From 6a3804ba2764242d311934caeac92656d5f24419 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 14 Aug 2022 17:55:51 +0100 Subject: [PATCH 1/3] Update application documentation with: ``` make -C doc/ updaterst ``` --- doc/Makefile | 3 +- doc/source/lib/galaxy.actions.rst | 8 - doc/source/lib/galaxy.app_unittest_utils.rst | 34 ++++ doc/source/lib/galaxy.celery.rst | 18 +++ .../lib/galaxy.datatypes.converters.rst | 8 + doc/source/lib/galaxy.datatypes.rst | 32 ++++ doc/source/lib/galaxy.eggs.rst | 7 - doc/source/lib/galaxy.files.rst | 1 + doc/source/lib/galaxy.files.sources.rst | 64 ++++++++ ...rs.rst => galaxy.files.unittest_utils.rst} | 4 +- ...s.rst => galaxy.job_execution.actions.rst} | 8 +- doc/source/lib/galaxy.job_execution.rst | 9 ++ doc/source/lib/galaxy.jobs.rst | 9 -- .../lib/galaxy.jobs.runners.util.cli.job.rst | 8 + doc/source/lib/galaxy.managers.rst | 96 +++++++++++- doc/source/lib/galaxy.model.migrate.rst | 1 + .../lib/galaxy.model.migrate.triggers.rst | 26 ++++ .../lib/galaxy.model.migrate.versions.rst | 64 ++++++++ doc/source/lib/galaxy.model.rst | 25 ++- ...galaxy.model.tool_shed_install.migrate.rst | 8 + ...del.tool_shed_install.migrate.versions.rst | 146 ++++++++++++++++++ .../lib/galaxy.model.unittest_utils.rst | 18 +++ doc/source/lib/galaxy.objectstore.rst | 8 + .../lib/galaxy.objectstore.unittest_utils.rst | 7 + doc/source/lib/galaxy.openid.rst | 26 ---- doc/source/lib/galaxy.rst | 28 +++- doc/source/lib/galaxy.schema.rst | 16 ++ doc/source/lib/galaxy.security.rst | 24 +++ ...alaxy.tool_shed.galaxy_install.migrate.rst | 34 ---- ...l_shed.galaxy_install.migrate.versions.rst | 106 ------------- .../lib/galaxy.tool_shed.galaxy_install.rst | 9 -- doc/source/lib/galaxy.tool_util.biotools.rst | 26 ++++ .../lib/galaxy.tool_util.deps.mulled.rst | 8 + doc/source/lib/galaxy.tool_util.rst | 11 ++ .../lib/galaxy.tool_util.toolbox.filters.rst | 7 + .../lib/galaxy.tool_util.toolbox.lineages.rst | 26 ++++ doc/source/lib/galaxy.tool_util.toolbox.rst | 68 ++++++++ .../lib/galaxy.tool_util.toolbox.views.rst | 50 ++++++ .../lib/galaxy.tool_util.unittest_utils.rst | 18 +++ doc/source/lib/galaxy.tools.rst | 18 ++- .../lib/galaxy.tools.toolbox.lineages.rst | 26 ---- doc/source/lib/galaxy.tools.toolbox.rst | 67 -------- doc/source/lib/galaxy.util.rst | 48 ++++-- .../lib/galaxy.web.framework.middleware.rst | 8 - doc/source/lib/galaxy.web.rst | 16 -- doc/source/lib/galaxy.web_stack.rst | 8 + doc/source/lib/galaxy.webapps.base.rst | 8 + doc/source/lib/galaxy.webapps.galaxy.api.rst | 16 ++ .../lib/galaxy.webapps.galaxy.controllers.rst | 8 - doc/source/lib/galaxy.webapps.galaxy.rst | 17 ++ .../lib/galaxy.webapps.galaxy.services.rst | 106 +++++++++++++ doc/source/lib/galaxy.webapps.reports.api.rst | 7 + doc/source/lib/galaxy.webapps.reports.rst | 17 ++ doc/source/lib/galaxy_test.api.cwl.rst | 7 + doc/source/lib/galaxy_test.api.rst | 78 +++++++++- doc/source/lib/galaxy_test.base.rst | 16 +- doc/source/lib/galaxy_test.driver.rst | 8 + doc/source/lib/galaxy_test.performance.rst | 26 ++++ doc/source/lib/galaxy_test.rst | 1 + doc/source/lib/galaxy_test.selenium.rst | 40 +++++ doc/source/lib/tool_shed.webapp.framework.rst | 11 ++ doc/source/lib/tool_shed.webapp.rst | 16 ++ 62 files changed, 1264 insertions(+), 378 deletions(-) create mode 100644 doc/source/lib/galaxy.app_unittest_utils.rst create mode 100644 doc/source/lib/galaxy.celery.rst delete mode 100644 doc/source/lib/galaxy.eggs.rst rename doc/source/lib/{galaxy.tools.toolbox.filters.rst => galaxy.files.unittest_utils.rst} (52%) rename doc/source/lib/{galaxy.jobs.actions.rst => galaxy.job_execution.actions.rst} (58%) create mode 100644 doc/source/lib/galaxy.model.migrate.triggers.rst create mode 100644 doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst create mode 100644 doc/source/lib/galaxy.model.unittest_utils.rst create mode 100644 doc/source/lib/galaxy.objectstore.unittest_utils.rst delete mode 100644 doc/source/lib/galaxy.openid.rst delete mode 100644 doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst delete mode 100644 doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst create mode 100644 doc/source/lib/galaxy.tool_util.biotools.rst create mode 100644 doc/source/lib/galaxy.tool_util.toolbox.filters.rst create mode 100644 doc/source/lib/galaxy.tool_util.toolbox.lineages.rst create mode 100644 doc/source/lib/galaxy.tool_util.toolbox.rst create mode 100644 doc/source/lib/galaxy.tool_util.toolbox.views.rst create mode 100644 doc/source/lib/galaxy.tool_util.unittest_utils.rst delete mode 100644 doc/source/lib/galaxy.tools.toolbox.lineages.rst delete mode 100644 doc/source/lib/galaxy.tools.toolbox.rst create mode 100644 doc/source/lib/galaxy.webapps.galaxy.services.rst create mode 100644 doc/source/lib/galaxy.webapps.reports.api.rst create mode 100644 doc/source/lib/galaxy_test.api.cwl.rst create mode 100644 doc/source/lib/galaxy_test.performance.rst diff --git a/doc/Makefile b/doc/Makefile index de5921267ad..fc986bd6376 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -54,8 +54,6 @@ source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config/__init__.py printf ' logging:\n ' >> $@ PYTHONPATH=../lib python -c 'from __future__ import print_function; import yaml, galaxy.config; print("\n ".join(yaml.dump(galaxy.config.LOGGING_CONFIG_DEFAULT, indent=2, default_flow_style=False).splitlines()))' >> $@ -# might also want to do -# cd source/lib; hg revert; rm *.rst.orig; or not. clean: -rm -rf $(BUILDDIR)/* $(GENERATED_RST) @@ -172,4 +170,5 @@ doctest: $(GENERATED_RST) # Update Sphinx RST files for lib/ to reflect code structure changes updaterst: + -rm -rf source/lib/ $(SPHINXAPIDOC) -M --force -o source/lib/ ../lib/ diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index a1229c02b41..e1807df5d8e 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -9,14 +9,6 @@ galaxy.actions package Submodules ---------- -galaxy.actions.admin module ---------------------------- - -.. automodule:: galaxy.actions.admin - :members: - :undoc-members: - :show-inheritance: - galaxy.actions.library module ----------------------------- diff --git a/doc/source/lib/galaxy.app_unittest_utils.rst b/doc/source/lib/galaxy.app_unittest_utils.rst new file mode 100644 index 00000000000..b7102289a47 --- /dev/null +++ b/doc/source/lib/galaxy.app_unittest_utils.rst @@ -0,0 +1,34 @@ +galaxy.app\_unittest\_utils package +=================================== + +.. automodule:: galaxy.app_unittest_utils + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.app\_unittest\_utils.celery\_helper module +------------------------------------------------- + +.. automodule:: galaxy.app_unittest_utils.celery_helper + :members: + :undoc-members: + :show-inheritance: + +galaxy.app\_unittest\_utils.galaxy\_mock module +----------------------------------------------- + +.. automodule:: galaxy.app_unittest_utils.galaxy_mock + :members: + :undoc-members: + :show-inheritance: + +galaxy.app\_unittest\_utils.tools\_support module +------------------------------------------------- + +.. automodule:: galaxy.app_unittest_utils.tools_support + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.celery.rst b/doc/source/lib/galaxy.celery.rst new file mode 100644 index 00000000000..d0d4877a654 --- /dev/null +++ b/doc/source/lib/galaxy.celery.rst @@ -0,0 +1,18 @@ +galaxy.celery package +===================== + +.. automodule:: galaxy.celery + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.celery.tasks module +-------------------------- + +.. automodule:: galaxy.celery.tasks + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index e62c824cf74..f12929b8ab3 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -161,6 +161,14 @@ galaxy.datatypes.converters.maf\_to\_interval\_converter module :undoc-members: :show-inheritance: +galaxy.datatypes.converters.parquet\_to\_csv\_converter module +-------------------------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.parquet_to_csv_converter + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.converters.pbed\_ldreduced\_converter module ------------------------------------------------------------- diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index 11fcfd910db..ba4f5c2ed25 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -100,6 +100,14 @@ galaxy.datatypes.data module :undoc-members: :show-inheritance: +galaxy.datatypes.flow module +---------------------------- + +.. automodule:: galaxy.datatypes.flow + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.genetics module -------------------------------- @@ -116,6 +124,14 @@ galaxy.datatypes.gis module :undoc-members: :show-inheritance: +galaxy.datatypes.goldenpath module +---------------------------------- + +.. automodule:: galaxy.datatypes.goldenpath + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.graph module ----------------------------- @@ -124,6 +140,14 @@ galaxy.datatypes.graph module :undoc-members: :show-inheritance: +galaxy.datatypes.hdf5 module +---------------------------- + +.. automodule:: galaxy.datatypes.hdf5 + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.images module ------------------------------ @@ -156,6 +180,14 @@ galaxy.datatypes.media module :undoc-members: :show-inheritance: +galaxy.datatypes.metacyto module +-------------------------------- + +.. automodule:: galaxy.datatypes.metacyto + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.metadata module -------------------------------- diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst deleted file mode 100644 index 2c4bf2f535a..00000000000 --- a/doc/source/lib/galaxy.eggs.rst +++ /dev/null @@ -1,7 +0,0 @@ -galaxy.eggs package -=================== - -.. automodule:: galaxy.eggs - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.files.rst b/doc/source/lib/galaxy.files.rst index e5d3cda4660..47b7e4bf13d 100644 --- a/doc/source/lib/galaxy.files.rst +++ b/doc/source/lib/galaxy.files.rst @@ -13,3 +13,4 @@ Subpackages :maxdepth: 4 galaxy.files.sources + galaxy.files.unittest_utils diff --git a/doc/source/lib/galaxy.files.sources.rst b/doc/source/lib/galaxy.files.sources.rst index bee1d7000d1..49297bcb159 100644 --- a/doc/source/lib/galaxy.files.sources.rst +++ b/doc/source/lib/galaxy.files.sources.rst @@ -9,6 +9,22 @@ galaxy.files.sources package Submodules ---------- +galaxy.files.sources.anvil module +--------------------------------- + +.. automodule:: galaxy.files.sources.anvil + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.basespace module +------------------------------------- + +.. automodule:: galaxy.files.sources.basespace + :members: + :undoc-members: + :show-inheritance: + galaxy.files.sources.dropbox module ----------------------------------- @@ -17,6 +33,14 @@ galaxy.files.sources.dropbox module :undoc-members: :show-inheritance: +galaxy.files.sources.ftp module +------------------------------- + +.. automodule:: galaxy.files.sources.ftp + :members: + :undoc-members: + :show-inheritance: + galaxy.files.sources.galaxy module ---------------------------------- @@ -25,6 +49,30 @@ galaxy.files.sources.galaxy module :undoc-members: :show-inheritance: +galaxy.files.sources.googlecloudstorage module +---------------------------------------------- + +.. automodule:: galaxy.files.sources.googlecloudstorage + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.googledrive module +--------------------------------------- + +.. automodule:: galaxy.files.sources.googledrive + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.onedata module +----------------------------------- + +.. automodule:: galaxy.files.sources.onedata + :members: + :undoc-members: + :show-inheritance: + galaxy.files.sources.posix module --------------------------------- @@ -41,6 +89,22 @@ galaxy.files.sources.s3 module :undoc-members: :show-inheritance: +galaxy.files.sources.s3fs module +-------------------------------- + +.. automodule:: galaxy.files.sources.s3fs + :members: + :undoc-members: + :show-inheritance: + +galaxy.files.sources.ssh module +------------------------------- + +.. automodule:: galaxy.files.sources.ssh + :members: + :undoc-members: + :show-inheritance: + galaxy.files.sources.webdav module ---------------------------------- diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.files.unittest_utils.rst similarity index 52% rename from doc/source/lib/galaxy.tools.toolbox.filters.rst rename to doc/source/lib/galaxy.files.unittest_utils.rst index 1d5157fd251..46aaa937d29 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.files.unittest_utils.rst @@ -1,7 +1,7 @@ -galaxy.tools.toolbox.filters package +galaxy.files.unittest\_utils package ==================================== -.. automodule:: galaxy.tools.toolbox.filters +.. automodule:: galaxy.files.unittest_utils :members: :undoc-members: :show-inheritance: diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.job_execution.actions.rst similarity index 58% rename from doc/source/lib/galaxy.jobs.actions.rst rename to doc/source/lib/galaxy.job_execution.actions.rst index 22358a11128..65b962a4962 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.job_execution.actions.rst @@ -1,5 +1,5 @@ -galaxy.job_execution.actions package -=========================== +galaxy.job\_execution.actions package +===================================== .. automodule:: galaxy.job_execution.actions :members: @@ -9,8 +9,8 @@ galaxy.job_execution.actions package Submodules ---------- -galaxy.job_execution.actions.post module -------------------------------- +galaxy.job\_execution.actions.post module +----------------------------------------- .. automodule:: galaxy.job_execution.actions.post :members: diff --git a/doc/source/lib/galaxy.job_execution.rst b/doc/source/lib/galaxy.job_execution.rst index 4e144d62cda..7550669924b 100644 --- a/doc/source/lib/galaxy.job_execution.rst +++ b/doc/source/lib/galaxy.job_execution.rst @@ -12,11 +12,20 @@ Subpackages .. toctree:: :maxdepth: 4 + galaxy.job_execution.actions galaxy.job_execution.ports Submodules ---------- +galaxy.job\_execution.compute\_environment module +------------------------------------------------- + +.. automodule:: galaxy.job_execution.compute_environment + :members: + :undoc-members: + :show-inheritance: + galaxy.job\_execution.datasets module ------------------------------------- diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index aa64cbdbe49..3a03255bc2f 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -12,7 +12,6 @@ Subpackages .. toctree:: :maxdepth: 4 - galaxy.job_execution.actions galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters @@ -75,11 +74,3 @@ galaxy.jobs.stock\_rules module :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.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst index b931eb319b4..bbcb8618cc7 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -17,6 +17,14 @@ galaxy.jobs.runners.util.cli.job.lsf module :undoc-members: :show-inheritance: +galaxy.jobs.runners.util.cli.job.pbs module +------------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.cli.job.pbs + :members: + :undoc-members: + :show-inheritance: + galaxy.jobs.runners.util.cli.job.slurm module --------------------------------------------- diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index a0186296841..0a1c0bebbc1 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -81,14 +81,6 @@ galaxy.managers.configuration module :undoc-members: :show-inheritance: -galaxy.managers.containers module ---------------------------------- - -.. automodule:: galaxy.managers.containers - :members: - :undoc-members: - :show-inheritance: - galaxy.managers.context module ------------------------------ @@ -105,6 +97,14 @@ galaxy.managers.datasets module :undoc-members: :show-inheritance: +galaxy.managers.datatypes module +-------------------------------- + +.. automodule:: galaxy.managers.datatypes + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.deletable module -------------------------------- @@ -113,6 +113,14 @@ galaxy.managers.deletable module :undoc-members: :show-inheritance: +galaxy.managers.display\_applications module +-------------------------------------------- + +.. automodule:: galaxy.managers.display_applications + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.executables module ---------------------------------- @@ -129,6 +137,38 @@ galaxy.managers.folders module :undoc-members: :show-inheritance: +galaxy.managers.genomes module +------------------------------ + +.. automodule:: galaxy.managers.genomes + :members: + :undoc-members: + :show-inheritance: + +galaxy.managers.group\_roles module +----------------------------------- + +.. automodule:: galaxy.managers.group_roles + :members: + :undoc-members: + :show-inheritance: + +galaxy.managers.group\_users module +----------------------------------- + +.. automodule:: galaxy.managers.group_users + :members: + :undoc-members: + :show-inheritance: + +galaxy.managers.groups module +----------------------------- + +.. automodule:: galaxy.managers.groups + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.hdas module --------------------------- @@ -225,6 +265,14 @@ galaxy.managers.markdown\_util module :undoc-members: :show-inheritance: +galaxy.managers.metrics module +------------------------------ + +.. automodule:: galaxy.managers.metrics + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.pages module ---------------------------- @@ -233,6 +281,14 @@ galaxy.managers.pages module :undoc-members: :show-inheritance: +galaxy.managers.quotas module +----------------------------- + +.. automodule:: galaxy.managers.quotas + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.ratable module ------------------------------ @@ -249,6 +305,14 @@ galaxy.managers.rbac\_secured module :undoc-members: :show-inheritance: +galaxy.managers.remote\_files module +------------------------------------ + +.. automodule:: galaxy.managers.remote_files + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.roles module ---------------------------- @@ -289,6 +353,22 @@ galaxy.managers.taggable module :undoc-members: :show-inheritance: +galaxy.managers.tags module +--------------------------- + +.. automodule:: galaxy.managers.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.managers.tool\_data module +--------------------------------- + +.. automodule:: galaxy.managers.tool_data + :members: + :undoc-members: + :show-inheritance: + galaxy.managers.tools module ---------------------------- diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 0a8f979a501..7f78af9078c 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -12,6 +12,7 @@ Subpackages .. toctree:: :maxdepth: 4 + galaxy.model.migrate.triggers galaxy.model.migrate.versions Submodules diff --git a/doc/source/lib/galaxy.model.migrate.triggers.rst b/doc/source/lib/galaxy.model.migrate.triggers.rst new file mode 100644 index 00000000000..7297f66154f --- /dev/null +++ b/doc/source/lib/galaxy.model.migrate.triggers.rst @@ -0,0 +1,26 @@ +galaxy.model.migrate.triggers package +===================================== + +.. automodule:: galaxy.model.migrate.triggers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrate.triggers.history\_update\_time\_field module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.triggers.history_update_time_field + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.triggers.update\_audit\_table module +--------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.triggers.update_audit_table + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.migrate.versions.rst b/doc/source/lib/galaxy.model.migrate.versions.rst index 8f98e0ca607..07d2348277c 100644 --- a/doc/source/lib/galaxy.model.migrate.versions.rst +++ b/doc/source/lib/galaxy.model.migrate.versions.rst @@ -1385,6 +1385,70 @@ galaxy.model.migrate.versions.0172\_it\_entrypoint\_requires\_domain module :undoc-members: :show-inheritance: +galaxy.model.migrate.versions.0173\_add\_job\_id\_to\_dataset module +-------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0173_add_job_id_to_dataset + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0174\_readd\_update\_time\_triggers module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0174_readd_update_time_triggers + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0175\_history\_audit module +--------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0175_history_audit + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0176\_add\_indexes\_on\_update\_time module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0176_add_indexes_on_update_time + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0177\_update\_job\_state\_summary module +---------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0177_update_job_state_summary + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0178\_drop\_deferredjob\_table module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0178_drop_deferredjob_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0179\_drop\_transferjob\_table module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0179_drop_transferjob_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0180\_add\_vault\_table module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0180_add_vault_table + :members: + :undoc-members: + :show-inheritance: + galaxy.model.migrate.versions.util module ----------------------------------------- diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index ec0c3266eb8..5805dce314f 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -17,6 +17,7 @@ Subpackages galaxy.model.orm galaxy.model.store galaxy.model.tool_shed_install + galaxy.model.unittest_utils galaxy.model.view Submodules @@ -46,6 +47,14 @@ galaxy.model.database\_heartbeat module :undoc-members: :show-inheritance: +galaxy.model.database\_utils module +----------------------------------- + +.. automodule:: galaxy.model.database_utils + :members: + :undoc-members: + :show-inheritance: + galaxy.model.item\_attrs module ------------------------------- @@ -78,6 +87,14 @@ galaxy.model.none\_like module :undoc-members: :show-inheritance: +galaxy.model.scoped\_session module +----------------------------------- + +.. automodule:: galaxy.model.scoped_session + :members: + :undoc-members: + :show-inheritance: + galaxy.model.search module -------------------------- @@ -101,11 +118,3 @@ galaxy.model.tags module :members: :undoc-members: :show-inheritance: - -galaxy.model.triggers module ----------------------------- - -.. automodule:: galaxy.model.triggers - :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 1c8d6340e27..6fbecd637b3 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -6,6 +6,14 @@ galaxy.model.tool\_shed\_install.migrate package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + galaxy.model.tool_shed_install.migrate.versions + Submodules ---------- diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst new file mode 100644 index 00000000000..9c39abe91a3 --- /dev/null +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst @@ -0,0 +1,146 @@ +galaxy.model.tool\_shed\_install.migrate.versions package +========================================================= + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.tool\_shed\_install.migrate.versions.0001\_add\_tool\_shed\_repository\_table module +------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0001_add_tool_shed_repository_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0002\_add\_tool\_shed\_repository\_table\_columns module +---------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0002_add_tool_shed_repository_table_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0003\_tool\_id\_guid\_map\_table module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0003_tool_id_guid_map_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0004\_add\_installed\_changeset\_revison\_column module +--------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0005\_add\_tool\_shed\_repository\_table\_columns module +---------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0005_add_tool_shed_repository_table_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0006\_add\_tool\_version\_tables module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0006_add_tool_version_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0007\_add\_migrate\_tools\_table module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0007_add_migrate_tools_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0008\_add\_ctx\_rev\_column module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0008_add_ctx_rev_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0009\_add\_tool\_dependency\_table module +------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0009_add_tool_dependency_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0010\_alter\_tool\_dependency\_table\_version\_column module +-------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0011\_drop\_installed\_changeset\_revision\_column module +----------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0011_drop_installed_changeset_revision_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0012\_add\_tool\_dependency\_status\_columns module +----------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0012_add_tool_dependency_status_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0013\_add\_tool\_shed\_repository\_status\_columns module +----------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0013_add_tool_shed_repository_status_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0014\_add\_repository\_dependency\_tables module +-------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0014_add_repository_dependency_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0015\_update\_migrate\_tools\_table module +-------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0015_update_migrate_tools_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0016\_update\_migrate\_tools\_table\_again module +--------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0016_update_migrate_tools_table_again + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tool\_shed\_install.migrate.versions.0017\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module +------------------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0017_drop_update_available_col_add_tool_shed_status_col + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.model.unittest_utils.rst b/doc/source/lib/galaxy.model.unittest_utils.rst new file mode 100644 index 00000000000..b6b8fc19959 --- /dev/null +++ b/doc/source/lib/galaxy.model.unittest_utils.rst @@ -0,0 +1,18 @@ +galaxy.model.unittest\_utils package +==================================== + +.. automodule:: galaxy.model.unittest_utils + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.unittest\_utils.data\_app module +--------------------------------------------- + +.. automodule:: galaxy.model.unittest_utils.data_app + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 61b92f89d14..38009c61d91 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -6,6 +6,14 @@ galaxy.objectstore package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + galaxy.objectstore.unittest_utils + Submodules ---------- diff --git a/doc/source/lib/galaxy.objectstore.unittest_utils.rst b/doc/source/lib/galaxy.objectstore.unittest_utils.rst new file mode 100644 index 00000000000..11a2cc6e51f --- /dev/null +++ b/doc/source/lib/galaxy.objectstore.unittest_utils.rst @@ -0,0 +1,7 @@ +galaxy.objectstore.unittest\_utils package +========================================== + +.. automodule:: galaxy.objectstore.unittest_utils + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst deleted file mode 100644 index 86451bafb5e..00000000000 --- a/doc/source/lib/galaxy.openid.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.openid package -===================== - -.. automodule:: galaxy.openid - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.openid.openid\_manager module ------------------------------------- - -.. automodule:: galaxy.openid.openid_manager - :members: - :undoc-members: - :show-inheritance: - -galaxy.openid.providers module ------------------------------- - -.. automodule:: galaxy.openid.providers - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index b911e3634b2..5220a7fd12b 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -13,13 +13,14 @@ Subpackages :maxdepth: 4 galaxy.actions + galaxy.app_unittest_utils galaxy.auth galaxy.authnz + galaxy.celery galaxy.config galaxy.containers galaxy.datatypes galaxy.dependencies - galaxy.eggs galaxy.exceptions galaxy.files galaxy.forms @@ -30,7 +31,6 @@ Subpackages galaxy.metadata galaxy.model galaxy.objectstore - galaxy.openid galaxy.quota galaxy.schema galaxy.security @@ -67,6 +67,14 @@ galaxy.config\_watchers module :undoc-members: :show-inheritance: +galaxy.di module +---------------- + +.. automodule:: galaxy.di + :members: + :undoc-members: + :show-inheritance: + galaxy.main module ------------------ @@ -75,6 +83,14 @@ galaxy.main module :undoc-members: :show-inheritance: +galaxy.main\_config module +-------------------------- + +.. automodule:: galaxy.main_config + :members: + :undoc-members: + :show-inheritance: + galaxy.queue\_worker module --------------------------- @@ -91,6 +107,14 @@ galaxy.queues module :undoc-members: :show-inheritance: +galaxy.structured\_app module +----------------------------- + +.. automodule:: galaxy.structured_app + :members: + :undoc-members: + :show-inheritance: + galaxy.version module --------------------- diff --git a/doc/source/lib/galaxy.schema.rst b/doc/source/lib/galaxy.schema.rst index 38ec22b6fdc..0e245468d5d 100644 --- a/doc/source/lib/galaxy.schema.rst +++ b/doc/source/lib/galaxy.schema.rst @@ -17,6 +17,14 @@ galaxy.schema.fields module :undoc-members: :show-inheritance: +galaxy.schema.remote\_files module +---------------------------------- + +.. automodule:: galaxy.schema.remote_files + :members: + :undoc-members: + :show-inheritance: + galaxy.schema.schema module --------------------------- @@ -24,3 +32,11 @@ galaxy.schema.schema module :members: :undoc-members: :show-inheritance: + +galaxy.schema.types module +-------------------------- + +.. automodule:: galaxy.schema.types + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index 62e9f4d264a..90f9b907498 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -17,6 +17,14 @@ galaxy.security.idencoding module :undoc-members: :show-inheritance: +galaxy.security.object\_wrapper module +-------------------------------------- + +.. automodule:: galaxy.security.object_wrapper + :members: + :undoc-members: + :show-inheritance: + galaxy.security.passwords module -------------------------------- @@ -25,6 +33,14 @@ galaxy.security.passwords module :undoc-members: :show-inheritance: +galaxy.security.ssh\_util module +-------------------------------- + +.. automodule:: galaxy.security.ssh_util + :members: + :undoc-members: + :show-inheritance: + galaxy.security.validate\_user\_input module -------------------------------------------- @@ -32,3 +48,11 @@ galaxy.security.validate\_user\_input module :members: :undoc-members: :show-inheritance: + +galaxy.security.vault module +---------------------------- + +.. automodule:: galaxy.security.vault + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst deleted file mode 100644 index 937d4510298..00000000000 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst +++ /dev/null @@ -1,34 +0,0 @@ -galaxy.tool\_shed.galaxy\_install.migrate package -================================================= - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - galaxy.tool_shed.galaxy_install.migrate.versions - -Submodules ----------- - -galaxy.tool\_shed.galaxy\_install.migrate.check module ------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.check - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.common module -------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.common - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst deleted file mode 100644 index dea11083e28..00000000000 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst +++ /dev/null @@ -1,106 +0,0 @@ -galaxy.tool\_shed.galaxy\_install.migrate.versions package -========================================================== - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0001\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0002\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0003\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0004\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0005\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0006\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0007\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0008\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0009\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0010\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0011\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.tool\_shed.galaxy\_install.migrate.versions.0012\_tools module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst index e0cbc6d5ac7..bc765a12beb 100644 --- a/doc/source/lib/galaxy.tool_shed.galaxy_install.rst +++ b/doc/source/lib/galaxy.tool_shed.galaxy_install.rst @@ -14,7 +14,6 @@ Subpackages galaxy.tool_shed.galaxy_install.datatypes galaxy.tool_shed.galaxy_install.metadata - galaxy.tool_shed.galaxy_install.migrate galaxy.tool_shed.galaxy_install.repository_dependencies galaxy.tool_shed.galaxy_install.tool_dependencies galaxy.tool_shed.galaxy_install.tools @@ -38,14 +37,6 @@ galaxy.tool\_shed.galaxy\_install.installed\_repository\_manager module :undoc-members: :show-inheritance: -galaxy.tool\_shed.galaxy\_install.tool\_migration\_manager module ------------------------------------------------------------------ - -.. automodule:: galaxy.tool_shed.galaxy_install.tool_migration_manager - :members: - :undoc-members: - :show-inheritance: - galaxy.tool\_shed.galaxy\_install.update\_repository\_manager module -------------------------------------------------------------------- diff --git a/doc/source/lib/galaxy.tool_util.biotools.rst b/doc/source/lib/galaxy.tool_util.biotools.rst new file mode 100644 index 00000000000..201838c5019 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.biotools.rst @@ -0,0 +1,26 @@ +galaxy.tool\_util.biotools package +================================== + +.. automodule:: galaxy.tool_util.biotools + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.biotools.interface module +------------------------------------------- + +.. automodule:: galaxy.tool_util.biotools.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.biotools.source module +---------------------------------------- + +.. automodule:: galaxy.tool_util.biotools.source + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.deps.mulled.rst b/doc/source/lib/galaxy.tool_util.deps.mulled.rst index cd84c1ddbe5..eda9ec0e8d4 100644 --- a/doc/source/lib/galaxy.tool_util.deps.mulled.rst +++ b/doc/source/lib/galaxy.tool_util.deps.mulled.rst @@ -49,6 +49,14 @@ galaxy.tool\_util.deps.mulled.mulled\_build\_tool module :undoc-members: :show-inheritance: +galaxy.tool\_util.deps.mulled.mulled\_hash module +------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_hash + :members: + :undoc-members: + :show-inheritance: + galaxy.tool\_util.deps.mulled.mulled\_list module ------------------------------------------------- diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst index 7693a34b76e..e8150cd1d9c 100644 --- a/doc/source/lib/galaxy.tool_util.rst +++ b/doc/source/lib/galaxy.tool_util.rst @@ -12,17 +12,28 @@ Subpackages .. toctree:: :maxdepth: 4 + galaxy.tool_util.biotools galaxy.tool_util.client galaxy.tool_util.cwl galaxy.tool_util.deps galaxy.tool_util.linters galaxy.tool_util.locations galaxy.tool_util.parser + galaxy.tool_util.toolbox + galaxy.tool_util.unittest_utils galaxy.tool_util.verify Submodules ---------- +galaxy.tool\_util.edam\_util module +----------------------------------- + +.. automodule:: galaxy.tool_util.edam_util + :members: + :undoc-members: + :show-inheritance: + galaxy.tool\_util.fetcher module -------------------------------- diff --git a/doc/source/lib/galaxy.tool_util.toolbox.filters.rst b/doc/source/lib/galaxy.tool_util.toolbox.filters.rst new file mode 100644 index 00000000000..be1c548b2fb --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.toolbox.filters.rst @@ -0,0 +1,7 @@ +galaxy.tool\_util.toolbox.filters package +========================================= + +.. automodule:: galaxy.tool_util.toolbox.filters + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.toolbox.lineages.rst b/doc/source/lib/galaxy.tool_util.toolbox.lineages.rst new file mode 100644 index 00000000000..efff36a4630 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.toolbox.lineages.rst @@ -0,0 +1,26 @@ +galaxy.tool\_util.toolbox.lineages package +========================================== + +.. automodule:: galaxy.tool_util.toolbox.lineages + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.toolbox.lineages.factory module +------------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.lineages.factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.lineages.interface module +--------------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.lineages.interface + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.toolbox.rst b/doc/source/lib/galaxy.tool_util.toolbox.rst new file mode 100644 index 00000000000..b4b6938512f --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.toolbox.rst @@ -0,0 +1,68 @@ +galaxy.tool\_util.toolbox package +================================= + +.. automodule:: galaxy.tool_util.toolbox + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + galaxy.tool_util.toolbox.filters + galaxy.tool_util.toolbox.lineages + galaxy.tool_util.toolbox.views + +Submodules +---------- + +galaxy.tool\_util.toolbox.base module +------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.integrated\_panel module +-------------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.integrated_panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.panel module +-------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.panel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.parser module +--------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.parser + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.tags module +------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.watcher module +---------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.watcher + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.toolbox.views.rst b/doc/source/lib/galaxy.tool_util.toolbox.views.rst new file mode 100644 index 00000000000..18d2055042d --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.toolbox.views.rst @@ -0,0 +1,50 @@ +galaxy.tool\_util.toolbox.views package +======================================= + +.. automodule:: galaxy.tool_util.toolbox.views + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.toolbox.views.definitions module +-------------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.views.definitions + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.views.edam module +------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.views.edam + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.views.interface module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.toolbox.views.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.views.sources module +---------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.views.sources + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.toolbox.views.static module +--------------------------------------------- + +.. automodule:: galaxy.tool_util.toolbox.views.static + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tool_util.unittest_utils.rst b/doc/source/lib/galaxy.tool_util.unittest_utils.rst new file mode 100644 index 00000000000..3641e3a2596 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.unittest_utils.rst @@ -0,0 +1,18 @@ +galaxy.tool\_util.unittest\_utils package +========================================= + +.. automodule:: galaxy.tool_util.unittest_utils + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.unittest\_utils.sample\_data module +----------------------------------------------------- + +.. automodule:: galaxy.tool_util.unittest_utils.sample_data + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 1b65b6a1275..d4f7ac0a4e4 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -13,6 +13,7 @@ Subpackages :maxdepth: 4 galaxy.tools.actions + galaxy.tools.bundled galaxy.tools.data galaxy.tools.data_manager galaxy.tools.error_reports @@ -21,12 +22,19 @@ Subpackages galaxy.tools.imp_exp galaxy.tools.parameters galaxy.tools.search - galaxy.tools.toolbox galaxy.tools.util Submodules ---------- +galaxy.tools.biotools module +---------------------------- + +.. automodule:: galaxy.tools.biotools + :members: + :undoc-members: + :show-inheritance: + galaxy.tools.cache module ------------------------- @@ -83,6 +91,14 @@ galaxy.tools.recommendations module :undoc-members: :show-inheritance: +galaxy.tools.remote\_tool\_eval module +-------------------------------------- + +.. automodule:: galaxy.tools.remote_tool_eval + :members: + :undoc-members: + :show-inheritance: + galaxy.tools.repositories module -------------------------------- diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst deleted file mode 100644 index e21361b648e..00000000000 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ /dev/null @@ -1,26 +0,0 @@ -galaxy.tools.toolbox.lineages package -===================================== - -.. automodule:: galaxy.tools.toolbox.lineages - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.tools.toolbox.lineages.factory module --------------------------------------------- - -.. automodule:: galaxy.tools.toolbox.lineages.factory - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.toolbox.lineages.interface module ----------------------------------------------- - -.. automodule:: galaxy.tools.toolbox.lineages.interface - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst deleted file mode 100644 index 3e8a1628caf..00000000000 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ /dev/null @@ -1,67 +0,0 @@ -galaxy.tools.toolbox package -============================ - -.. automodule:: galaxy.tools.toolbox - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - 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.parser module ----------------------------------- - -.. automodule:: galaxy.tools.toolbox.parser - :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.util.rst b/doc/source/lib/galaxy.util.rst index 2a251a7ca04..8a7703a412d 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -28,6 +28,14 @@ galaxy.util.aliaspickler module :undoc-members: :show-inheritance: +galaxy.util.bool\_expressions module +------------------------------------ + +.. automodule:: galaxy.util.bool_expressions + :members: + :undoc-members: + :show-inheritance: + galaxy.util.bunch module ------------------------ @@ -84,6 +92,14 @@ galaxy.util.dictifiable module :undoc-members: :show-inheritance: +galaxy.util.dynamic module +-------------------------- + +.. automodule:: galaxy.util.dynamic + :members: + :undoc-members: + :show-inheritance: + galaxy.util.expressions module ------------------------------ @@ -116,14 +132,6 @@ galaxy.util.form\_builder module :undoc-members: :show-inheritance: -galaxy.util.getargspec module ------------------------------ - -.. automodule:: galaxy.util.getargspec - :members: - :undoc-members: - :show-inheritance: - galaxy.util.hash\_util module ----------------------------- @@ -188,14 +196,6 @@ galaxy.util.monitors module :undoc-members: :show-inheritance: -galaxy.util.object\_wrapper module ----------------------------------- - -.. automodule:: galaxy.util.object_wrapper - :members: - :undoc-members: - :show-inheritance: - galaxy.util.odict module ------------------------ @@ -244,6 +244,14 @@ galaxy.util.renamed\_temporary\_file module :undoc-members: :show-inheritance: +galaxy.util.resources module +---------------------------- + +.. automodule:: galaxy.util.resources + :members: + :undoc-members: + :show-inheritance: + galaxy.util.rules\_dsl module ----------------------------- @@ -324,6 +332,14 @@ galaxy.util.submodules module :undoc-members: :show-inheritance: +galaxy.util.task module +----------------------- + +.. automodule:: galaxy.util.task + :members: + :undoc-members: + :show-inheritance: + galaxy.util.template module --------------------------- diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index db25934e8d6..f86afbd143d 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -49,14 +49,6 @@ galaxy.web.framework.middleware.request\_id module :undoc-members: :show-inheritance: -galaxy.web.framework.middleware.sentry module ---------------------------------------------- - -.. automodule:: galaxy.web.framework.middleware.sentry - :members: - :undoc-members: - :show-inheritance: - galaxy.web.framework.middleware.sqldebug module ----------------------------------------------- diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index c836eb35a4f..d32dba66462 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -35,22 +35,6 @@ galaxy.web.form\_builder module :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: - galaxy.web.statsd\_client module -------------------------------- diff --git a/doc/source/lib/galaxy.web_stack.rst b/doc/source/lib/galaxy.web_stack.rst index 8ef43b9ffe5..9bde52b36b3 100644 --- a/doc/source/lib/galaxy.web_stack.rst +++ b/doc/source/lib/galaxy.web_stack.rst @@ -9,6 +9,14 @@ galaxy.web\_stack package Submodules ---------- +galaxy.web\_stack.gunicorn\_config module +----------------------------------------- + +.. automodule:: galaxy.web_stack.gunicorn_config + :members: + :undoc-members: + :show-inheritance: + galaxy.web\_stack.handlers module --------------------------------- diff --git a/doc/source/lib/galaxy.webapps.base.rst b/doc/source/lib/galaxy.webapps.base.rst index f8fdff600df..ded91cfab01 100644 --- a/doc/source/lib/galaxy.webapps.base.rst +++ b/doc/source/lib/galaxy.webapps.base.rst @@ -9,6 +9,14 @@ galaxy.webapps.base package Submodules ---------- +galaxy.webapps.base.api module +------------------------------ + +.. automodule:: galaxy.webapps.base.api + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.base.controller module ------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 19033eb0d39..54995bc1dd9 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -41,6 +41,14 @@ galaxy.webapps.galaxy.api.cloudauthz module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.api.common module +--------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.common + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.api.configuration module ---------------------------------------------- @@ -313,6 +321,14 @@ galaxy.webapps.galaxy.api.roles module :undoc-members: :show-inheritance: +galaxy.webapps.galaxy.api.sanitize\_allow module +------------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.sanitize_allow + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.galaxy.api.search module --------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index 5207edd910f..d60ce2330bd 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -97,14 +97,6 @@ galaxy.webapps.galaxy.controllers.library module :undoc-members: :show-inheritance: -galaxy.webapps.galaxy.controllers.openid module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.controllers.openid - :members: - :undoc-members: - :show-inheritance: - galaxy.webapps.galaxy.controllers.page module --------------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index 1db3649afd7..f73ef973438 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -14,6 +14,7 @@ Subpackages galaxy.webapps.galaxy.api galaxy.webapps.galaxy.controllers + galaxy.webapps.galaxy.services Submodules ---------- @@ -33,3 +34,19 @@ galaxy.webapps.galaxy.fast\_app module :members: :undoc-members: :show-inheritance: + +galaxy.webapps.galaxy.fast\_factory module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.fast_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.workers module +------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.workers + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.services.rst b/doc/source/lib/galaxy.webapps.galaxy.services.rst new file mode 100644 index 00000000000..871a56dad7e --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.services.rst @@ -0,0 +1,106 @@ +galaxy.webapps.galaxy.services package +====================================== + +.. automodule:: galaxy.webapps.galaxy.services + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.galaxy.services.base module +------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.services.base + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.dataset\_collections module +---------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.dataset_collections + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.datasets module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.datasets + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.histories module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.histories + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.history\_contents module +------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.history_contents + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.libraries module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.libraries + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.library\_folder\_contents module +--------------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.library_folder_contents + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.library\_folders module +------------------------------------------------------ + +.. automodule:: galaxy.webapps.galaxy.services.library_folders + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.pages module +------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.pages + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.quotas module +-------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.quotas + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.sharable module +---------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.sharable + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.services.visualizations module +---------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.services.visualizations + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.reports.api.rst b/doc/source/lib/galaxy.webapps.reports.api.rst new file mode 100644 index 00000000000..e03f438a004 --- /dev/null +++ b/doc/source/lib/galaxy.webapps.reports.api.rst @@ -0,0 +1,7 @@ +galaxy.webapps.reports.api package +================================== + +.. automodule:: galaxy.webapps.reports.api + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index bd30d9fc3b9..4c8d2814e4e 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -12,6 +12,7 @@ Subpackages .. toctree:: :maxdepth: 4 + galaxy.webapps.reports.api galaxy.webapps.reports.controllers Submodules @@ -40,3 +41,19 @@ galaxy.webapps.reports.config module :members: :undoc-members: :show-inheritance: + +galaxy.webapps.reports.fast\_app module +--------------------------------------- + +.. automodule:: galaxy.webapps.reports.fast_app + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.reports.fast\_factory module +------------------------------------------- + +.. automodule:: galaxy.webapps.reports.fast_factory + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.api.cwl.rst b/doc/source/lib/galaxy_test.api.cwl.rst new file mode 100644 index 00000000000..11bcb542801 --- /dev/null +++ b/doc/source/lib/galaxy_test.api.cwl.rst @@ -0,0 +1,7 @@ +galaxy\_test.api.cwl package +============================ + +.. automodule:: galaxy_test.api.cwl + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.api.rst b/doc/source/lib/galaxy_test.api.rst index d453bb577bd..12049df9da5 100644 --- a/doc/source/lib/galaxy_test.api.rst +++ b/doc/source/lib/galaxy_test.api.rst @@ -6,9 +6,33 @@ galaxy\_test.api package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + galaxy_test.api.cwl + Submodules ---------- +galaxy\_test.api.conftest module +-------------------------------- + +.. automodule:: galaxy_test.api.conftest + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.api.sharable module +-------------------------------- + +.. automodule:: galaxy_test.api.sharable + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.api.test\_api\_batch module ---------------------------------------- @@ -57,6 +81,30 @@ galaxy\_test.api.test\_datatypes module :undoc-members: :show-inheritance: +galaxy\_test.api.test\_display\_applications module +--------------------------------------------------- + +.. automodule:: galaxy_test.api.test_display_applications + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.api.test\_folder\_contents module +---------------------------------------------- + +.. automodule:: galaxy_test.api.test_folder_contents + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.api.test\_folders module +------------------------------------- + +.. automodule:: galaxy_test.api.test_folders + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.api.test\_framework module --------------------------------------- @@ -65,10 +113,26 @@ galaxy\_test.api.test\_framework module :undoc-members: :show-inheritance: -galaxy\_test.api.test\_galaxy\_interactor module ------------------------------------------------- +galaxy\_test.api.test\_group\_roles module +------------------------------------------ -.. automodule:: galaxy_test.api.test_galaxy_interactor +.. automodule:: galaxy_test.api.test_group_roles + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.api.test\_group\_users module +------------------------------------------ + +.. automodule:: galaxy_test.api.test_group_users + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.api.test\_groups module +------------------------------------ + +.. automodule:: galaxy_test.api.test_groups :members: :undoc-members: :show-inheritance: @@ -225,6 +289,14 @@ galaxy\_test.api.test\_workflows module :undoc-members: :show-inheritance: +galaxy\_test.api.test\_workflows\_cwl module +-------------------------------------------- + +.. automodule:: galaxy_test.api.test_workflows_cwl + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.api.test\_workflows\_from\_yaml module --------------------------------------------------- diff --git a/doc/source/lib/galaxy_test.base.rst b/doc/source/lib/galaxy_test.base.rst index f3c83ac8519..142ae112a58 100644 --- a/doc/source/lib/galaxy_test.base.rst +++ b/doc/source/lib/galaxy_test.base.rst @@ -89,14 +89,6 @@ galaxy\_test.base.rules\_test\_data module :undoc-members: :show-inheritance: -galaxy\_test.base.ssh\_util module ----------------------------------- - -.. automodule:: galaxy_test.base.ssh_util - :members: - :undoc-members: - :show-inheritance: - galaxy\_test.base.testcase module --------------------------------- @@ -105,6 +97,14 @@ galaxy\_test.base.testcase module :undoc-members: :show-inheritance: +galaxy\_test.base.uses\_shed module +----------------------------------- + +.. automodule:: galaxy_test.base.uses_shed + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.base.workflow\_fixtures module ------------------------------------------- diff --git a/doc/source/lib/galaxy_test.driver.rst b/doc/source/lib/galaxy_test.driver.rst index 03abce0b64c..38d11dc3a91 100644 --- a/doc/source/lib/galaxy_test.driver.rst +++ b/doc/source/lib/galaxy_test.driver.rst @@ -17,6 +17,14 @@ galaxy\_test.driver.driver\_util module :undoc-members: :show-inheritance: +galaxy\_test.driver.integration\_setup module +--------------------------------------------- + +.. automodule:: galaxy_test.driver.integration_setup + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.driver.integration\_util module -------------------------------------------- diff --git a/doc/source/lib/galaxy_test.performance.rst b/doc/source/lib/galaxy_test.performance.rst new file mode 100644 index 00000000000..5930228cd0b --- /dev/null +++ b/doc/source/lib/galaxy_test.performance.rst @@ -0,0 +1,26 @@ +galaxy\_test.performance package +================================ + +.. automodule:: galaxy_test.performance + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy\_test.performance.conftest module +---------------------------------------- + +.. automodule:: galaxy_test.performance.conftest + :members: + :undoc-members: + :show-inheritance: + +galaxy\_test.performance.test\_workflow\_framework\_performance module +---------------------------------------------------------------------- + +.. automodule:: galaxy_test.performance.test_workflow_framework_performance + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/galaxy_test.rst b/doc/source/lib/galaxy_test.rst index 756ea47eeb8..00eb52df606 100644 --- a/doc/source/lib/galaxy_test.rst +++ b/doc/source/lib/galaxy_test.rst @@ -15,4 +15,5 @@ Subpackages galaxy_test.api galaxy_test.base galaxy_test.driver + galaxy_test.performance galaxy_test.selenium diff --git a/doc/source/lib/galaxy_test.selenium.rst b/doc/source/lib/galaxy_test.selenium.rst index a73bc11d7e8..fbfa28b243c 100644 --- a/doc/source/lib/galaxy_test.selenium.rst +++ b/doc/source/lib/galaxy_test.selenium.rst @@ -17,6 +17,14 @@ Subpackages Submodules ---------- +galaxy\_test.selenium.conftest module +------------------------------------- + +.. automodule:: galaxy_test.selenium.conftest + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.framework module -------------------------------------- @@ -65,6 +73,14 @@ galaxy\_test.selenium.test\_collection\_builders module :undoc-members: :show-inheritance: +galaxy\_test.selenium.test\_collection\_edit module +--------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_collection_edit + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.test\_custom\_builds module ------------------------------------------------- @@ -73,6 +89,14 @@ galaxy\_test.selenium.test\_custom\_builds module :undoc-members: :show-inheritance: +galaxy\_test.selenium.test\_data\_source\_tools module +------------------------------------------------------ + +.. automodule:: galaxy_test.selenium.test_data_source_tools + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.test\_histories\_list module -------------------------------------------------- @@ -97,6 +121,14 @@ galaxy\_test.selenium.test\_history\_dataset\_state module :undoc-members: :show-inheritance: +galaxy\_test.selenium.test\_history\_export module +-------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_history_export + :members: + :undoc-members: + :show-inheritance: + galaxy\_test.selenium.test\_history\_multi\_view module ------------------------------------------------------- @@ -312,3 +344,11 @@ galaxy\_test.selenium.test\_workflow\_run module :members: :undoc-members: :show-inheritance: + +galaxy\_test.selenium.test\_workflow\_sharing module +---------------------------------------------------- + +.. automodule:: galaxy_test.selenium.test_workflow_sharing + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.framework.rst b/doc/source/lib/tool_shed.webapp.framework.rst index ec00b6b50b7..e1acf78e162 100644 --- a/doc/source/lib/tool_shed.webapp.framework.rst +++ b/doc/source/lib/tool_shed.webapp.framework.rst @@ -13,3 +13,14 @@ Subpackages :maxdepth: 4 tool_shed.webapp.framework.middleware + +Submodules +---------- + +tool\_shed.webapp.framework.decorators module +--------------------------------------------- + +.. automodule:: tool_shed.webapp.framework.decorators + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/tool_shed.webapp.rst b/doc/source/lib/tool_shed.webapp.rst index 03e9896effc..61201f61437 100644 --- a/doc/source/lib/tool_shed.webapp.rst +++ b/doc/source/lib/tool_shed.webapp.rst @@ -46,3 +46,19 @@ tool\_shed.webapp.config module :members: :undoc-members: :show-inheritance: + +tool\_shed.webapp.fast\_app module +---------------------------------- + +.. automodule:: tool_shed.webapp.fast_app + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.webapp.fast\_factory module +-------------------------------------- + +.. automodule:: tool_shed.webapp.fast_factory + :members: + :undoc-members: + :show-inheritance: From 69defb7a20641e7a9eaca96b4d28d5980477ea0a Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 14 Aug 2022 18:33:42 +0100 Subject: [PATCH 2/3] Doc fixes --- doc/source/admin/nginx.md | 2 +- .../special_topics/performance_tracking.rst | 9 ++- doc/source/dev/debugging_galaxy_slurm.md | 20 +++---- doc/source/dev/interactive_environments.rst | 2 +- doc/source/dev/translating.rst | 8 +-- doc/source/releases/19.01_announce_user.rst | 2 +- doc/source/releases/19.05_announce_user.rst | 2 +- doc/source/releases/19.09_announce_user.rst | 2 +- doc/source/releases/20.01_announce_user.rst | 2 +- doc/source/releases/20.05_announce_user.rst | 2 +- doc/source/releases/20.09_announce_user.rst | 2 +- doc/source/releases/21.01_announce_user.rst | 2 +- doc/source/releases/21.01_prs.rst | 2 + doc/source/releases/21.05_announce_user.rst | 2 +- doc/source/releases/21.09_announce_user.rst | 2 +- doc/source/releases/22.01_announce_user.rst | 6 +- lib/galaxy/datatypes/binary.py | 11 ++++ .../datatypes/constructive_solid_geometry.py | 53 ++++++++++------- lib/galaxy/datatypes/images.py | 6 +- lib/galaxy/datatypes/microarrays.py | 2 + lib/galaxy/datatypes/molecules.py | 5 +- lib/galaxy/jobs/runners/util/pykube_util.py | 17 +++--- lib/galaxy/selenium/has_driver.py | 7 +-- lib/galaxy/selenium/navigates_galaxy.py | 20 +++---- lib/galaxy/tool_util/lint.py | 42 +++++++------ lib/galaxy/util/bool_expressions.py | 3 +- .../webapps/galaxy/api/history_contents.py | 59 +++++++++++-------- .../galaxy/services/history_contents.py | 23 ++++---- ...170_complex_prior_installation_required.py | 6 +- ...test_0420_citable_urls_for_repositories.py | 18 +++--- ...190_complex_prior_installation_required.py | 6 +- ...test_1450_installing_datatypes_sniffers.py | 21 +++---- scripts/bootstrap_history.py | 2 +- 33 files changed, 200 insertions(+), 168 deletions(-) diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md index ba377f5a713..377fb039755 100644 --- a/doc/source/admin/nginx.md +++ b/doc/source/admin/nginx.md @@ -325,7 +325,7 @@ If you serve Galaxy at a prefix exchange `/api/upload/resumable_upload` with `/p After reloading the nginx configuration you can verify that this configuration works correctly by uploading a file to Galaxy. Make sure the tusd server logs the request. It should look similar to the following -```log +``` [tusd] 2021/10/12 13:30:14 Using '/Users/mvandenb/src/galaxy/database/tmp' as directory storage. [tusd] 2021/10/12 13:30:14 Using 0.00MB as maximum size. [tusd] 2021/10/12 13:30:14 Using 'http://localhost:8000/api/upload/hooks' as the endpoint for hooks diff --git a/doc/source/admin/special_topics/performance_tracking.rst b/doc/source/admin/special_topics/performance_tracking.rst index 5958a0a1614..c354bdd9d2b 100644 --- a/doc/source/admin/special_topics/performance_tracking.rst +++ b/doc/source/admin/special_topics/performance_tracking.rst @@ -2,22 +2,21 @@ Galaxy Performance Tracking =========================== Tracking performance over time and identifying slow queries in your Galaxy can be an extremely important thing to do, especially for larger Galaxies. -[A more in-depth tutorial is available at the Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html). +A more `in-depth tutorial `__ is available at the Galaxy Training Network. Most performance tracking requires sending metrics to a metrics collection server such as `StatsD `__. This document assumes you have already deployed StatsD. Gunicorn ------ +-------- There is some built-in `Gunicorn `__ support for performance logging. You can send Gunicorn's internal metrics to a StatsD server by setting the `--statsd-host` and `--statsd-prefix` command line options for Gunicorn in the `gravity` section of `galaxy.yml`: .. code-block:: yaml gravity: - ... + #... gunicorn: - extra_args: `--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn` - ... + extra_args: '--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn' API / Route Timing Statistics ----------------------------- diff --git a/doc/source/dev/debugging_galaxy_slurm.md b/doc/source/dev/debugging_galaxy_slurm.md index fd0965a7da5..75dc6173ba7 100644 --- a/doc/source/dev/debugging_galaxy_slurm.md +++ b/doc/source/dev/debugging_galaxy_slurm.md @@ -2,15 +2,15 @@ # Debugging Galaxy: Slurm Compute Cluster This document explains how to debug a Galaxy instance that uses a Slurm compute cluster (not the -default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's -VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with -4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to -successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode, -and Docker (if using Irods storage). Finally, These instructions are intended for developers who -want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible +default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's +VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with +4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to +successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode, +and Docker (if using Irods storage). Finally, These instructions are intended for developers who +want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible playbooks for that). -## Debugging Galaxy in VS Code +## Debugging Galaxy in VS Code 1. Install libslurm-dev * `sudo apt install libslurm-dev` @@ -19,7 +19,7 @@ playbooks for that). 2. Install slurm-drmaa * Download slurm-drmaa tar file from https://github.com/natefoo/slurm-drmaa/releases/download/1.1.2/slurm-drmaa-1.1.2.tar.gz - * Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~` + * Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~` * To compile and install slurm-drmaa * `cd ~/slurm-drmaa-1.1.2` * `./configure --with-slurm-inc=/usr/include --with-slurm-lib=/usr/lib/x86_64-linux-gpu` @@ -71,6 +71,6 @@ playbooks for that). * `sudo service slurmd start` * `sudo service slurmctld start` -6. Follow the instructions [here](./debuging_galaxy.md) to setup VSCode for debugging. +6. Follow the instructions [here](debugging_galaxy) to setup VSCode for debugging. -Enjoy debugging session your Galaxy instance backed by a Slurm cluster! +Enjoy debugging session your Galaxy instance backed by a Slurm cluster! diff --git a/doc/source/dev/interactive_environments.rst b/doc/source/dev/interactive_environments.rst index e7eb5462657..ea66b7794ce 100644 --- a/doc/source/dev/interactive_environments.rst +++ b/doc/source/dev/interactive_environments.rst @@ -1,5 +1,5 @@ Interactive Environments ========================= -Galaxy Interactive Environments are deprecated and were the precursors to the current :doc:`Galaxy Interactive Tools <../admin/special_topics/interactivetools>`. +Galaxy Interactive Environments are deprecated and were the precursors to the current :ref:`Galaxy Interactive Tools `. You can find information about Galaxy Interactive Environments in `older versions `__ of this document. diff --git a/doc/source/dev/translating.rst b/doc/source/dev/translating.rst index 2f64ddffc75..6dc19189a61 100644 --- a/doc/source/dev/translating.rst +++ b/doc/source/dev/translating.rst @@ -45,19 +45,19 @@ There are a number of ways text gets used in the codebase, especially the new Vu 1. Text within an element: - .. code-block:: js + .. code-block:: html Some Text 2. Text within a more complex element: - .. code-block:: javascript + .. code-block:: html Some Text 3. Attribute or placeholder text - .. code-block:: javascript + .. code-block:: html @@ -88,7 +88,7 @@ The first one is the easiest, we can just add the ``v-localize`` tag and we're d For those you'll need to have a quick overview of the structure of a Vue component to localize the correct place to set the variable. The exact structure will not always be identical but it should be similar. At the top is a ``