.runners.lwr_client.transport :members: :undoc-members: :show-inheritance: -:mod:`curl` Module ------------------- +Submodules +---------- + +galaxy.jobs.runners.lwr_client.transport.curl module +---------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.transport.curl :members: :undoc-members: :show-inheritance: -:mod:`standard` Module ----------------------- +galaxy.jobs.runners.lwr_client.transport.standard module +-------------------------------------------------------- .. automodule:: galaxy.jobs.runners.lwr_client.transport.standard :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index 83cf3a5a41e..30c2f598717 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -1,94 +1,11 @@ -runners Package -=============== - -:mod:`runners` Package ----------------------- +galaxy.jobs.runners package +=========================== .. automodule:: galaxy.jobs.runners :members: :undoc-members: :show-inheritance: -:mod:`cli` Module ------------------ - -.. automodule:: galaxy.jobs.runners.cli - :members: - :undoc-members: - :show-inheritance: - -:mod:`condor` Module --------------------- - -.. automodule:: galaxy.jobs.runners.condor - :members: - :undoc-members: - :show-inheritance: - -:mod:`drmaa` Module -------------------- - -.. automodule:: galaxy.jobs.runners.drmaa - :members: - :undoc-members: - :show-inheritance: - -:mod:`local` Module -------------------- - -.. automodule:: galaxy.jobs.runners.local - :members: - :undoc-members: - :show-inheritance: - -:mod:`lwr` Module ------------------ - -.. automodule:: galaxy.jobs.runners.lwr - :members: - :undoc-members: - :show-inheritance: - -:mod:`pbs` Module ------------------ - -.. automodule:: galaxy.jobs.runners.pbs - :members: - :undoc-members: - :show-inheritance: - -:mod:`pulsar` Module --------------------- - -.. automodule:: galaxy.jobs.runners.pulsar - :members: - :undoc-members: - :show-inheritance: - -:mod:`slurm` Module -------------------- - -.. automodule:: galaxy.jobs.runners.slurm - :members: - :undoc-members: - :show-inheritance: - -:mod:`state_handler_factory` Module ------------------------------------ - -.. automodule:: galaxy.jobs.runners.state_handler_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`tasks` Module -------------------- - -.. automodule:: galaxy.jobs.runners.tasks - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -98,3 +15,87 @@ Subpackages galaxy.jobs.runners.state_handlers galaxy.jobs.runners.util +Submodules +---------- + +galaxy.jobs.runners.cli module +------------------------------ + +.. automodule:: galaxy.jobs.runners.cli + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.condor module +--------------------------------- + +.. automodule:: galaxy.jobs.runners.condor + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.drmaa module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.drmaa + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.local module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.local + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.lwr module +------------------------------ + +.. automodule:: galaxy.jobs.runners.lwr + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.pbs module +------------------------------ + +.. automodule:: galaxy.jobs.runners.pbs + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.pulsar module +--------------------------------- + +.. automodule:: galaxy.jobs.runners.pulsar + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.slurm module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.slurm + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.state_handler_factory module +------------------------------------------------ + +.. automodule:: galaxy.jobs.runners.state_handler_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.tasks module +-------------------------------- + +.. automodule:: galaxy.jobs.runners.tasks + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst index bbf8577287a..06b15dd3f54 100644 --- a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -1,11 +1,20 @@ -state_handlers Package -====================== +galaxy.jobs.runners.state_handlers package +========================================== -:mod:`resubmit` Module ----------------------- +.. automodule:: galaxy.jobs.runners.state_handlers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.jobs.runners.state_handlers.resubmit module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handlers.resubmit :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst index f98c1cb988a..ec1149a0d87 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -1,35 +1,36 @@ -job Package -=========== - -:mod:`job` Package ------------------- +galaxy.jobs.runners.util.cli.job package +======================================== .. automodule:: galaxy.jobs.runners.util.cli.job :members: :undoc-members: :show-inheritance: -:mod:`slurm` Module -------------------- +Submodules +---------- + +galaxy.jobs.runners.util.cli.job.slurm module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`torque` Module --------------------- +galaxy.jobs.runners.util.cli.job.torque module +---------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.torque :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst index b3426fc78f8..dadd626718b 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -1,22 +1,11 @@ -cli Package -=========== - -:mod:`cli` Package ------------------- +galaxy.jobs.runners.util.cli package +==================================== .. automodule:: galaxy.jobs.runners.util.cli :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- - -.. automodule:: galaxy.jobs.runners.util.cli.factory - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -25,3 +14,15 @@ Subpackages galaxy.jobs.runners.util.cli.job galaxy.jobs.runners.util.cli.shell +Submodules +---------- + +galaxy.jobs.runners.util.cli.factory module +------------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.factory + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst index 115c1cfc0dd..42e5c7ffe73 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -1,27 +1,28 @@ -shell Package -============= - -:mod:`shell` Package --------------------- +galaxy.jobs.runners.util.cli.shell package +========================================== .. automodule:: galaxy.jobs.runners.util.cli.shell :members: :undoc-members: :show-inheritance: -:mod:`local` Module -------------------- +Submodules +---------- + +galaxy.jobs.runners.util.cli.shell.local module +----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.local :members: :undoc-members: :show-inheritance: -:mod:`rsh` Module ------------------ +galaxy.jobs.runners.util.cli.shell.rsh module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.rsh :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst index 8678f6a98a7..823ea51ac3e 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.condor.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -1,8 +1,5 @@ -condor Package -============== - -:mod:`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 7599d9a1f64..bcc2b16e9eb 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -1,8 +1,5 @@ -job_script Package -================== - -:mod:`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 410034390c9..8bdd25fc7b4 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -1,38 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.jobs.runners.util package +================================ .. automodule:: galaxy.jobs.runners.util :members: :undoc-members: :show-inheritance: -:mod:`env` Module ------------------ - -.. automodule:: galaxy.jobs.runners.util.env - :members: - :undoc-members: - :show-inheritance: - -:mod:`external` Module ----------------------- - -.. automodule:: galaxy.jobs.runners.util.external - :members: - :undoc-members: - :show-inheritance: - -:mod:`kill` Module ------------------- - -.. automodule:: galaxy.jobs.runners.util.kill - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -42,3 +15,31 @@ Subpackages galaxy.jobs.runners.util.condor galaxy.jobs.runners.util.job_script +Submodules +---------- + +galaxy.jobs.runners.util.env module +----------------------------------- + +.. automodule:: galaxy.jobs.runners.util.env + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.external module +---------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.external + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.kill module +------------------------------------ + +.. automodule:: galaxy.jobs.runners.util.kill + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst index 66545414b2e..d8af934e1be 100644 --- a/doc/source/lib/galaxy.jobs.splitters.rst +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -1,19 +1,28 @@ -splitters Package -================= +galaxy.jobs.splitters package +============================= -:mod:`basic` Module -------------------- +.. automodule:: galaxy.jobs.splitters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.jobs.splitters.basic module +---------------------------------- .. automodule:: galaxy.jobs.splitters.basic :members: :undoc-members: :show-inheritance: -:mod:`multi` Module -------------------- +galaxy.jobs.splitters.multi module +---------------------------------- .. automodule:: galaxy.jobs.splitters.multi :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index ae0ab647d05..5fab9245342 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -1,227 +1,228 @@ -managers Package -================ - -:mod:`managers` Package ------------------------ +galaxy.managers package +======================= .. automodule:: galaxy.managers :members: :undoc-members: :show-inheritance: -:mod:`annotatable` Module -------------------------- +Submodules +---------- + +galaxy.managers.annotatable module +---------------------------------- .. automodule:: galaxy.managers.annotatable :members: :undoc-members: :show-inheritance: -:mod:`api_keys` Module ----------------------- +galaxy.managers.api_keys module +------------------------------- .. automodule:: galaxy.managers.api_keys :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- +galaxy.managers.base module +--------------------------- .. automodule:: galaxy.managers.base :members: :undoc-members: :show-inheritance: -:mod:`citations` Module ------------------------ +galaxy.managers.citations module +-------------------------------- .. automodule:: galaxy.managers.citations :members: :undoc-members: :show-inheritance: -:mod:`collections` Module -------------------------- +galaxy.managers.collections module +---------------------------------- .. automodule:: galaxy.managers.collections :members: :undoc-members: :show-inheritance: -:mod:`collections_util` Module ------------------------------- +galaxy.managers.collections_util module +--------------------------------------- .. automodule:: galaxy.managers.collections_util :members: :undoc-members: :show-inheritance: -:mod:`configuration` Module ---------------------------- +galaxy.managers.configuration module +------------------------------------ .. automodule:: galaxy.managers.configuration :members: :undoc-members: :show-inheritance: -:mod:`containers` Module ------------------------- +galaxy.managers.containers module +--------------------------------- .. automodule:: galaxy.managers.containers :members: :undoc-members: :show-inheritance: -:mod:`context` Module ---------------------- +galaxy.managers.context module +------------------------------ .. automodule:: galaxy.managers.context :members: :undoc-members: :show-inheritance: -:mod:`datasets` Module ----------------------- +galaxy.managers.datasets module +------------------------------- .. automodule:: galaxy.managers.datasets :members: :undoc-members: :show-inheritance: -:mod:`deletable` Module ------------------------ +galaxy.managers.deletable module +-------------------------------- .. automodule:: galaxy.managers.deletable :members: :undoc-members: :show-inheritance: -:mod:`folders` Module ---------------------- +galaxy.managers.folders module +------------------------------ .. automodule:: galaxy.managers.folders :members: :undoc-members: :show-inheritance: -:mod:`hdas` Module ------------------- +galaxy.managers.hdas module +--------------------------- .. automodule:: galaxy.managers.hdas :members: :undoc-members: :show-inheritance: -:mod:`histories` Module ------------------------ +galaxy.managers.histories module +-------------------------------- .. automodule:: galaxy.managers.histories :members: :undoc-members: :show-inheritance: -:mod:`lddas` Module -------------------- +galaxy.managers.lddas module +---------------------------- .. automodule:: galaxy.managers.lddas :members: :undoc-members: :show-inheritance: -:mod:`libraries` Module ------------------------ +galaxy.managers.libraries module +-------------------------------- .. automodule:: galaxy.managers.libraries :members: :undoc-members: :show-inheritance: -:mod:`pages` Module -------------------- +galaxy.managers.pages module +---------------------------- .. automodule:: galaxy.managers.pages :members: :undoc-members: :show-inheritance: -:mod:`ratable` Module ---------------------- +galaxy.managers.ratable module +------------------------------ .. automodule:: galaxy.managers.ratable :members: :undoc-members: :show-inheritance: -:mod:`rbac_secured` Module --------------------------- +galaxy.managers.rbac_secured module +----------------------------------- .. automodule:: galaxy.managers.rbac_secured :members: :undoc-members: :show-inheritance: -:mod:`roles` Module -------------------- +galaxy.managers.roles module +---------------------------- .. automodule:: galaxy.managers.roles :members: :undoc-members: :show-inheritance: -:mod:`secured` Module ---------------------- +galaxy.managers.secured module +------------------------------ .. automodule:: galaxy.managers.secured :members: :undoc-members: :show-inheritance: -:mod:`sharable` Module ----------------------- +galaxy.managers.sharable module +------------------------------- .. automodule:: galaxy.managers.sharable :members: :undoc-members: :show-inheritance: -:mod:`taggable` Module ----------------------- +galaxy.managers.taggable module +------------------------------- .. automodule:: galaxy.managers.taggable :members: :undoc-members: :show-inheritance: -:mod:`tags` Module ------------------- +galaxy.managers.tags module +--------------------------- .. automodule:: galaxy.managers.tags :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.managers.users module +---------------------------- .. automodule:: galaxy.managers.users :members: :undoc-members: :show-inheritance: -:mod:`visualizations` Module ----------------------------- +galaxy.managers.visualizations module +------------------------------------- .. automodule:: galaxy.managers.visualizations :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.managers.workflows module +-------------------------------- .. automodule:: galaxy.managers.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 7218eff3296..60857c84097 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.model.migrate package +============================ -:mod:`check` Module -------------------- +.. automodule:: galaxy.model.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrate.check module +--------------------------------- .. automodule:: galaxy.model.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 379141b94ed..b6896869c00 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -1,43 +1,44 @@ -orm Package -=========== - -:mod:`orm` Package ------------------- +galaxy.model.orm package +======================== .. automodule:: galaxy.model.orm :members: :undoc-members: :show-inheritance: -:mod:`engine_factory` Module ----------------------------- +Submodules +---------- + +galaxy.model.orm.engine_factory module +-------------------------------------- .. automodule:: galaxy.model.orm.engine_factory :members: :undoc-members: :show-inheritance: -:mod:`logging_connection_proxy` Module --------------------------------------- +galaxy.model.orm.logging_connection_proxy module +------------------------------------------------ .. automodule:: galaxy.model.orm.logging_connection_proxy :members: :undoc-members: :show-inheritance: -:mod:`now` Module ------------------ +galaxy.model.orm.now module +--------------------------- .. automodule:: galaxy.model.orm.now :members: :undoc-members: :show-inheritance: -:mod:`scripts` Module ---------------------- +galaxy.model.orm.scripts module +------------------------------- .. automodule:: galaxy.model.orm.scripts :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index e063ff3d456..748a7ba7710 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -1,62 +1,11 @@ -model Package -============= - -:mod:`model` Package --------------------- +galaxy.model package +==================== .. automodule:: galaxy.model :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.model.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`custom_types` Module --------------------------- - -.. automodule:: galaxy.model.custom_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`item_attrs` Module ------------------------- - -.. automodule:: galaxy.model.item_attrs - :members: - :undoc-members: - :show-inheritance: - -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.model.mapping - :members: - :undoc-members: - :show-inheritance: - -:mod:`search` Module --------------------- - -.. automodule:: galaxy.model.search - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: galaxy.model.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -66,3 +15,55 @@ Subpackages galaxy.model.orm galaxy.model.tool_shed_install +Submodules +---------- + +galaxy.model.base module +------------------------ + +.. automodule:: galaxy.model.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.custom_types module +-------------------------------- + +.. automodule:: galaxy.model.custom_types + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.item_attrs module +------------------------------ + +.. automodule:: galaxy.model.item_attrs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.mapping module +--------------------------- + +.. automodule:: galaxy.model.mapping + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.search module +-------------------------- + +.. automodule:: galaxy.model.search + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.util module +------------------------ + +.. automodule:: galaxy.model.util + :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 f117f24a115..56b44de4bc7 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.model.tool_shed_install.migrate package +============================================== -:mod:`check` Module -------------------- +.. automodule:: galaxy.model.tool_shed_install.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.tool_shed_install.migrate.check module +--------------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index 3d311847ab5..24e6b47e45b 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -1,22 +1,11 @@ -tool_shed_install Package -========================= - -:mod:`tool_shed_install` Package --------------------------------- +galaxy.model.tool_shed_install package +====================================== .. automodule:: galaxy.model.tool_shed_install :members: :undoc-members: :show-inheritance: -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.model.tool_shed_install.mapping - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.model.tool_shed_install.migrate +Submodules +---------- + +galaxy.model.tool_shed_install.mapping module +--------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.mapping + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 19343f88e39..71457af109e 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -1,43 +1,44 @@ -objectstore Package -=================== - -:mod:`objectstore` Package --------------------------- +galaxy.objectstore package +========================== .. automodule:: galaxy.objectstore :members: :undoc-members: :show-inheritance: -:mod:`pulsar` Module --------------------- +Submodules +---------- + +galaxy.objectstore.pulsar module +-------------------------------- .. automodule:: galaxy.objectstore.pulsar :members: :undoc-members: :show-inheritance: -:mod:`rods` Module ------------------- +galaxy.objectstore.rods module +------------------------------ .. automodule:: galaxy.objectstore.rods :members: :undoc-members: :show-inheritance: -:mod:`s3` Module ----------------- +galaxy.objectstore.s3 module +---------------------------- .. automodule:: galaxy.objectstore.s3 :members: :undoc-members: :show-inheritance: -:mod:`s3_multipart_upload` Module ---------------------------------- +galaxy.objectstore.s3_multipart_upload module +--------------------------------------------- .. automodule:: galaxy.objectstore.s3_multipart_upload :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst index d5dd49a08d3..ccd8057cfce 100644 --- a/doc/source/lib/galaxy.openid.rst +++ b/doc/source/lib/galaxy.openid.rst @@ -1,19 +1,20 @@ -openid Package -============== - -:mod:`openid` Package ---------------------- +galaxy.openid package +===================== .. automodule:: galaxy.openid :members: :undoc-members: :show-inheritance: -:mod:`providers` Module ------------------------ +Submodules +---------- + +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 b06c6ba33d3..36802033ce1 100644 --- a/doc/source/lib/galaxy.quota.rst +++ b/doc/source/lib/galaxy.quota.rst @@ -1,8 +1,5 @@ -quota Package -============= - -:mod:`quota` Package --------------------- +galaxy.quota package +==================== .. automodule:: galaxy.quota :members: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index a1a42e221e4..b811fd86a1a 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -1,62 +1,11 @@ -galaxy Package +galaxy package ============== -:mod:`galaxy` Package ---------------------- - .. automodule:: galaxy :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.config - :members: - :undoc-members: - :show-inheritance: - -:mod:`main` Module ------------------- - -.. automodule:: galaxy.main - :members: - :undoc-members: - :show-inheritance: - -:mod:`queue_worker` Module --------------------------- - -.. automodule:: galaxy.queue_worker - :members: - :undoc-members: - :show-inheritance: - -:mod:`queues` Module --------------------- - -.. automodule:: galaxy.queues - :members: - :undoc-members: - :show-inheritance: - -:mod:`version` Module ---------------------- - -.. automodule:: galaxy.version - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -88,3 +37,55 @@ Subpackages galaxy.work galaxy.workflow +Submodules +---------- + +galaxy.app module +----------------- + +.. automodule:: galaxy.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.config module +-------------------- + +.. automodule:: galaxy.config + :members: + :undoc-members: + :show-inheritance: + +galaxy.main module +------------------ + +.. automodule:: galaxy.main + :members: + :undoc-members: + :show-inheritance: + +galaxy.queue_worker module +-------------------------- + +.. automodule:: galaxy.queue_worker + :members: + :undoc-members: + :show-inheritance: + +galaxy.queues module +-------------------- + +.. automodule:: galaxy.queues + :members: + :undoc-members: + :show-inheritance: + +galaxy.version module +--------------------- + +.. automodule:: galaxy.version + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.sample_tracking.rst b/doc/source/lib/galaxy.sample_tracking.rst index 52dd1e6c7f6..dbef4b76139 100644 --- a/doc/source/lib/galaxy.sample_tracking.rst +++ b/doc/source/lib/galaxy.sample_tracking.rst @@ -1,35 +1,44 @@ -sample_tracking Package -======================= +galaxy.sample_tracking package +============================== -:mod:`data_transfer` Module ---------------------------- +.. automodule:: galaxy.sample_tracking + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.sample_tracking.data_transfer module +------------------------------------------- .. automodule:: galaxy.sample_tracking.data_transfer :members: :undoc-members: :show-inheritance: -:mod:`external_service_types` Module ------------------------------------- +galaxy.sample_tracking.external_service_types module +---------------------------------------------------- .. automodule:: galaxy.sample_tracking.external_service_types :members: :undoc-members: :show-inheritance: -:mod:`request_types` Module ---------------------------- +galaxy.sample_tracking.request_types module +------------------------------------------- .. automodule:: galaxy.sample_tracking.request_types :members: :undoc-members: :show-inheritance: -:mod:`sample` Module --------------------- +galaxy.sample_tracking.sample module +------------------------------------ .. automodule:: galaxy.sample_tracking.sample :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index ff90ef6e6e2..5f1ab5fe123 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -1,27 +1,28 @@ -security Package -================ - -:mod:`security` Package ------------------------ +galaxy.security package +======================= .. automodule:: galaxy.security :members: :undoc-members: :show-inheritance: -:mod:`passwords` Module ------------------------ +Submodules +---------- + +galaxy.security.passwords module +-------------------------------- .. automodule:: galaxy.security.passwords :members: :undoc-members: :show-inheritance: -:mod:`validate_user_input` Module ---------------------------------- +galaxy.security.validate_user_input module +------------------------------------------ .. automodule:: galaxy.security.validate_user_input :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tags.rst b/doc/source/lib/galaxy.tags.rst index 38d5152b8e7..d61869f22bd 100644 --- a/doc/source/lib/galaxy.tags.rst +++ b/doc/source/lib/galaxy.tags.rst @@ -1,8 +1,5 @@ -tags Package -============ - -:mod:`tags` Package -------------------- +galaxy.tags package +=================== .. automodule:: galaxy.tags :members: diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 870cc2ca31b..1cf4863c217 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -1,59 +1,60 @@ -actions Package -=============== - -:mod:`actions` Package ----------------------- +galaxy.tools.actions package +============================ .. automodule:: galaxy.tools.actions :members: :undoc-members: :show-inheritance: -:mod:`data_manager` Module --------------------------- +Submodules +---------- + +galaxy.tools.actions.data_manager module +---------------------------------------- .. automodule:: galaxy.tools.actions.data_manager :members: :undoc-members: :show-inheritance: -:mod:`data_source` Module -------------------------- +galaxy.tools.actions.data_source module +--------------------------------------- .. automodule:: galaxy.tools.actions.data_source :members: :undoc-members: :show-inheritance: -:mod:`history_imp_exp` Module ------------------------------ +galaxy.tools.actions.history_imp_exp module +------------------------------------------- .. automodule:: galaxy.tools.actions.history_imp_exp :members: :undoc-members: :show-inheritance: -:mod:`metadata` Module ----------------------- +galaxy.tools.actions.metadata module +------------------------------------ .. automodule:: galaxy.tools.actions.metadata :members: :undoc-members: :show-inheritance: -:mod:`upload` Module --------------------- +galaxy.tools.actions.upload module +---------------------------------- .. automodule:: galaxy.tools.actions.upload :members: :undoc-members: :show-inheritance: -:mod:`upload_common` Module ---------------------------- +galaxy.tools.actions.upload_common module +----------------------------------------- .. automodule:: galaxy.tools.actions.upload_common :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst index 92641efedcb..4435ba549f8 100644 --- a/doc/source/lib/galaxy.tools.data.rst +++ b/doc/source/lib/galaxy.tools.data.rst @@ -1,8 +1,5 @@ -data Package -============ - -:mod:`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 bbf07acd662..02c75fa28ad 100644 --- a/doc/source/lib/galaxy.tools.data_manager.rst +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -1,19 +1,20 @@ -data_manager Package -==================== - -:mod:`data_manager` Package ---------------------------- +galaxy.tools.data_manager package +================================= .. automodule:: galaxy.tools.data_manager :members: :undoc-members: :show-inheritance: -:mod:`manager` Module ---------------------- +Submodules +---------- + +galaxy.tools.data_manager.manager module +---------------------------------------- .. automodule:: galaxy.tools.data_manager.manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst index 5890b4eed38..ef2282bb8d3 100644 --- a/doc/source/lib/galaxy.tools.deps.resolvers.rst +++ b/doc/source/lib/galaxy.tools.deps.resolvers.rst @@ -1,59 +1,60 @@ -resolvers Package -================= - -:mod:`resolvers` Package ------------------------- +galaxy.tools.deps.resolvers package +=================================== .. automodule:: galaxy.tools.deps.resolvers :members: :undoc-members: :show-inheritance: -:mod:`brewed_tool_shed_packages` Module ---------------------------------------- +Submodules +---------- + +galaxy.tools.deps.resolvers.brewed_tool_shed_packages module +------------------------------------------------------------ .. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages :members: :undoc-members: :show-inheritance: -:mod:`galaxy_packages` Module ------------------------------ +galaxy.tools.deps.resolvers.galaxy_packages module +-------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.galaxy_packages :members: :undoc-members: :show-inheritance: -:mod:`homebrew` Module ----------------------- +galaxy.tools.deps.resolvers.homebrew module +------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.homebrew :members: :undoc-members: :show-inheritance: -:mod:`modules` Module ---------------------- +galaxy.tools.deps.resolvers.modules module +------------------------------------------ .. automodule:: galaxy.tools.deps.resolvers.modules :members: :undoc-members: :show-inheritance: -:mod:`resolver_mixins` Module ------------------------------ +galaxy.tools.deps.resolvers.resolver_mixins module +-------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.resolver_mixins :members: :undoc-members: :show-inheritance: -:mod:`tool_shed_packages` Module --------------------------------- +galaxy.tools.deps.resolvers.tool_shed_packages module +----------------------------------------------------- .. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst index 404d660628e..f64c423dc22 100644 --- a/doc/source/lib/galaxy.tools.deps.rst +++ b/doc/source/lib/galaxy.tools.deps.rst @@ -1,78 +1,11 @@ -deps Package -============ - -:mod:`deps` Package -------------------- +galaxy.tools.deps package +========================= .. automodule:: galaxy.tools.deps :members: :undoc-members: :show-inheritance: -:mod:`brew_exts` Module ------------------------ - -.. automodule:: galaxy.tools.deps.brew_exts - :members: - :undoc-members: - :show-inheritance: - -:mod:`brew_util` Module ------------------------ - -.. automodule:: galaxy.tools.deps.brew_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`commands` Module ----------------------- - -.. automodule:: galaxy.tools.deps.commands - :members: - :undoc-members: - :show-inheritance: - -:mod:`containers` Module ------------------------- - -.. automodule:: galaxy.tools.deps.containers - :members: - :undoc-members: - :show-inheritance: - -:mod:`dependencies` Module --------------------------- - -.. automodule:: galaxy.tools.deps.dependencies - :members: - :undoc-members: - :show-inheritance: - -:mod:`docker_util` Module -------------------------- - -.. automodule:: galaxy.tools.deps.docker_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`dockerfiles` Module -------------------------- - -.. automodule:: galaxy.tools.deps.dockerfiles - :members: - :undoc-members: - :show-inheritance: - -:mod:`requirements` Module --------------------------- - -.. automodule:: galaxy.tools.deps.requirements - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -80,3 +13,71 @@ Subpackages galaxy.tools.deps.resolvers +Submodules +---------- + +galaxy.tools.deps.brew_exts module +---------------------------------- + +.. automodule:: galaxy.tools.deps.brew_exts + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.brew_util module +---------------------------------- + +.. automodule:: galaxy.tools.deps.brew_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.commands module +--------------------------------- + +.. automodule:: galaxy.tools.deps.commands + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.containers module +----------------------------------- + +.. automodule:: galaxy.tools.deps.containers + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.dependencies module +------------------------------------- + +.. automodule:: galaxy.tools.deps.dependencies + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.docker_util module +------------------------------------ + +.. automodule:: galaxy.tools.deps.docker_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.dockerfiles module +------------------------------------ + +.. automodule:: galaxy.tools.deps.dockerfiles + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.deps.requirements module +------------------------------------- + +.. automodule:: galaxy.tools.deps.requirements + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst index e31664e9cd3..bbea7ec45e4 100644 --- a/doc/source/lib/galaxy.tools.filters.rst +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -1,8 +1,5 @@ -filters Package -=============== - -:mod:`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 2801da055dd..e466f86b0a4 100644 --- a/doc/source/lib/galaxy.tools.imp_exp.rst +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -1,27 +1,28 @@ -imp_exp Package -=============== - -:mod:`imp_exp` Package ----------------------- +galaxy.tools.imp_exp package +============================ .. automodule:: galaxy.tools.imp_exp :members: :undoc-members: :show-inheritance: -:mod:`export_history` Module ----------------------------- +Submodules +---------- + +galaxy.tools.imp_exp.export_history module +------------------------------------------ .. automodule:: galaxy.tools.imp_exp.export_history :members: :undoc-members: :show-inheritance: -:mod:`unpack_tar_gz_archive` Module ------------------------------------ +galaxy.tools.imp_exp.unpack_tar_gz_archive module +------------------------------------------------- .. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst index e8e91a60b88..a27e6bf42bd 100644 --- a/doc/source/lib/galaxy.tools.linters.rst +++ b/doc/source/lib/galaxy.tools.linters.rst @@ -1,67 +1,68 @@ -linters Package -=============== - -:mod:`linters` Package ----------------------- +galaxy.tools.linters package +============================ .. automodule:: galaxy.tools.linters :members: :undoc-members: :show-inheritance: -:mod:`citations` Module ------------------------ +Submodules +---------- + +galaxy.tools.linters.citations module +------------------------------------- .. automodule:: galaxy.tools.linters.citations :members: :undoc-members: :show-inheritance: -:mod:`command` Module ---------------------- +galaxy.tools.linters.command module +----------------------------------- .. automodule:: galaxy.tools.linters.command :members: :undoc-members: :show-inheritance: -:mod:`help` Module ------------------- +galaxy.tools.linters.help module +-------------------------------- .. automodule:: galaxy.tools.linters.help :members: :undoc-members: :show-inheritance: -:mod:`inputs` Module --------------------- +galaxy.tools.linters.inputs module +---------------------------------- .. automodule:: galaxy.tools.linters.inputs :members: :undoc-members: :show-inheritance: -:mod:`outputs` Module ---------------------- +galaxy.tools.linters.outputs module +----------------------------------- .. automodule:: galaxy.tools.linters.outputs :members: :undoc-members: :show-inheritance: -:mod:`tests` Module -------------------- +galaxy.tools.linters.tests module +--------------------------------- .. automodule:: galaxy.tools.linters.tests :members: :undoc-members: :show-inheritance: -:mod:`top_level` Module ------------------------ +galaxy.tools.linters.top_level module +------------------------------------- .. automodule:: galaxy.tools.linters.top_level :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 183d17cb295..28309e13f58 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -1,107 +1,108 @@ -parameters Package -================== - -:mod:`parameters` Package -------------------------- +galaxy.tools.parameters package +=============================== .. automodule:: galaxy.tools.parameters :members: :undoc-members: :show-inheritance: -:mod:`basic` Module -------------------- +Submodules +---------- + +galaxy.tools.parameters.basic module +------------------------------------ .. automodule:: galaxy.tools.parameters.basic :members: :undoc-members: :show-inheritance: -:mod:`dataset_matcher` Module ------------------------------ +galaxy.tools.parameters.dataset_matcher module +---------------------------------------------- .. automodule:: galaxy.tools.parameters.dataset_matcher :members: :undoc-members: :show-inheritance: -:mod:`dynamic_options` Module ------------------------------ +galaxy.tools.parameters.dynamic_options module +---------------------------------------------- .. automodule:: galaxy.tools.parameters.dynamic_options :members: :undoc-members: :show-inheritance: -:mod:`grouping` Module ----------------------- +galaxy.tools.parameters.grouping module +--------------------------------------- .. automodule:: galaxy.tools.parameters.grouping :members: :undoc-members: :show-inheritance: -:mod:`history_query` Module ---------------------------- +galaxy.tools.parameters.history_query module +-------------------------------------------- .. automodule:: galaxy.tools.parameters.history_query :members: :undoc-members: :show-inheritance: -:mod:`input_translation` Module -------------------------------- +galaxy.tools.parameters.input_translation module +------------------------------------------------ .. automodule:: galaxy.tools.parameters.input_translation :members: :undoc-members: :show-inheritance: -:mod:`meta` Module ------------------- +galaxy.tools.parameters.meta module +----------------------------------- .. automodule:: galaxy.tools.parameters.meta :members: :undoc-members: :show-inheritance: -:mod:`output` Module --------------------- +galaxy.tools.parameters.output module +------------------------------------- .. automodule:: galaxy.tools.parameters.output :members: :undoc-members: :show-inheritance: -:mod:`output_collect` Module ----------------------------- +galaxy.tools.parameters.output_collect module +--------------------------------------------- .. automodule:: galaxy.tools.parameters.output_collect :members: :undoc-members: :show-inheritance: -:mod:`sanitize` Module ----------------------- +galaxy.tools.parameters.sanitize module +--------------------------------------- .. automodule:: galaxy.tools.parameters.sanitize :members: :undoc-members: :show-inheritance: -:mod:`validation` Module ------------------------- +galaxy.tools.parameters.validation module +----------------------------------------- .. automodule:: galaxy.tools.parameters.validation :members: :undoc-members: :show-inheritance: -:mod:`wrapped` Module ---------------------- +galaxy.tools.parameters.wrapped module +-------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst index 8c316098d72..ecdc2b15feb 100644 --- a/doc/source/lib/galaxy.tools.parser.rst +++ b/doc/source/lib/galaxy.tools.parser.rst @@ -1,51 +1,52 @@ -parser Package -============== - -:mod:`parser` Package ---------------------- +galaxy.tools.parser package +=========================== .. automodule:: galaxy.tools.parser :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- +Submodules +---------- + +galaxy.tools.parser.factory module +---------------------------------- .. automodule:: galaxy.tools.parser.factory :members: :undoc-members: :show-inheritance: -:mod:`interface` Module ------------------------ +galaxy.tools.parser.interface module +------------------------------------ .. automodule:: galaxy.tools.parser.interface :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +galaxy.tools.parser.util module +------------------------------- .. automodule:: galaxy.tools.parser.util :members: :undoc-members: :show-inheritance: -:mod:`xml` Module ------------------ +galaxy.tools.parser.xml module +------------------------------ .. automodule:: galaxy.tools.parser.xml :members: :undoc-members: :show-inheritance: -:mod:`yaml` Module ------------------- +galaxy.tools.parser.yaml module +------------------------------- .. automodule:: galaxy.tools.parser.yaml :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 90bb129cbd4..01add8d971c 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -1,86 +1,11 @@ -tools Package -============= - -:mod:`tools` Package --------------------- +galaxy.tools package +==================== .. automodule:: galaxy.tools :members: :undoc-members: :show-inheritance: -:mod:`errors` Module --------------------- - -.. automodule:: galaxy.tools.errors - :members: - :undoc-members: - :show-inheritance: - -:mod:`evaluation` Module ------------------------- - -.. automodule:: galaxy.tools.evaluation - :members: - :undoc-members: - :show-inheritance: - -:mod:`exception_handling` Module --------------------------------- - -.. automodule:: galaxy.tools.exception_handling - :members: - :undoc-members: - :show-inheritance: - -:mod:`execute` Module ---------------------- - -.. automodule:: galaxy.tools.execute - :members: - :undoc-members: - :show-inheritance: - -:mod:`lint` Module ------------------- - -.. automodule:: galaxy.tools.lint - :members: - :undoc-members: - :show-inheritance: - -:mod:`loader` Module --------------------- - -.. automodule:: galaxy.tools.loader - :members: - :undoc-members: - :show-inheritance: - -:mod:`loader_directory` Module ------------------------------- - -.. automodule:: galaxy.tools.loader_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`test` Module ------------------- - -.. automodule:: galaxy.tools.test - :members: - :undoc-members: - :show-inheritance: - -:mod:`wrappers` Module ----------------------- - -.. automodule:: galaxy.tools.wrappers - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -99,3 +24,79 @@ Subpackages galaxy.tools.toolbox galaxy.tools.util +Submodules +---------- + +galaxy.tools.errors module +-------------------------- + +.. automodule:: galaxy.tools.errors + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.evaluation module +------------------------------ + +.. automodule:: galaxy.tools.evaluation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.exception_handling module +-------------------------------------- + +.. automodule:: galaxy.tools.exception_handling + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.execute module +--------------------------- + +.. automodule:: galaxy.tools.execute + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.lint module +------------------------ + +.. automodule:: galaxy.tools.lint + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.loader module +-------------------------- + +.. automodule:: galaxy.tools.loader + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.loader_directory module +------------------------------------ + +.. automodule:: galaxy.tools.loader_directory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.test module +------------------------ + +.. automodule:: galaxy.tools.test + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.wrappers module +---------------------------- + +.. automodule:: galaxy.tools.wrappers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst index 616079f69b7..edbb5bf3c79 100644 --- a/doc/source/lib/galaxy.tools.search.rst +++ b/doc/source/lib/galaxy.tools.search.rst @@ -1,8 +1,5 @@ -search Package -============== - -:mod:`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 d168b000a9e..a5a81d279fb 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -1,8 +1,5 @@ -filters Package -=============== - -:mod:`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 bd3811cdb1e..3159c8d248d 100644 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -1,43 +1,44 @@ -lineages Package -================ - -:mod:`lineages` Package ------------------------ +galaxy.tools.toolbox.lineages package +===================================== .. automodule:: galaxy.tools.toolbox.lineages :members: :undoc-members: :show-inheritance: -:mod:`factory` Module ---------------------- +Submodules +---------- + +galaxy.tools.toolbox.lineages.factory module +-------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.factory :members: :undoc-members: :show-inheritance: -:mod:`interface` Module ------------------------ +galaxy.tools.toolbox.lineages.interface module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.interface :members: :undoc-members: :show-inheritance: -:mod:`stock` Module -------------------- +galaxy.tools.toolbox.lineages.stock module +------------------------------------------ .. automodule:: galaxy.tools.toolbox.lineages.stock :members: :undoc-members: :show-inheritance: -:mod:`tool_shed` Module ------------------------ +galaxy.tools.toolbox.lineages.tool_shed module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.tool_shed :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst index 8739d4fb201..7528cb77e08 100644 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -1,54 +1,11 @@ -toolbox Package -=============== - -:mod:`toolbox` Package ----------------------- +galaxy.tools.toolbox package +============================ .. automodule:: galaxy.tools.toolbox :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.tools.toolbox.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`integrated_panel` Module ------------------------------- - -.. automodule:: galaxy.tools.toolbox.integrated_panel - :members: - :undoc-members: - :show-inheritance: - -:mod:`panel` Module -------------------- - -.. automodule:: galaxy.tools.toolbox.panel - :members: - :undoc-members: - :show-inheritance: - -:mod:`tags` Module ------------------- - -.. automodule:: galaxy.tools.toolbox.tags - :members: - :undoc-members: - :show-inheritance: - -:mod:`watcher` Module ---------------------- - -.. automodule:: galaxy.tools.toolbox.watcher - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -57,3 +14,47 @@ Subpackages galaxy.tools.toolbox.filters galaxy.tools.toolbox.lineages +Submodules +---------- + +galaxy.tools.toolbox.base module +-------------------------------- + +.. automodule:: galaxy.tools.toolbox.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.integrated_panel module +-------------------------------------------- + +.. automodule:: galaxy.tools.toolbox.integrated_panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.panel module +--------------------------------- + +.. automodule:: galaxy.tools.toolbox.panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.tags module +-------------------------------- + +.. automodule:: galaxy.tools.toolbox.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.toolbox.watcher module +----------------------------------- + +.. automodule:: galaxy.tools.toolbox.watcher + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst index 2e749eefb13..4ea949a2fac 100644 --- a/doc/source/lib/galaxy.tools.util.galaxyops.rst +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -1,8 +1,5 @@ -galaxyops Package -================= - -:mod:`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 04efb192a74..f7b6b6f32d0 100644 --- a/doc/source/lib/galaxy.tools.util.rst +++ b/doc/source/lib/galaxy.tools.util.rst @@ -1,22 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.tools.util package +========================= .. automodule:: galaxy.tools.util :members: :undoc-members: :show-inheritance: -:mod:`maf_utilities` Module ---------------------------- - -.. automodule:: galaxy.tools.util.maf_utilities - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.tools.util.galaxyops +Submodules +---------- + +galaxy.tools.util.maf_utilities module +-------------------------------------- + +.. automodule:: galaxy.tools.util.maf_utilities + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.util.backports.importlib.rst b/doc/source/lib/galaxy.util.backports.importlib.rst index 765830ac0bc..974cf47f98d 100644 --- a/doc/source/lib/galaxy.util.backports.importlib.rst +++ b/doc/source/lib/galaxy.util.backports.importlib.rst @@ -1,8 +1,5 @@ -importlib Package -================= - -:mod:`importlib` Package ------------------------- +galaxy.util.backports.importlib package +======================================= .. automodule:: galaxy.util.backports.importlib :members: diff --git a/doc/source/lib/galaxy.util.backports.rst b/doc/source/lib/galaxy.util.backports.rst index ead946d6eca..69356d80fcd 100644 --- a/doc/source/lib/galaxy.util.backports.rst +++ b/doc/source/lib/galaxy.util.backports.rst @@ -1,8 +1,5 @@ -backports Package -================= - -:mod:`backports` Package ------------------------- +galaxy.util.backports package +============================= .. automodule:: galaxy.util.backports :members: diff --git a/doc/source/lib/galaxy.util.log.rst b/doc/source/lib/galaxy.util.log.rst index c3aa8056511..0f81bc0115c 100644 --- a/doc/source/lib/galaxy.util.log.rst +++ b/doc/source/lib/galaxy.util.log.rst @@ -1,19 +1,20 @@ -log Package -=========== - -:mod:`log` Package ------------------- +galaxy.util.log package +======================= .. automodule:: galaxy.util.log :members: :undoc-members: :show-inheritance: -:mod:`fluent_log` Module ------------------------- +Submodules +---------- + +galaxy.util.log.fluent_log module +--------------------------------- .. automodule:: galaxy.util.log.fluent_log :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst index beb1f826ebe..0a861eb5a4f 100644 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -1,27 +1,28 @@ -pastescript Package -=================== - -:mod:`pastescript` Package --------------------------- +galaxy.util.pastescript package +=============================== .. automodule:: galaxy.util.pastescript :members: :undoc-members: :show-inheritance: -:mod:`loadwsgi` Module ----------------------- +Submodules +---------- + +galaxy.util.pastescript.loadwsgi module +--------------------------------------- .. automodule:: galaxy.util.pastescript.loadwsgi :members: :undoc-members: :show-inheritance: -:mod:`serve` Module -------------------- +galaxy.util.pastescript.serve module +------------------------------------ .. automodule:: galaxy.util.pastescript.serve :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index e37346a6b6b..dd2eca1c66b 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -1,278 +1,11 @@ -util Package -============ - -:mod:`util` Package -------------------- +galaxy.util package +=================== .. automodule:: galaxy.util :members: :undoc-members: :show-inheritance: -:mod:`aliaspickler` Module --------------------------- - -.. automodule:: galaxy.util.aliaspickler - :members: - :undoc-members: - :show-inheritance: - -:mod:`biostar` Module ---------------------- - -.. automodule:: galaxy.util.biostar - :members: - :undoc-members: - :show-inheritance: - -:mod:`bunch` Module -------------------- - -.. automodule:: galaxy.util.bunch - :members: - :undoc-members: - :show-inheritance: - -:mod:`dbkeys` Module --------------------- - -.. automodule:: galaxy.util.dbkeys - :members: - :undoc-members: - :show-inheritance: - -:mod:`debugging` Module ------------------------ - -.. automodule:: galaxy.util.debugging - :members: - :undoc-members: - :show-inheritance: - -:mod:`dictobj` Module ---------------------- - -.. automodule:: galaxy.util.dictobj - :members: - :undoc-members: - :show-inheritance: - -:mod:`directory_hash` Module ----------------------------- - -.. automodule:: galaxy.util.directory_hash - :members: - :undoc-members: - :show-inheritance: - -:mod:`expressions` Module -------------------------- - -.. automodule:: galaxy.util.expressions - :members: - :undoc-members: - :show-inheritance: - -:mod:`hash_util` Module ------------------------ - -.. automodule:: galaxy.util.hash_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`heartbeat` Module ------------------------ - -.. automodule:: galaxy.util.heartbeat - :members: - :undoc-members: - :show-inheritance: - -:mod:`inflection` Module ------------------------- - -.. automodule:: galaxy.util.inflection - :members: - :undoc-members: - :show-inheritance: - -:mod:`json` Module ------------------- - -.. automodule:: galaxy.util.json - :members: - :undoc-members: - :show-inheritance: - -:mod:`jstree` Module --------------------- - -.. automodule:: galaxy.util.jstree - :members: - :undoc-members: - :show-inheritance: - -:mod:`lazy_process` Module --------------------------- - -.. automodule:: galaxy.util.lazy_process - :members: - :undoc-members: - :show-inheritance: - -:mod:`lrucache` Module ----------------------- - -.. automodule:: galaxy.util.lrucache - :members: - :undoc-members: - :show-inheritance: - -:mod:`none_like` Module ------------------------ - -.. automodule:: galaxy.util.none_like - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_wrapper` Module ----------------------------- - -.. automodule:: galaxy.util.object_wrapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`odict` Module -------------------- - -.. automodule:: galaxy.util.odict - :members: - :undoc-members: - :show-inheritance: - -:mod:`permutations` Module --------------------------- - -.. automodule:: galaxy.util.permutations - :members: - :undoc-members: - :show-inheritance: - -:mod:`plugin_config` Module ---------------------------- - -.. automodule:: galaxy.util.plugin_config - :members: - :undoc-members: - :show-inheritance: - -:mod:`properties` Module ------------------------- - -.. automodule:: galaxy.util.properties - :members: - :undoc-members: - :show-inheritance: - -:mod:`sanitize_html` Module ---------------------------- - -.. automodule:: galaxy.util.sanitize_html - :members: - :undoc-members: - :show-inheritance: - -:mod:`simplegraph` Module -------------------------- - -.. automodule:: galaxy.util.simplegraph - :members: - :undoc-members: - :show-inheritance: - -:mod:`sleeper` Module ---------------------- - -.. automodule:: galaxy.util.sleeper - :members: - :undoc-members: - :show-inheritance: - -:mod:`sockets` Module ---------------------- - -.. automodule:: galaxy.util.sockets - :members: - :undoc-members: - :show-inheritance: - -:mod:`specs` Module -------------------- - -.. automodule:: galaxy.util.specs - :members: - :undoc-members: - :show-inheritance: - -:mod:`sqlite` Module --------------------- - -.. automodule:: galaxy.util.sqlite - :members: - :undoc-members: - :show-inheritance: - -:mod:`streamball` Module ------------------------- - -.. automodule:: galaxy.util.streamball - :members: - :undoc-members: - :show-inheritance: - -:mod:`submodules` Module ------------------------- - -.. automodule:: galaxy.util.submodules - :members: - :undoc-members: - :show-inheritance: - -:mod:`template` Module ----------------------- - -.. automodule:: galaxy.util.template - :members: - :undoc-members: - :show-inheritance: - -:mod:`topsort` Module ---------------------- - -.. automodule:: galaxy.util.topsort - :members: - :undoc-members: - :show-inheritance: - -:mod:`validation` Module ------------------------- - -.. automodule:: galaxy.util.validation - :members: - :undoc-members: - :show-inheritance: - -:mod:`xml_macros` Module ------------------------- - -.. automodule:: galaxy.util.xml_macros - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -282,3 +15,271 @@ Subpackages galaxy.util.log galaxy.util.pastescript +Submodules +---------- + +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 +------------------------ + +.. automodule:: galaxy.util.bunch + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.dbkeys module +------------------------- + +.. automodule:: galaxy.util.dbkeys + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.debugging module +---------------------------- + +.. automodule:: galaxy.util.debugging + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.dictobj module +-------------------------- + +.. automodule:: galaxy.util.dictobj + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.directory_hash module +--------------------------------- + +.. automodule:: galaxy.util.directory_hash + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.expressions module +------------------------------ + +.. automodule:: galaxy.util.expressions + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.hash_util module +---------------------------- + +.. automodule:: galaxy.util.hash_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.heartbeat module +---------------------------- + +.. automodule:: galaxy.util.heartbeat + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.inflection module +----------------------------- + +.. automodule:: galaxy.util.inflection + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.json module +----------------------- + +.. automodule:: galaxy.util.json + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.jstree module +------------------------- + +.. automodule:: galaxy.util.jstree + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.lazy_process module +------------------------------- + +.. automodule:: galaxy.util.lazy_process + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.lrucache module +--------------------------- + +.. automodule:: galaxy.util.lrucache + :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 +--------------------------------- + +.. automodule:: galaxy.util.object_wrapper + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.odict module +------------------------ + +.. automodule:: galaxy.util.odict + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.permutations module +------------------------------- + +.. automodule:: galaxy.util.permutations + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.plugin_config module +-------------------------------- + +.. automodule:: galaxy.util.plugin_config + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.properties module +----------------------------- + +.. automodule:: galaxy.util.properties + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sanitize_html module +-------------------------------- + +.. automodule:: galaxy.util.sanitize_html + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.simplegraph module +------------------------------ + +.. automodule:: galaxy.util.simplegraph + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sleeper module +-------------------------- + +.. automodule:: galaxy.util.sleeper + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sockets module +-------------------------- + +.. automodule:: galaxy.util.sockets + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.specs module +------------------------ + +.. automodule:: galaxy.util.specs + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.sqlite module +------------------------- + +.. automodule:: galaxy.util.sqlite + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.streamball module +----------------------------- + +.. automodule:: galaxy.util.streamball + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.submodules module +----------------------------- + +.. automodule:: galaxy.util.submodules + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.template module +--------------------------- + +.. automodule:: galaxy.util.template + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.topsort module +-------------------------- + +.. automodule:: galaxy.util.topsort + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.validation module +----------------------------- + +.. automodule:: galaxy.util.validation + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.xml_macros module +----------------------------- + +.. automodule:: galaxy.util.xml_macros + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst index 7d51bfb4f84..26b7cb913ca 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -1,43 +1,44 @@ -phyloviz Package -================ - -:mod:`phyloviz` Package ------------------------ +galaxy.visualization.data_providers.phyloviz package +==================================================== .. automodule:: galaxy.visualization.data_providers.phyloviz :members: :undoc-members: :show-inheritance: -:mod:`baseparser` Module ------------------------- +Submodules +---------- + +galaxy.visualization.data_providers.phyloviz.baseparser module +-------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser :members: :undoc-members: :show-inheritance: -:mod:`newickparser` Module --------------------------- +galaxy.visualization.data_providers.phyloviz.newickparser module +---------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser :members: :undoc-members: :show-inheritance: -:mod:`nexusparser` Module -------------------------- +galaxy.visualization.data_providers.phyloviz.nexusparser module +--------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser :members: :undoc-members: :show-inheritance: -:mod:`phyloxmlparser` Module ----------------------------- +galaxy.visualization.data_providers.phyloviz.phyloxmlparser module +------------------------------------------------------------------ .. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index ba55a961528..3180ac79181 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -1,46 +1,11 @@ -data_providers Package -====================== - -:mod:`data_providers` Package ------------------------------ +galaxy.visualization.data_providers package +=========================================== .. automodule:: galaxy.visualization.data_providers :members: :undoc-members: :show-inheritance: -:mod:`basic` Module -------------------- - -.. automodule:: galaxy.visualization.data_providers.basic - :members: - :undoc-members: - :show-inheritance: - -:mod:`cigar` Module -------------------- - -.. automodule:: galaxy.visualization.data_providers.cigar - :members: - :undoc-members: - :show-inheritance: - -:mod:`genome` Module --------------------- - -.. automodule:: galaxy.visualization.data_providers.genome - :members: - :undoc-members: - :show-inheritance: - -:mod:`registry` Module ----------------------- - -.. automodule:: galaxy.visualization.data_providers.registry - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -48,3 +13,39 @@ Subpackages galaxy.visualization.data_providers.phyloviz +Submodules +---------- + +galaxy.visualization.data_providers.basic module +------------------------------------------------ + +.. automodule:: galaxy.visualization.data_providers.basic + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.cigar module +------------------------------------------------ + +.. automodule:: galaxy.visualization.data_providers.cigar + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.genome module +------------------------------------------------- + +.. automodule:: galaxy.visualization.data_providers.genome + :members: + :undoc-members: + :show-inheritance: + +galaxy.visualization.data_providers.registry module +--------------------------------------------------- + +.. automodule:: galaxy.visualization.data_providers.registry + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index 8e880dd6b5f..9097529321c 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -1,8 +1,5 @@ -genome Package -============== - -:mod:`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 d276f6d2c32..b8ded7d9b6d 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -1,43 +1,52 @@ -plugins Package -=============== +galaxy.visualization.plugins package +==================================== -:mod:`config_parser` Module ---------------------------- +.. automodule:: galaxy.visualization.plugins + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.visualization.plugins.config_parser module +------------------------------------------------- .. automodule:: galaxy.visualization.plugins.config_parser :members: :undoc-members: :show-inheritance: -:mod:`plugin` Module --------------------- +galaxy.visualization.plugins.plugin module +------------------------------------------ .. automodule:: galaxy.visualization.plugins.plugin :members: :undoc-members: :show-inheritance: -:mod:`registry` Module ----------------------- +galaxy.visualization.plugins.registry module +-------------------------------------------- .. automodule:: galaxy.visualization.plugins.registry :members: :undoc-members: :show-inheritance: -:mod:`resource_parser` Module ------------------------------ +galaxy.visualization.plugins.resource_parser module +--------------------------------------------------- .. automodule:: galaxy.visualization.plugins.resource_parser :members: :undoc-members: :show-inheritance: -:mod:`utils` Module -------------------- +galaxy.visualization.plugins.utils module +----------------------------------------- .. automodule:: galaxy.visualization.plugins.utils :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index ba80d9719ce..1f334499e29 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -1,22 +1,11 @@ -visualization Package -===================== - -:mod:`visualization` Package ----------------------------- +galaxy.visualization package +============================ .. automodule:: galaxy.visualization :members: :undoc-members: :show-inheritance: -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.visualization.genomes - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -27,3 +16,15 @@ Subpackages galaxy.visualization.plugins galaxy.visualization.tracks +Submodules +---------- + +galaxy.visualization.genomes module +----------------------------------- + +.. automodule:: galaxy.visualization.genomes + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 9823b4191df..2d279399ef6 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -1,8 +1,5 @@ -tracks Package -============== - -:mod:`tracks` Package ---------------------- +galaxy.visualization.tracks package +=================================== .. automodule:: galaxy.visualization.tracks :members: diff --git a/doc/source/lib/galaxy.web.base.controllers.rst b/doc/source/lib/galaxy.web.base.controllers.rst index a37900b0aa5..6c153a18d4d 100644 --- a/doc/source/lib/galaxy.web.base.controllers.rst +++ b/doc/source/lib/galaxy.web.base.controllers.rst @@ -1,11 +1,20 @@ -controllers Package -=================== +galaxy.web.base.controllers package +=================================== -:mod:`admin` Module -------------------- +.. automodule:: galaxy.web.base.controllers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.web.base.controllers.admin module +---------------------------------------- .. automodule:: galaxy.web.base.controllers.admin :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index 8b12d23d8c2..3ac90729275 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -1,26 +1,7 @@ -base Package -============ +galaxy.web.base package +======================= -:mod:`controller` Module ------------------------- - -.. automodule:: galaxy.web.base.controller - :members: - :undoc-members: - :show-inheritance: - -:mod:`interactive_environments` Module --------------------------------------- - -.. automodule:: galaxy.web.base.interactive_environments - :members: - :undoc-members: - :show-inheritance: - -:mod:`pluginframework` Module ------------------------------ - -.. automodule:: galaxy.web.base.pluginframework +.. automodule:: galaxy.web.base :members: :undoc-members: :show-inheritance: @@ -32,3 +13,31 @@ Subpackages galaxy.web.base.controllers +Submodules +---------- + +galaxy.web.base.controller module +--------------------------------- + +.. automodule:: galaxy.web.base.controller + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.base.interactive_environments module +----------------------------------------------- + +.. automodule:: galaxy.web.base.interactive_environments + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.base.pluginframework module +-------------------------------------- + +.. automodule:: galaxy.web.base.pluginframework + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst index 690122ac045..d1916931133 100644 --- a/doc/source/lib/galaxy.web.framework.helpers.rst +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -1,19 +1,20 @@ -helpers Package -=============== - -:mod:`helpers` Package ----------------------- +galaxy.web.framework.helpers package +==================================== .. automodule:: galaxy.web.framework.helpers :members: :undoc-members: :show-inheritance: -:mod:`grids` Module -------------------- +Submodules +---------- + +galaxy.web.framework.helpers.grids module +----------------------------------------- .. automodule:: galaxy.web.framework.helpers.grids :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index ddaff84b275..3eb2cbe0ed2 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -1,75 +1,76 @@ -middleware Package -================== - -:mod:`middleware` Package -------------------------- +galaxy.web.framework.middleware package +======================================= .. automodule:: galaxy.web.framework.middleware :members: :undoc-members: :show-inheritance: -:mod:`error` Module -------------------- +Submodules +---------- + +galaxy.web.framework.middleware.error module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.error :members: :undoc-members: :show-inheritance: -:mod:`profile` Module ---------------------- +galaxy.web.framework.middleware.profile module +---------------------------------------------- .. automodule:: galaxy.web.framework.middleware.profile :members: :undoc-members: :show-inheritance: -:mod:`remoteuser` Module ------------------------- +galaxy.web.framework.middleware.remoteuser module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: -:mod:`request_id` Module ------------------------- +galaxy.web.framework.middleware.request_id module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.request_id :members: :undoc-members: :show-inheritance: -:mod:`sentry` Module --------------------- +galaxy.web.framework.middleware.sentry module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sentry :members: :undoc-members: :show-inheritance: -:mod:`static` Module --------------------- +galaxy.web.framework.middleware.static module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.static :members: :undoc-members: :show-inheritance: -:mod:`translogger` Module -------------------------- +galaxy.web.framework.middleware.translogger module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.translogger :members: :undoc-members: :show-inheritance: -:mod:`xforwardedhost` Module ----------------------------- +galaxy.web.framework.middleware.xforwardedhost module +----------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.xforwardedhost :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index 7e02bd99e5b..f6357d01eb2 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -1,54 +1,11 @@ -framework Package -================= - -:mod:`framework` Package ------------------------- +galaxy.web.framework package +============================ .. automodule:: galaxy.web.framework :members: :undoc-members: :show-inheritance: -:mod:`base` Module ------------------- - -.. automodule:: galaxy.web.framework.base - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: galaxy.web.framework.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`formbuilder` Module -------------------------- - -.. automodule:: galaxy.web.framework.formbuilder - :members: - :undoc-members: - :show-inheritance: - -:mod:`openid_manager` Module ----------------------------- - -.. automodule:: galaxy.web.framework.openid_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`webapp` Module --------------------- - -.. automodule:: galaxy.web.framework.webapp - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -57,3 +14,47 @@ Subpackages galaxy.web.framework.helpers galaxy.web.framework.middleware +Submodules +---------- + +galaxy.web.framework.base module +-------------------------------- + +.. automodule:: galaxy.web.framework.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.decorators module +-------------------------------------- + +.. automodule:: galaxy.web.framework.decorators + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.formbuilder module +--------------------------------------- + +.. automodule:: galaxy.web.framework.formbuilder + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.openid_manager module +------------------------------------------ + +.. automodule:: galaxy.web.framework.openid_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.framework.webapp module +---------------------------------- + +.. automodule:: galaxy.web.framework.webapp + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst index a9f49e364e8..53c7c4bbca7 100644 --- a/doc/source/lib/galaxy.web.proxy.rst +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -1,19 +1,20 @@ -proxy Package -============= - -:mod:`proxy` Package --------------------- +galaxy.web.proxy package +======================== .. automodule:: galaxy.web.proxy :members: :undoc-members: :show-inheritance: -:mod:`filelock` Module ----------------------- +Submodules +---------- + +galaxy.web.proxy.filelock module +-------------------------------- .. automodule:: galaxy.web.proxy.filelock :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index 5d721616340..762db65e65b 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -1,46 +1,11 @@ -web Package -=========== - -:mod:`web` Package ------------------- +galaxy.web package +================== .. automodule:: galaxy.web :members: :undoc-members: :show-inheritance: -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.web.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`form_builder` Module --------------------------- - -.. automodule:: galaxy.web.form_builder - :members: - :undoc-members: - :show-inheritance: - -:mod:`formatting` Module ------------------------- - -.. automodule:: galaxy.web.formatting - :members: - :undoc-members: - :show-inheritance: - -:mod:`params` Module --------------------- - -.. automodule:: galaxy.web.params - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -51,3 +16,39 @@ Subpackages galaxy.web.proxy galaxy.web.security +Submodules +---------- + +galaxy.web.buildapp module +-------------------------- + +.. automodule:: galaxy.web.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.form_builder module +------------------------------ + +.. automodule:: galaxy.web.form_builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.formatting module +---------------------------- + +.. automodule:: galaxy.web.formatting + :members: + :undoc-members: + :show-inheritance: + +galaxy.web.params module +------------------------ + +.. automodule:: galaxy.web.params + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.security.rst b/doc/source/lib/galaxy.web.security.rst index 2904ea1e5cb..276b543abb7 100644 --- a/doc/source/lib/galaxy.web.security.rst +++ b/doc/source/lib/galaxy.web.security.rst @@ -1,8 +1,5 @@ -security Package -================ - -:mod:`security` Package ------------------------ +galaxy.web.security package +=========================== .. automodule:: galaxy.web.security :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 5ff9d716e45..657035ef368 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -1,315 +1,324 @@ galaxy.webapps.galaxy.api package ================================= -:mod:`annotations` Module -------------------------- +.. automodule:: galaxy.webapps.galaxy.api + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.galaxy.api.annotations module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations :members: :undoc-members: :show-inheritance: -:mod:`authenticate` Module --------------------------- +galaxy.webapps.galaxy.api.authenticate module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate :members: :undoc-members: :show-inheritance: -:mod:`configuration` Module ---------------------------- +galaxy.webapps.galaxy.api.configuration module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration :members: :undoc-members: :show-inheritance: -:mod:`dataset_collections` Module ---------------------------------- +galaxy.webapps.galaxy.api.dataset_collections module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections :members: :undoc-members: :show-inheritance: -:mod:`datasets` Module ----------------------- +galaxy.webapps.galaxy.api.datasets module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets :members: :undoc-members: :show-inheritance: -:mod:`datatypes` Module ------------------------ +galaxy.webapps.galaxy.api.datatypes module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.datatypes :members: :undoc-members: :show-inheritance: -:mod:`extended_metadata` Module -------------------------------- +galaxy.webapps.galaxy.api.extended_metadata module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata :members: :undoc-members: :show-inheritance: -:mod:`folder_contents` Module ------------------------------ +galaxy.webapps.galaxy.api.folder_contents module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.folder_contents :members: :undoc-members: :show-inheritance: -:mod:`folders` Module ---------------------- +galaxy.webapps.galaxy.api.folders module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folders :members: :undoc-members: :show-inheritance: -:mod:`forms` Module -------------------- +galaxy.webapps.galaxy.api.forms module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.forms :members: :undoc-members: :show-inheritance: -:mod:`genomes` Module ---------------------- +galaxy.webapps.galaxy.api.genomes module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes :members: :undoc-members: :show-inheritance: -:mod:`group_roles` Module -------------------------- +galaxy.webapps.galaxy.api.group_roles module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles :members: :undoc-members: :show-inheritance: -:mod:`group_users` Module -------------------------- +galaxy.webapps.galaxy.api.group_users module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.galaxy.api.groups module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.groups :members: :undoc-members: :show-inheritance: -:mod:`histories` Module ------------------------ +galaxy.webapps.galaxy.api.histories module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.histories :members: :undoc-members: :show-inheritance: -:mod:`history_contents` Module ------------------------------- +galaxy.webapps.galaxy.api.history_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.history_contents :members: :undoc-members: :show-inheritance: -:mod:`item_tags` Module ------------------------ +galaxy.webapps.galaxy.api.item_tags module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.item_tags :members: :undoc-members: :show-inheritance: -:mod:`job_files` Module ------------------------ +galaxy.webapps.galaxy.api.job_files module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.job_files :members: :undoc-members: :show-inheritance: -:mod:`jobs` Module ------------------- +galaxy.webapps.galaxy.api.jobs module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.jobs :members: :undoc-members: :show-inheritance: -:mod:`lda_datasets` Module --------------------------- +galaxy.webapps.galaxy.api.lda_datasets module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.lda_datasets :members: :undoc-members: :show-inheritance: -:mod:`libraries` Module ------------------------ +galaxy.webapps.galaxy.api.libraries module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.libraries :members: :undoc-members: :show-inheritance: -:mod:`library_contents` Module ------------------------------- +galaxy.webapps.galaxy.api.library_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_contents :members: :undoc-members: :show-inheritance: -:mod:`metrics` Module ---------------------- +galaxy.webapps.galaxy.api.metrics module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics :members: :undoc-members: :show-inheritance: -:mod:`page_revisions` Module ----------------------------- +galaxy.webapps.galaxy.api.page_revisions module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.page_revisions :members: :undoc-members: :show-inheritance: -:mod:`pages` Module -------------------- +galaxy.webapps.galaxy.api.pages module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.pages :members: :undoc-members: :show-inheritance: -:mod:`provenance` Module ------------------------- +galaxy.webapps.galaxy.api.provenance module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.provenance :members: :undoc-members: :show-inheritance: -:mod:`quotas` Module --------------------- +galaxy.webapps.galaxy.api.quotas module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas :members: :undoc-members: :show-inheritance: -:mod:`remote_files` Module --------------------------- +galaxy.webapps.galaxy.api.remote_files module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files :members: :undoc-members: :show-inheritance: -:mod:`request_types` Module ---------------------------- +galaxy.webapps.galaxy.api.request_types module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.request_types :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +galaxy.webapps.galaxy.api.requests module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.requests :members: :undoc-members: :show-inheritance: -:mod:`roles` Module -------------------- +galaxy.webapps.galaxy.api.roles module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.roles :members: :undoc-members: :show-inheritance: -:mod:`samples` Module ---------------------- +galaxy.webapps.galaxy.api.samples module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.samples :members: :undoc-members: :show-inheritance: -:mod:`search` Module --------------------- +galaxy.webapps.galaxy.api.search module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.search :members: :undoc-members: :show-inheritance: -:mod:`tool_data` Module ------------------------ +galaxy.webapps.galaxy.api.tool_data module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.tool_data :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`tools` Module -------------------- +galaxy.webapps.galaxy.api.tools module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tools :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.galaxy.api.users module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.users :members: :undoc-members: :show-inheritance: -:mod:`visualizations` Module ----------------------------- +galaxy.webapps.galaxy.api.visualizations module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.webapps.galaxy.api.workflows module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index 3b870bf2092..5a59cc4af81 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -1,251 +1,252 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.galaxy.controllers package +========================================= .. automodule:: galaxy.webapps.galaxy.controllers :members: :undoc-members: :show-inheritance: -:mod:`admin` Module -------------------- +Submodules +---------- + +galaxy.webapps.galaxy.controllers.admin module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin :members: :undoc-members: :show-inheritance: -:mod:`admin_toolshed` Module ----------------------------- +galaxy.webapps.galaxy.controllers.admin_toolshed module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed :members: :undoc-members: :show-inheritance: -:mod:`async` Module -------------------- +galaxy.webapps.galaxy.controllers.async module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.async :members: :undoc-members: :show-inheritance: -:mod:`biostar` Module ---------------------- +galaxy.webapps.galaxy.controllers.biostar module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.biostar :members: :undoc-members: :show-inheritance: -:mod:`cloudlaunch` Module -------------------------- +galaxy.webapps.galaxy.controllers.cloudlaunch module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch :members: :undoc-members: :show-inheritance: -:mod:`data_manager` Module --------------------------- +galaxy.webapps.galaxy.controllers.data_manager module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.data_manager :members: :undoc-members: :show-inheritance: -:mod:`dataset` Module ---------------------- +galaxy.webapps.galaxy.controllers.dataset module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.dataset :members: :undoc-members: :show-inheritance: -:mod:`error` Module -------------------- +galaxy.webapps.galaxy.controllers.error module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.error :members: :undoc-members: :show-inheritance: -:mod:`external_service` Module ------------------------------- +galaxy.webapps.galaxy.controllers.external_service module +--------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.external_service :members: :undoc-members: :show-inheritance: -:mod:`external_services` Module -------------------------------- +galaxy.webapps.galaxy.controllers.external_services module +---------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.external_services :members: :undoc-members: :show-inheritance: -:mod:`forms` Module -------------------- +galaxy.webapps.galaxy.controllers.forms module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.forms :members: :undoc-members: :show-inheritance: -:mod:`history` Module ---------------------- +galaxy.webapps.galaxy.controllers.history module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.history :members: :undoc-members: :show-inheritance: -:mod:`library` Module ---------------------- +galaxy.webapps.galaxy.controllers.library module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library :members: :undoc-members: :show-inheritance: -:mod:`library_admin` Module ---------------------------- +galaxy.webapps.galaxy.controllers.library_admin module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library_admin :members: :undoc-members: :show-inheritance: -:mod:`library_common` Module ----------------------------- +galaxy.webapps.galaxy.controllers.library_common module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.library_common :members: :undoc-members: :show-inheritance: -:mod:`mobile` Module --------------------- +galaxy.webapps.galaxy.controllers.mobile module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.mobile :members: :undoc-members: :show-inheritance: -:mod:`page` Module ------------------- +galaxy.webapps.galaxy.controllers.page module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.page :members: :undoc-members: :show-inheritance: -:mod:`request_type` Module --------------------------- +galaxy.webapps.galaxy.controllers.request_type module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.request_type :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +galaxy.webapps.galaxy.controllers.requests module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests :members: :undoc-members: :show-inheritance: -:mod:`requests_admin` Module ----------------------------- +galaxy.webapps.galaxy.controllers.requests_admin module +------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests_admin :members: :undoc-members: :show-inheritance: -:mod:`requests_common` Module ------------------------------ +galaxy.webapps.galaxy.controllers.requests_common module +-------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.requests_common :members: :undoc-members: :show-inheritance: -:mod:`root` Module ------------------- +galaxy.webapps.galaxy.controllers.root module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.root :members: :undoc-members: :show-inheritance: -:mod:`search` Module --------------------- +galaxy.webapps.galaxy.controllers.search module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.search :members: :undoc-members: :show-inheritance: -:mod:`tag` Module ------------------ +galaxy.webapps.galaxy.controllers.tag module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tag :members: :undoc-members: :show-inheritance: -:mod:`tool_runner` Module -------------------------- +galaxy.webapps.galaxy.controllers.tool_runner module +---------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tool_runner :members: :undoc-members: :show-inheritance: -:mod:`ucsc_proxy` Module ------------------------- +galaxy.webapps.galaxy.controllers.ucsc_proxy module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy :members: :undoc-members: :show-inheritance: -:mod:`user` Module ------------------- +galaxy.webapps.galaxy.controllers.user module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.user :members: :undoc-members: :show-inheritance: -:mod:`userskeys` Module ------------------------ +galaxy.webapps.galaxy.controllers.userskeys module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.userskeys :members: :undoc-members: :show-inheritance: -:mod:`visualization` Module ---------------------------- +galaxy.webapps.galaxy.controllers.visualization module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.visualization :members: :undoc-members: :show-inheritance: -:mod:`workflow` Module ----------------------- +galaxy.webapps.galaxy.controllers.workflow module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.workflow :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index 42642bec26c..5256155b1ed 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -1,10 +1,7 @@ -galaxy Package -============== +galaxy.webapps.galaxy package +============================= -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.galaxy.buildapp +.. automodule:: galaxy.webapps.galaxy :members: :undoc-members: :show-inheritance: @@ -17,3 +14,15 @@ Subpackages galaxy.webapps.galaxy.api galaxy.webapps.galaxy.controllers +Submodules +---------- + +galaxy.webapps.galaxy.buildapp module +------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.buildapp + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index 72e2b6da340..122b8e286ba 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -1,67 +1,68 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.reports.controllers package +========================================== .. automodule:: galaxy.webapps.reports.controllers :members: :undoc-members: :show-inheritance: -:mod:`jobs` Module ------------------- +Submodules +---------- + +galaxy.webapps.reports.controllers.jobs module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.jobs :members: :undoc-members: :show-inheritance: -:mod:`query` Module -------------------- +galaxy.webapps.reports.controllers.query module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.query :members: :undoc-members: :show-inheritance: -:mod:`root` Module ------------------- +galaxy.webapps.reports.controllers.root module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.root :members: :undoc-members: :show-inheritance: -:mod:`sample_tracking` Module ------------------------------ +galaxy.webapps.reports.controllers.sample_tracking module +--------------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.sample_tracking :members: :undoc-members: :show-inheritance: -:mod:`system` Module --------------------- +galaxy.webapps.reports.controllers.system module +------------------------------------------------ .. automodule:: galaxy.webapps.reports.controllers.system :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.reports.controllers.users module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.users :members: :undoc-members: :show-inheritance: -:mod:`workflows` Module ------------------------ +galaxy.webapps.reports.controllers.workflows module +--------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.workflows :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index 59231f71951..8e9fff62be8 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -1,38 +1,11 @@ -reports Package -=============== - -:mod:`reports` Package ----------------------- +galaxy.webapps.reports package +============================== .. automodule:: galaxy.webapps.reports :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.reports.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.reports.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.reports.config - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -40,3 +13,31 @@ Subpackages galaxy.webapps.reports.controllers +Submodules +---------- + +galaxy.webapps.reports.app module +--------------------------------- + +.. automodule:: galaxy.webapps.reports.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.reports.buildapp module +-------------------------------------- + +.. automodule:: galaxy.webapps.reports.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.reports.config module +------------------------------------ + +.. automodule:: galaxy.webapps.reports.config + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 7b0597ba68c..2e301191c77 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -1,8 +1,5 @@ -webapps Package -=============== - -:mod:`webapps` Package ----------------------- +galaxy.webapps package +====================== .. automodule:: galaxy.webapps :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index 98dae6f2fd8..ae4c3b45f24 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -1,59 +1,68 @@ -api Package -=========== +galaxy.webapps.tool_shed.api package +==================================== -:mod:`authenticate` Module --------------------------- +.. automodule:: galaxy.webapps.tool_shed.api + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.api.authenticate module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.authenticate :members: :undoc-members: :show-inheritance: -:mod:`categories` Module ------------------------- +galaxy.webapps.tool_shed.api.categories module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.categories :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.tool_shed.api.groups module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.groups :members: :undoc-members: :show-inheritance: -:mod:`repositories` Module --------------------------- +galaxy.webapps.tool_shed.api.repositories module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.repositories :members: :undoc-members: :show-inheritance: -:mod:`repository_revisions` Module ----------------------------------- +galaxy.webapps.tool_shed.api.repository_revisions module +-------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repository_revisions :members: :undoc-members: :show-inheritance: -:mod:`tools` Module -------------------- +galaxy.webapps.tool_shed.api.tools module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.tools :members: :undoc-members: :show-inheritance: -:mod:`users` Module -------------------- +galaxy.webapps.tool_shed.api.users module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.users :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst index 986d7fe3f57..6e9e7914c46 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -1,67 +1,68 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- +galaxy.webapps.tool_shed.controllers package +============================================ .. automodule:: galaxy.webapps.tool_shed.controllers :members: :undoc-members: :show-inheritance: -:mod:`admin` Module -------------------- +Submodules +---------- + +galaxy.webapps.tool_shed.controllers.admin module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.admin :members: :undoc-members: :show-inheritance: -:mod:`groups` Module --------------------- +galaxy.webapps.tool_shed.controllers.groups module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.groups :members: :undoc-members: :show-inheritance: -:mod:`hg` Module ----------------- +galaxy.webapps.tool_shed.controllers.hg module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.hg :members: :undoc-members: :show-inheritance: -:mod:`repository` Module ------------------------- +galaxy.webapps.tool_shed.controllers.repository module +------------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.controllers.repository :members: :undoc-members: :show-inheritance: -:mod:`repository_review` Module -------------------------------- +galaxy.webapps.tool_shed.controllers.repository_review module +------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository_review :members: :undoc-members: :show-inheritance: -:mod:`upload` Module --------------------- +galaxy.webapps.tool_shed.controllers.upload module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.upload :members: :undoc-members: :show-inheritance: -:mod:`user` Module ------------------- +galaxy.webapps.tool_shed.controllers.user module +------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.controllers.user :members: :undoc-members: :show-inheritance: + 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 4de7ea427c2..361baef5268 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -1,27 +1,28 @@ -middleware Package -================== - -:mod:`middleware` Package -------------------------- +galaxy.webapps.tool_shed.framework.middleware package +===================================================== .. automodule:: galaxy.webapps.tool_shed.framework.middleware :members: :undoc-members: :show-inheritance: -:mod:`hg` Module ----------------- +Submodules +---------- + +galaxy.webapps.tool_shed.framework.middleware.hg module +------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.hg :members: :undoc-members: :show-inheritance: -:mod:`remoteuser` Module ------------------------- +galaxy.webapps.tool_shed.framework.middleware.remoteuser module +--------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst index d0f4b8abdf8..0276dcbd1c4 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -1,8 +1,5 @@ -framework Package -================= - -:mod:`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 2d4197c30a3..9fd4bd531e8 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -1,11 +1,20 @@ -migrate Package -=============== +galaxy.webapps.tool_shed.model.migrate package +============================================== -:mod:`check` Module -------------------- +.. automodule:: galaxy.webapps.tool_shed.model.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.model.migrate.check module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.migrate.check :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.rst index 429f0d57917..bc60bd734c3 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -1,22 +1,11 @@ -model Package -============= - -:mod:`model` Package --------------------- +galaxy.webapps.tool_shed.model package +====================================== .. automodule:: galaxy.webapps.tool_shed.model :members: :undoc-members: :show-inheritance: -:mod:`mapping` Module ---------------------- - -.. automodule:: galaxy.webapps.tool_shed.model.mapping - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -24,3 +13,15 @@ Subpackages galaxy.webapps.tool_shed.model.migrate +Submodules +---------- + +galaxy.webapps.tool_shed.model.mapping module +--------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.mapping + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst index e358e871712..836aa571014 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -1,38 +1,11 @@ -tool_shed Package -================= - -:mod:`tool_shed` Package ------------------------- +galaxy.webapps.tool_shed package +================================ .. automodule:: galaxy.webapps.tool_shed :members: :undoc-members: :show-inheritance: -:mod:`app` Module ------------------ - -.. automodule:: galaxy.webapps.tool_shed.app - :members: - :undoc-members: - :show-inheritance: - -:mod:`buildapp` Module ----------------------- - -.. automodule:: galaxy.webapps.tool_shed.buildapp - :members: - :undoc-members: - :show-inheritance: - -:mod:`config` Module --------------------- - -.. automodule:: galaxy.webapps.tool_shed.config - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -46,3 +19,31 @@ Subpackages galaxy.webapps.tool_shed.security galaxy.webapps.tool_shed.util +Submodules +---------- + +galaxy.webapps.tool_shed.app module +----------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.app + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool_shed.buildapp module +---------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.buildapp + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool_shed.config module +-------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.config + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst index 78ccaa6cffb..9daeff111f0 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.search.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst @@ -1,19 +1,28 @@ -search Package -============== +galaxy.webapps.tool_shed.search package +======================================= -:mod:`repo_search` Module -------------------------- +.. automodule:: galaxy.webapps.tool_shed.search + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.search.repo_search module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.repo_search :members: :undoc-members: :show-inheritance: -:mod:`tool_search` Module -------------------------- +galaxy.webapps.tool_shed.search.tool_search module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.tool_search :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.security.rst b/doc/source/lib/galaxy.webapps.tool_shed.security.rst index ac3f17fb38d..4e39d99210a 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.security.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -1,8 +1,5 @@ -security Package -================ - -:mod:`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 8eff5d41834..6ee1d6c7a9f 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -1,27 +1,36 @@ -util Package -============ +galaxy.webapps.tool_shed.util package +===================================== -:mod:`hgweb_config` Module --------------------------- +.. automodule:: galaxy.webapps.tool_shed.util + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool_shed.util.hgweb_config module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.hgweb_config :members: :undoc-members: :show-inheritance: -:mod:`ratings_util` Module --------------------------- +galaxy.webapps.tool_shed.util.ratings_util module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.ratings_util :members: :undoc-members: :show-inheritance: -:mod:`shed_statistics` Module ------------------------------ +galaxy.webapps.tool_shed.util.shed_statistics module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.shed_statistics :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst index 00f74832bc8..415a5b881c8 100644 --- a/doc/source/lib/galaxy.work.rst +++ b/doc/source/lib/galaxy.work.rst @@ -1,11 +1,20 @@ -work Package -============ +galaxy.work package +=================== -:mod:`context` Module ---------------------- +.. automodule:: galaxy.work + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.work.context module +-------------------------- .. automodule:: galaxy.work.context :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 7f41691fc77..8d0a2c4dfb6 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -1,58 +1,7 @@ -workflow Package -================ +galaxy.workflow package +======================= -:mod:`extract` Module ---------------------- - -.. automodule:: galaxy.workflow.extract - :members: - :undoc-members: - :show-inheritance: - -:mod:`modules` Module ---------------------- - -.. automodule:: galaxy.workflow.modules - :members: - :undoc-members: - :show-inheritance: - -:mod:`render` Module --------------------- - -.. automodule:: galaxy.workflow.render - :members: - :undoc-members: - :show-inheritance: - -:mod:`run` Module ------------------ - -.. automodule:: galaxy.workflow.run - :members: - :undoc-members: - :show-inheritance: - -:mod:`run_request` Module -------------------------- - -.. automodule:: galaxy.workflow.run_request - :members: - :undoc-members: - :show-inheritance: - -:mod:`scheduling_manager` Module --------------------------------- - -.. automodule:: galaxy.workflow.scheduling_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`steps` Module -------------------- - -.. automodule:: galaxy.workflow.steps +.. automodule:: galaxy.workflow :members: :undoc-members: :show-inheritance: @@ -64,3 +13,63 @@ Subpackages galaxy.workflow.schedulers +Submodules +---------- + +galaxy.workflow.extract module +------------------------------ + +.. automodule:: galaxy.workflow.extract + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.modules module +------------------------------ + +.. automodule:: galaxy.workflow.modules + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.render module +----------------------------- + +.. automodule:: galaxy.workflow.render + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.run module +-------------------------- + +.. automodule:: galaxy.workflow.run + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.run_request module +---------------------------------- + +.. automodule:: galaxy.workflow.run_request + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.scheduling_manager module +----------------------------------------- + +.. automodule:: galaxy.workflow.scheduling_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.workflow.steps module +---------------------------- + +.. automodule:: galaxy.workflow.steps + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst index 792b5f500ea..43801194aa8 100644 --- a/doc/source/lib/galaxy.workflow.schedulers.rst +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -1,19 +1,20 @@ -schedulers Package -================== - -:mod:`schedulers` Package -------------------------- +galaxy.workflow.schedulers package +================================== .. automodule:: galaxy.workflow.schedulers :members: :undoc-members: :show-inheritance: -:mod:`core` Module ------------------- +Submodules +---------- + +galaxy.workflow.schedulers.core module +-------------------------------------- .. automodule:: galaxy.workflow.schedulers.core :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst index c475fafca7c..489f529521f 100644 --- a/doc/source/lib/galaxy_ext.metadata.rst +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -1,19 +1,20 @@ -metadata Package -================ - -:mod:`metadata` Package ------------------------ +galaxy_ext.metadata package +=========================== .. automodule:: galaxy_ext.metadata :members: :undoc-members: :show-inheritance: -:mod:`set_metadata` Module --------------------------- +Submodules +---------- + +galaxy_ext.metadata.set_metadata module +--------------------------------------- .. automodule:: galaxy_ext.metadata.set_metadata :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index 1c13d00470b..040ba0b19c6 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -1,9 +1,6 @@ -galaxy_ext Package +galaxy_ext package ================== -:mod:`galaxy_ext` Package -------------------------- - .. automodule:: galaxy_ext :members: :undoc-members: diff --git a/doc/source/lib/galaxy_utils.rst b/doc/source/lib/galaxy_utils.rst index 3ed28649f1b..c17a7199d73 100644 --- a/doc/source/lib/galaxy_utils.rst +++ b/doc/source/lib/galaxy_utils.rst @@ -1,6 +1,11 @@ -galaxy_utils Package +galaxy_utils package ==================== +.. automodule:: galaxy_utils + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/galaxy_utils.sequence.rst b/doc/source/lib/galaxy_utils.sequence.rst index b1900d7421f..f047ab6e219 100644 --- a/doc/source/lib/galaxy_utils.sequence.rst +++ b/doc/source/lib/galaxy_utils.sequence.rst @@ -1,43 +1,52 @@ -sequence Package -================ +galaxy_utils.sequence package +============================= -:mod:`fasta` Module -------------------- +.. automodule:: galaxy_utils.sequence + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy_utils.sequence.fasta module +---------------------------------- .. automodule:: galaxy_utils.sequence.fasta :members: :undoc-members: :show-inheritance: -:mod:`fastq` Module -------------------- +galaxy_utils.sequence.fastq module +---------------------------------- .. automodule:: galaxy_utils.sequence.fastq :members: :undoc-members: :show-inheritance: -:mod:`sequence` Module ----------------------- +galaxy_utils.sequence.sequence module +------------------------------------- .. automodule:: galaxy_utils.sequence.sequence :members: :undoc-members: :show-inheritance: -:mod:`transform` Module ------------------------ +galaxy_utils.sequence.transform module +-------------------------------------- .. automodule:: galaxy_utils.sequence.transform :members: :undoc-members: :show-inheritance: -:mod:`vcf` Module ------------------ +galaxy_utils.sequence.vcf module +-------------------------------- .. automodule:: galaxy_utils.sequence.vcf :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/log_tempfile.rst b/doc/source/lib/log_tempfile.rst index a5ca8f23b82..51b904985f8 100644 --- a/doc/source/lib/log_tempfile.rst +++ b/doc/source/lib/log_tempfile.rst @@ -1,4 +1,4 @@ -log_tempfile Module +log_tempfile module =================== .. automodule:: log_tempfile diff --git a/doc/source/lib/mimeparse.rst b/doc/source/lib/mimeparse.rst index 0490cfdc8b3..afcdfa0c86b 100644 --- a/doc/source/lib/mimeparse.rst +++ b/doc/source/lib/mimeparse.rst @@ -1,4 +1,4 @@ -mimeparse Module +mimeparse module ================ .. automodule:: mimeparse diff --git a/doc/source/lib/pkg_resources.rst b/doc/source/lib/pkg_resources.rst index ef99aca6efc..e3082f69603 100644 --- a/doc/source/lib/pkg_resources.rst +++ b/doc/source/lib/pkg_resources.rst @@ -1,4 +1,4 @@ -pkg_resources Module +pkg_resources module ==================== .. automodule:: pkg_resources diff --git a/doc/source/lib/psyco_full.rst b/doc/source/lib/psyco_full.rst index 9e75f1b0955..370be05776f 100644 --- a/doc/source/lib/psyco_full.rst +++ b/doc/source/lib/psyco_full.rst @@ -1,4 +1,4 @@ -psyco_full Module +psyco_full module ================= .. automodule:: psyco_full diff --git a/doc/source/lib/pulsar.client.rst b/doc/source/lib/pulsar.client.rst index 6458d71332f..3a29f55ffae 100644 --- a/doc/source/lib/pulsar.client.rst +++ b/doc/source/lib/pulsar.client.rst @@ -1,126 +1,11 @@ -client Package -============== - -:mod:`client` Package ---------------------- +pulsar.client package +===================== .. automodule:: pulsar.client :members: :undoc-members: :show-inheritance: -:mod:`action_mapper` Module ---------------------------- - -.. automodule:: pulsar.client.action_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange` Module ---------------------------- - -.. automodule:: pulsar.client.amqp_exchange - :members: - :undoc-members: - :show-inheritance: - -:mod:`amqp_exchange_factory` Module ------------------------------------ - -.. automodule:: pulsar.client.amqp_exchange_factory - :members: - :undoc-members: - :show-inheritance: - -:mod:`client` Module --------------------- - -.. automodule:: pulsar.client.client - :members: - :undoc-members: - :show-inheritance: - -:mod:`config_util` Module -------------------------- - -.. automodule:: pulsar.client.config_util - :members: - :undoc-members: - :show-inheritance: - -:mod:`decorators` Module ------------------------- - -.. automodule:: pulsar.client.decorators - :members: - :undoc-members: - :show-inheritance: - -:mod:`destination` Module -------------------------- - -.. automodule:: pulsar.client.destination - :members: - :undoc-members: - :show-inheritance: - -:mod:`interface` Module ------------------------ - -.. automodule:: pulsar.client.interface - :members: - :undoc-members: - :show-inheritance: - -:mod:`job_directory` Module ---------------------------- - -.. automodule:: pulsar.client.job_directory - :members: - :undoc-members: - :show-inheritance: - -:mod:`manager` Module ---------------------- - -.. automodule:: pulsar.client.manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`object_client` Module ---------------------------- - -.. automodule:: pulsar.client.object_client - :members: - :undoc-members: - :show-inheritance: - -:mod:`path_mapper` Module -------------------------- - -.. automodule:: pulsar.client.path_mapper - :members: - :undoc-members: - :show-inheritance: - -:mod:`setup_handler` Module ---------------------------- - -.. automodule:: pulsar.client.setup_handler - :members: - :undoc-members: - :show-inheritance: - -:mod:`util` Module ------------------- - -.. automodule:: pulsar.client.util - :members: - :undoc-members: - :show-inheritance: - Subpackages ----------- @@ -129,3 +14,119 @@ Subpackages pulsar.client.staging pulsar.client.transport +Submodules +---------- + +pulsar.client.action_mapper module +---------------------------------- + +.. automodule:: pulsar.client.action_mapper + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.amqp_exchange module +---------------------------------- + +.. automodule:: pulsar.client.amqp_exchange + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.amqp_exchange_factory module +------------------------------------------ + +.. automodule:: pulsar.client.amqp_exchange_factory + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.client module +--------------------------- + +.. automodule:: pulsar.client.client + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.config_util module +-------------------------------- + +.. automodule:: pulsar.client.config_util + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.decorators module +------------------------------- + +.. automodule:: pulsar.client.decorators + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.destination module +-------------------------------- + +.. automodule:: pulsar.client.destination + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.interface module +------------------------------ + +.. automodule:: pulsar.client.interface + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.job_directory module +---------------------------------- + +.. automodule:: pulsar.client.job_directory + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.manager module +---------------------------- + +.. automodule:: pulsar.client.manager + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.object_client module +---------------------------------- + +.. automodule:: pulsar.client.object_client + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.path_mapper module +-------------------------------- + +.. automodule:: pulsar.client.path_mapper + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.setup_handler module +---------------------------------- + +.. automodule:: pulsar.client.setup_handler + :members: + :undoc-members: + :show-inheritance: + +pulsar.client.util module +------------------------- + +.. automodule:: pulsar.client.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/pulsar.client.staging.rst b/doc/source/lib/pulsar.client.staging.rst index 6731bc362b3..4d33f6676b8 100644 --- a/doc/source/lib/pulsar.client.staging.rst +++ b/doc/source/lib/pulsar.client.staging.rst @@ -1,27 +1,28 @@ -staging Package -=============== - -:mod:`staging` Package ----------------------- +pulsar.client.staging package +============================= .. automodule:: pulsar.client.staging :members: :undoc-members: :show-inheritance: -:mod:`down` Module ------------------- +Submodules +---------- + +pulsar.client.staging.down module +--------------------------------- .. automodule:: pulsar.client.staging.down :members: :undoc-members: :show-inheritance: -:mod:`up` Module ----------------- +pulsar.client.staging.up module +------------------------------- .. automodule:: pulsar.client.staging.up :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/pulsar.client.transport.rst b/doc/source/lib/pulsar.client.transport.rst index afeb8f24a3b..8b68dbb15a5 100644 --- a/doc/source/lib/pulsar.client.transport.rst +++ b/doc/source/lib/pulsar.client.transport.rst @@ -1,51 +1,52 @@ -transport Package -================= - -:mod:`transport` Package ------------------------- +pulsar.client.transport package +=============================== .. automodule:: pulsar.client.transport :members: :undoc-members: :show-inheritance: -:mod:`curl` Module ------------------- +Submodules +---------- + +pulsar.client.transport.curl module +----------------------------------- .. automodule:: pulsar.client.transport.curl :members: :undoc-members: :show-inheritance: -:mod:`poster` Module --------------------- +pulsar.client.transport.poster module +------------------------------------- .. automodule:: pulsar.client.transport.poster :members: :undoc-members: :show-inheritance: -:mod:`requests` Module ----------------------- +pulsar.client.transport.requests module +--------------------------------------- .. automodule:: pulsar.client.transport.requests :members: :undoc-members: :show-inheritance: -:mod:`ssh` Module ------------------ +pulsar.client.transport.ssh module +---------------------------------- .. automodule:: pulsar.client.transport.ssh :members: :undoc-members: :show-inheritance: -:mod:`standard` Module ----------------------- +pulsar.client.transport.standard module +--------------------------------------- .. automodule:: pulsar.client.transport.standard :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/pulsar.rst b/doc/source/lib/pulsar.rst index 754078e9094..c22c0a95bdb 100644 --- a/doc/source/lib/pulsar.rst +++ b/doc/source/lib/pulsar.rst @@ -1,6 +1,11 @@ -pulsar Package +pulsar package ============== +.. automodule:: pulsar + :members: + :undoc-members: + :show-inheritance: + Subpackages ----------- diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst index 9496653d044..3865f875806 100644 --- a/doc/source/lib/tool_shed.capsule.rst +++ b/doc/source/lib/tool_shed.capsule.rst @@ -1,11 +1,20 @@ -capsule Package -=============== +tool_shed.capsule package +========================= -:mod:`capsule_manager` Module ------------------------------ +.. automodule:: tool_shed.capsule + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.capsule.capsule_manager module +---------------------------------------- .. automodule:: tool_shed.capsule.capsule_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst index 5382a5ba40a..bd6356b7531 100644 --- a/doc/source/lib/tool_shed.dependencies.repository.rst +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -1,11 +1,20 @@ -repository Package -================== +tool_shed.dependencies.repository package +========================================= -:mod:`relation_builder` Module ------------------------------- +.. automodule:: tool_shed.dependencies.repository + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.dependencies.repository.relation_builder module +--------------------------------------------------------- .. automodule:: tool_shed.dependencies.repository.relation_builder :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst index e7b62a50159..563583e596f 100644 --- a/doc/source/lib/tool_shed.dependencies.rst +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -1,10 +1,7 @@ -dependencies Package -==================== +tool_shed.dependencies package +============================== -:mod:`attribute_handlers` Module --------------------------------- - -.. automodule:: tool_shed.dependencies.attribute_handlers +.. automodule:: tool_shed.dependencies :members: :undoc-members: :show-inheritance: @@ -17,3 +14,15 @@ Subpackages tool_shed.dependencies.repository tool_shed.dependencies.tool +Submodules +---------- + +tool_shed.dependencies.attribute_handlers module +------------------------------------------------ + +.. automodule:: tool_shed.dependencies.attribute_handlers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst index 9ba9c8b2472..3062aa20041 100644 --- a/doc/source/lib/tool_shed.dependencies.tool.rst +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -1,11 +1,20 @@ -tool Package -============ +tool_shed.dependencies.tool package +=================================== -:mod:`tag_attribute_handler` Module ------------------------------------ +.. automodule:: tool_shed.dependencies.tool + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.dependencies.tool.tag_attribute_handler module +-------------------------------------------------------- .. automodule:: tool_shed.dependencies.tool.tag_attribute_handler :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst index e5021e079c6..bab6f246f76 100644 --- a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst +++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst @@ -1,11 +1,20 @@ -datatypes Package -================= +tool_shed.galaxy_install.datatypes package +========================================== -:mod:`custom_datatype_manager` Module -------------------------------------- +.. automodule:: tool_shed.galaxy_install.datatypes + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.datatypes.custom_datatype_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst index c75c5c716ea..b01741c0d70 100644 --- a/doc/source/lib/tool_shed.galaxy_install.grids.rst +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -1,11 +1,20 @@ -grids Package -============= +tool_shed.galaxy_install.grids package +====================================== -:mod:`admin_toolshed_grids` Module ----------------------------------- +.. automodule:: tool_shed.galaxy_install.grids + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.grids.admin_toolshed_grids module +---------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst index a710cc6ad1b..8a63d06e5d0 100644 --- a/doc/source/lib/tool_shed.galaxy_install.metadata.rst +++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst @@ -1,11 +1,20 @@ -metadata Package -================ +tool_shed.galaxy_install.metadata package +========================================= -:mod:`installed_repository_metadata_manager` Module ---------------------------------------------------- +.. automodule:: tool_shed.galaxy_install.metadata + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.metadata.installed_repository_metadata_manager module +------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.rst index 5d553b446d1..4e3291da76b 100644 --- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -1,19 +1,28 @@ -migrate Package -=============== +tool_shed.galaxy_install.migrate package +======================================== -:mod:`check` Module -------------------- +.. automodule:: tool_shed.galaxy_install.migrate + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.migrate.check module +--------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.check :members: :undoc-members: :show-inheritance: -:mod:`common` Module --------------------- +tool_shed.galaxy_install.migrate.common module +---------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.common :members: :undoc-members: :show-inheritance: + 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 ac2c06dad4d..5110d9fb105 100644 --- a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst @@ -1,11 +1,20 @@ -repository_dependencies Package -=============================== +tool_shed.galaxy_install.repository_dependencies package +======================================================== -:mod:`repository_dependency_manager` Module -------------------------------------------- +.. automodule:: tool_shed.galaxy_install.repository_dependencies + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager module +------------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index c2da4ac3c55..f4510a24c13 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -1,50 +1,7 @@ -galaxy_install Package -====================== +tool_shed.galaxy_install package +================================ -:mod:`dependency_display` Module --------------------------------- - -.. automodule:: tool_shed.galaxy_install.dependency_display - :members: - :undoc-members: - :show-inheritance: - -:mod:`install_manager` Module ------------------------------ - -.. automodule:: tool_shed.galaxy_install.install_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`installed_repository_manager` Module ------------------------------------------- - -.. automodule:: tool_shed.galaxy_install.installed_repository_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`repair_repository_manager` Module ---------------------------------------- - -.. automodule:: tool_shed.galaxy_install.repair_repository_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_migration_manager` Module ------------------------------------- - -.. automodule:: tool_shed.galaxy_install.tool_migration_manager - :members: - :undoc-members: - :show-inheritance: - -:mod:`update_repository_manager` Module ---------------------------------------- - -.. automodule:: tool_shed.galaxy_install.update_repository_manager +.. automodule:: tool_shed.galaxy_install :members: :undoc-members: :show-inheritance: @@ -63,3 +20,55 @@ Subpackages tool_shed.galaxy_install.tools tool_shed.galaxy_install.utility_containers +Submodules +---------- + +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 +----------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.install_manager + :members: + :undoc-members: + :show-inheritance: + +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 +--------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.repair_repository_manager + :members: + :undoc-members: + :show-inheritance: + +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 +--------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.update_repository_manager + :members: + :undoc-members: + :show-inheritance: + + 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 6a7abd723fb..29d76529234 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 @@ -1,51 +1,60 @@ -recipe Package -============== +tool_shed.galaxy_install.tool_dependencies.recipe package +========================================================= -:mod:`asynchronous_reader` Module ---------------------------------- +.. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`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: -:mod:`tag_handler` Module -------------------------- +tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler module +-------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler :members: :undoc-members: :show-inheritance: + 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 c5b6ee4091f..5f67bad6c1e 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -1,10 +1,7 @@ -tool_dependencies Package -========================= +tool_shed.galaxy_install.tool_dependencies package +================================================== -:mod:`env_manager` Module -------------------------- - -.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager +.. automodule:: tool_shed.galaxy_install.tool_dependencies :members: :undoc-members: :show-inheritance: @@ -16,3 +13,15 @@ Subpackages tool_shed.galaxy_install.tool_dependencies.recipe +Submodules +---------- + +tool_shed.galaxy_install.tool_dependencies.env_manager module +------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst index 922667d523c..1d1d0f37243 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tools.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst @@ -1,19 +1,28 @@ -tools Package -============= +tool_shed.galaxy_install.tools package +====================================== -:mod:`data_manager` Module --------------------------- +.. automodule:: tool_shed.galaxy_install.tools + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.galaxy_install.tools.data_manager module +-------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.data_manager :members: :undoc-members: :show-inheritance: -:mod:`tool_panel_manager` Module --------------------------------- +tool_shed.galaxy_install.tools.tool_panel_manager module +-------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst index 60dd22914fc..347d7317fc2 100644 --- a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -1,8 +1,5 @@ -utility_containers Package -========================== - -:mod:`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 86c0bf2ee70..7ee5fb07ce8 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -1,43 +1,52 @@ -grids Package -============= +tool_shed.grids package +======================= -:mod:`admin_grids` Module -------------------------- +.. automodule:: tool_shed.grids + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.grids.admin_grids module +---------------------------------- .. automodule:: tool_shed.grids.admin_grids :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`repository_grids` Module ------------------------------- +tool_shed.grids.repository_grids module +--------------------------------------- .. automodule:: tool_shed.grids.repository_grids :members: :undoc-members: :show-inheritance: -:mod:`repository_review_grids` Module -------------------------------------- +tool_shed.grids.repository_review_grids module +---------------------------------------------- .. automodule:: tool_shed.grids.repository_review_grids :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +tool_shed.grids.util module +--------------------------- .. automodule:: tool_shed.grids.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst index f400d8d767e..04de3ce0371 100644 --- a/doc/source/lib/tool_shed.managers.rst +++ b/doc/source/lib/tool_shed.managers.rst @@ -1,19 +1,28 @@ -managers Package -================ +tool_shed.managers package +========================== -:mod:`groups` Module --------------------- +.. automodule:: tool_shed.managers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.managers.groups module +-------------------------------- .. automodule:: tool_shed.managers.groups :members: :undoc-members: :show-inheritance: -:mod:`repositories` Module --------------------------- +tool_shed.managers.repositories module +-------------------------------------- .. automodule:: tool_shed.managers.repositories :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst index 735acfd5e9d..7e2ba80941d 100644 --- a/doc/source/lib/tool_shed.metadata.rst +++ b/doc/source/lib/tool_shed.metadata.rst @@ -1,19 +1,28 @@ -metadata Package -================ +tool_shed.metadata package +========================== -:mod:`metadata_generator` Module --------------------------------- +.. automodule:: tool_shed.metadata + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.metadata.metadata_generator module +-------------------------------------------- .. automodule:: tool_shed.metadata.metadata_generator :members: :undoc-members: :show-inheritance: -:mod:`repository_metadata_manager` Module ------------------------------------------ +tool_shed.metadata.repository_metadata_manager module +----------------------------------------------------- .. automodule:: tool_shed.metadata.repository_metadata_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst index b64e85a7a18..5e5cff1b7de 100644 --- a/doc/source/lib/tool_shed.repository_types.rst +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -1,51 +1,60 @@ -repository_types Package -======================== +tool_shed.repository_types package +================================== -:mod:`metadata` Module ----------------------- +.. automodule:: tool_shed.repository_types + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.repository_types.metadata module +------------------------------------------ .. automodule:: tool_shed.repository_types.metadata :members: :undoc-members: :show-inheritance: -:mod:`registry` Module ----------------------- +tool_shed.repository_types.registry module +------------------------------------------ .. automodule:: tool_shed.repository_types.registry :members: :undoc-members: :show-inheritance: -:mod:`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: -:mod:`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: -:mod:`unrestricted` Module --------------------------- +tool_shed.repository_types.unrestricted module +---------------------------------------------- .. automodule:: tool_shed.repository_types.unrestricted :members: :undoc-members: :show-inheritance: -:mod:`util` Module ------------------- +tool_shed.repository_types.util module +-------------------------------------- .. automodule:: tool_shed.repository_types.util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index 4bf54d75b21..9ea2997d843 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -1,18 +1,7 @@ -tool_shed Package +tool_shed package ================= -:mod:`repository_registry` Module ---------------------------------- - -.. automodule:: tool_shed.repository_registry - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_shed_registry` Module --------------------------------- - -.. automodule:: tool_shed.tool_shed_registry +.. automodule:: tool_shed :members: :undoc-members: :show-inheritance: @@ -33,3 +22,23 @@ Subpackages tool_shed.util tool_shed.utility_containers +Submodules +---------- + +tool_shed.repository_registry module +------------------------------------ + +.. automodule:: tool_shed.repository_registry + :members: + :undoc-members: + :show-inheritance: + +tool_shed.tool_shed_registry module +----------------------------------- + +.. automodule:: tool_shed.tool_shed_registry + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst index a734ba26f96..bfc71f2f4eb 100644 --- a/doc/source/lib/tool_shed.tools.rst +++ b/doc/source/lib/tool_shed.tools.rst @@ -1,27 +1,36 @@ -tools Package -============= +tool_shed.tools package +======================= -:mod:`data_table_manager` Module --------------------------------- +.. automodule:: tool_shed.tools + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.tools.data_table_manager module +----------------------------------------- .. automodule:: tool_shed.tools.data_table_manager :members: :undoc-members: :show-inheritance: -:mod:`tool_validator` Module ----------------------------- +tool_shed.tools.tool_validator module +------------------------------------- .. automodule:: tool_shed.tools.tool_validator :members: :undoc-members: :show-inheritance: -:mod:`tool_version_manager` Module ----------------------------------- +tool_shed.tools.tool_version_manager module +------------------------------------------- .. automodule:: tool_shed.tools.tool_version_manager :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index add05826aee..47b221ed9b5 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -1,147 +1,156 @@ -util Package -============ +tool_shed.util package +====================== -:mod:`basic_util` Module ------------------------- +.. automodule:: tool_shed.util + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool_shed.util.basic_util module +-------------------------------- .. automodule:: tool_shed.util.basic_util :members: :undoc-members: :show-inheritance: -:mod:`commit_util` Module -------------------------- +tool_shed.util.commit_util module +--------------------------------- .. automodule:: tool_shed.util.commit_util :members: :undoc-members: :show-inheritance: -:mod:`common_util` Module -------------------------- +tool_shed.util.common_util module +--------------------------------- .. automodule:: tool_shed.util.common_util :members: :undoc-members: :show-inheritance: -:mod:`container_util` Module ----------------------------- +tool_shed.util.container_util module +------------------------------------ .. automodule:: tool_shed.util.container_util :members: :undoc-members: :show-inheritance: -:mod:`encoding_util` Module ---------------------------- +tool_shed.util.encoding_util module +----------------------------------- .. automodule:: tool_shed.util.encoding_util :members: :undoc-members: :show-inheritance: -:mod:`hg_util` Module ---------------------- +tool_shed.util.hg_util module +----------------------------- .. automodule:: tool_shed.util.hg_util :members: :undoc-members: :show-inheritance: -:mod:`metadata_util` Module ---------------------------- +tool_shed.util.metadata_util module +----------------------------------- .. automodule:: tool_shed.util.metadata_util :members: :undoc-members: :show-inheritance: -:mod:`readme_util` Module -------------------------- +tool_shed.util.readme_util module +--------------------------------- .. automodule:: tool_shed.util.readme_util :members: :undoc-members: :show-inheritance: -:mod:`repository_content_util` Module -------------------------------------- +tool_shed.util.repository_content_util module +--------------------------------------------- .. automodule:: tool_shed.util.repository_content_util :members: :undoc-members: :show-inheritance: -:mod:`repository_util` Module ------------------------------ +tool_shed.util.repository_util module +------------------------------------- .. automodule:: tool_shed.util.repository_util :members: :undoc-members: :show-inheritance: -:mod:`review_util` Module -------------------------- +tool_shed.util.review_util module +--------------------------------- .. automodule:: tool_shed.util.review_util :members: :undoc-members: :show-inheritance: -:mod:`search_util` Module -------------------------- +tool_shed.util.search_util module +--------------------------------- .. automodule:: tool_shed.util.search_util :members: :undoc-members: :show-inheritance: -:mod:`shed_util_common` Module ------------------------------- +tool_shed.util.shed_util_common module +-------------------------------------- .. automodule:: tool_shed.util.shed_util_common :members: :undoc-members: :show-inheritance: -:mod:`tool_dependency_util` Module ----------------------------------- +tool_shed.util.tool_dependency_util module +------------------------------------------ .. automodule:: tool_shed.util.tool_dependency_util :members: :undoc-members: :show-inheritance: -:mod:`tool_util` Module ------------------------ +tool_shed.util.tool_util module +------------------------------- .. automodule:: tool_shed.util.tool_util :members: :undoc-members: :show-inheritance: -:mod:`web_util` Module ----------------------- +tool_shed.util.web_util module +------------------------------ .. automodule:: tool_shed.util.web_util :members: :undoc-members: :show-inheritance: -:mod:`workflow_util` Module ---------------------------- +tool_shed.util.workflow_util module +----------------------------------- .. automodule:: tool_shed.util.workflow_util :members: :undoc-members: :show-inheritance: -:mod:`xml_util` Module ----------------------- +tool_shed.util.xml_util module +------------------------------ .. automodule:: tool_shed.util.xml_util :members: :undoc-members: :show-inheritance: + diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst index d5b2f756591..bfa484d7795 100644 --- a/doc/source/lib/tool_shed.utility_containers.rst +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -1,19 +1,20 @@ -utility_containers Package -========================== - -:mod:`utility_containers` Package ---------------------------------- +tool_shed.utility_containers package +==================================== .. automodule:: tool_shed.utility_containers :members: :undoc-members: :show-inheritance: -:mod:`utility_container_manager` Module ---------------------------------------- +Submodules +---------- + +tool_shed.utility_containers.utility_container_manager module +------------------------------------------------------------- .. automodule:: tool_shed.utility_containers.utility_container_manager :members: :undoc-members: :show-inheritance: +