From df5252c887ff211f934916d432f8b727bf32b563 Mon Sep 17 00:00:00 2001 From: Sergey Golitsynskiy Date: Sun, 21 Jul 2019 12:42:58 -0400 Subject: [PATCH] Update RST files to reflect code structure changes Also, clean out obsolete RST files. --- doc/source/lib/galaxy.config.rst | 20 ++ doc/source/lib/galaxy.datatypes.util.rst | 8 + doc/source/lib/galaxy.rst | 8 +- doc/source/lib/galaxy.selenium.rst | 83 +++++++ doc/source/lib/galaxy.selenium.scripts.rst | 20 ++ doc/source/lib/galaxy.tool_util.linters.rst | 92 ++++++++ doc/source/lib/galaxy.tool_util.rst | 10 + .../lib/galaxy.tool_util.verify.asserts.rst | 52 +++++ doc/source/lib/galaxy.tool_util.verify.rst | 43 ++++ doc/source/lib/galaxy.tools.linters.rst | 92 -------- doc/source/lib/galaxy.tools.rst | 18 -- .../lib/galaxy.tools.verify.asserts.rst | 52 ----- doc/source/lib/galaxy.tools.verify.rst | 43 ---- doc/source/lib/galaxy.util.rst | 1 + doc/source/lib/galaxy.util.tool_shed.rst | 36 +++ doc/source/lib/galaxy.web.base.rst | 20 -- doc/source/lib/galaxy.web.rst | 1 - doc/source/lib/galaxy.webapps.base.rst | 20 ++ doc/source/lib/galaxy.webapps.galaxy.rst | 8 - doc/source/lib/galaxy.webapps.rst | 1 + ...galaxy.webapps.tool_shed.model.migrate.rst | 7 + ...bapps.tool_shed.model.migrate.versions.rst | 220 ++++++++++++++++++ .../lib/tool_shed.galaxy_install.migrate.rst | 7 + ...l_shed.galaxy_install.migrate.versions.rst | 108 +++++++++ 24 files changed, 733 insertions(+), 237 deletions(-) create mode 100644 doc/source/lib/galaxy.config.rst create mode 100644 doc/source/lib/galaxy.selenium.rst create mode 100644 doc/source/lib/galaxy.selenium.scripts.rst create mode 100644 doc/source/lib/galaxy.tool_util.linters.rst create mode 100644 doc/source/lib/galaxy.tool_util.verify.asserts.rst create mode 100644 doc/source/lib/galaxy.tool_util.verify.rst delete mode 100644 doc/source/lib/galaxy.tools.linters.rst delete mode 100644 doc/source/lib/galaxy.tools.verify.asserts.rst delete mode 100644 doc/source/lib/galaxy.tools.verify.rst create mode 100644 doc/source/lib/galaxy.util.tool_shed.rst delete mode 100644 doc/source/lib/galaxy.web.base.rst create mode 100644 doc/source/lib/galaxy.webapps.base.rst create mode 100644 doc/source/lib/galaxy.webapps.tool_shed.model.migrate.versions.rst create mode 100644 doc/source/lib/tool_shed.galaxy_install.migrate.versions.rst diff --git a/doc/source/lib/galaxy.config.rst b/doc/source/lib/galaxy.config.rst new file mode 100644 index 00000000000..30d5b67c3ee --- /dev/null +++ b/doc/source/lib/galaxy.config.rst @@ -0,0 +1,20 @@ +galaxy.config package +===================== + +.. automodule:: galaxy.config + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.config.script module +--------------------------- + +.. automodule:: galaxy.config.script + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 8ac6f2c599d..9812c396a99 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -25,4 +25,12 @@ galaxy.datatypes.util.gff\_util module :undoc-members: :show-inheritance: +galaxy.datatypes.util.maf\_utilities module +------------------------------------------- + +.. automodule:: galaxy.datatypes.util.maf_utilities + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index 321bfcfcd7c..4c2425c5326 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -14,6 +14,7 @@ Subpackages galaxy.actions galaxy.auth galaxy.authnz + galaxy.config galaxy.containers galaxy.datatypes galaxy.dependencies @@ -30,6 +31,7 @@ Subpackages galaxy.openid galaxy.quota galaxy.security + galaxy.selenium galaxy.tool_util galaxy.tools galaxy.tours @@ -53,10 +55,10 @@ galaxy.app module :undoc-members: :show-inheritance: -galaxy.config module --------------------- +galaxy.config\_watchers module +------------------------------ -.. automodule:: galaxy.config +.. automodule:: galaxy.config_watchers :members: :undoc-members: :show-inheritance: diff --git a/doc/source/lib/galaxy.selenium.rst b/doc/source/lib/galaxy.selenium.rst new file mode 100644 index 00000000000..db4f0adfa64 --- /dev/null +++ b/doc/source/lib/galaxy.selenium.rst @@ -0,0 +1,83 @@ +galaxy.selenium package +======================= + +.. automodule:: galaxy.selenium + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.selenium.scripts + +Submodules +---------- + +galaxy.selenium.cli module +-------------------------- + +.. automodule:: galaxy.selenium.cli + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.components module +--------------------------------- + +.. automodule:: galaxy.selenium.components + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.data module +--------------------------- + +.. automodule:: galaxy.selenium.data + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.driver\_factory module +-------------------------------------- + +.. automodule:: galaxy.selenium.driver_factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.has\_driver module +---------------------------------- + +.. automodule:: galaxy.selenium.has_driver + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.navigates\_galaxy module +---------------------------------------- + +.. automodule:: galaxy.selenium.navigates_galaxy + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.sizzle module +----------------------------- + +.. automodule:: galaxy.selenium.sizzle + :members: + :undoc-members: + :show-inheritance: + +galaxy.selenium.smart\_components module +---------------------------------------- + +.. automodule:: galaxy.selenium.smart_components + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.selenium.scripts.rst b/doc/source/lib/galaxy.selenium.scripts.rst new file mode 100644 index 00000000000..9b1ca62862e --- /dev/null +++ b/doc/source/lib/galaxy.selenium.scripts.rst @@ -0,0 +1,20 @@ +galaxy.selenium.scripts package +=============================== + +.. automodule:: galaxy.selenium.scripts + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.selenium.scripts.dump\_tour module +----------------------------------------- + +.. automodule:: galaxy.selenium.scripts.dump_tour + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.linters.rst b/doc/source/lib/galaxy.tool_util.linters.rst new file mode 100644 index 00000000000..e87307309f8 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.linters.rst @@ -0,0 +1,92 @@ +galaxy.tool\_util.linters package +================================= + +.. automodule:: galaxy.tool_util.linters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.linters.citations module +------------------------------------------ + +.. automodule:: galaxy.tool_util.linters.citations + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.command module +---------------------------------------- + +.. automodule:: galaxy.tool_util.linters.command + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.cwl module +------------------------------------ + +.. automodule:: galaxy.tool_util.linters.cwl + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.general module +---------------------------------------- + +.. automodule:: galaxy.tool_util.linters.general + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.help module +------------------------------------- + +.. automodule:: galaxy.tool_util.linters.help + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.inputs module +--------------------------------------- + +.. automodule:: galaxy.tool_util.linters.inputs + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.outputs module +---------------------------------------- + +.. automodule:: galaxy.tool_util.linters.outputs + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.stdio module +-------------------------------------- + +.. automodule:: galaxy.tool_util.linters.stdio + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.tests module +-------------------------------------- + +.. automodule:: galaxy.tool_util.linters.tests + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.linters.xml\_order module +------------------------------------------- + +.. automodule:: galaxy.tool_util.linters.xml_order + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst index 02818574534..f09d5aa37f5 100644 --- a/doc/source/lib/galaxy.tool_util.rst +++ b/doc/source/lib/galaxy.tool_util.rst @@ -13,8 +13,10 @@ Subpackages galaxy.tool_util.cwl galaxy.tool_util.deps + galaxy.tool_util.linters galaxy.tool_util.locations galaxy.tool_util.parser + galaxy.tool_util.verify Submodules ---------- @@ -27,6 +29,14 @@ galaxy.tool\_util.fetcher module :undoc-members: :show-inheritance: +galaxy.tool\_util.lint module +----------------------------- + +.. automodule:: galaxy.tool_util.lint + :members: + :undoc-members: + :show-inheritance: + galaxy.tool\_util.loader module ------------------------------- diff --git a/doc/source/lib/galaxy.tool_util.verify.asserts.rst b/doc/source/lib/galaxy.tool_util.verify.asserts.rst new file mode 100644 index 00000000000..b252cd0806c --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.verify.asserts.rst @@ -0,0 +1,52 @@ +galaxy.tool\_util.verify.asserts package +======================================== + +.. automodule:: galaxy.tool_util.verify.asserts + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.verify.asserts.archive module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.verify.asserts.archive + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.asserts.hdf5 module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.verify.asserts.hdf5 + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.asserts.tabular module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.verify.asserts.tabular + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.asserts.text module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.verify.asserts.text + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.asserts.xml module +------------------------------------------- + +.. automodule:: galaxy.tool_util.verify.asserts.xml + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.verify.rst b/doc/source/lib/galaxy.tool_util.verify.rst new file mode 100644 index 00000000000..99469adf02d --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.verify.rst @@ -0,0 +1,43 @@ +galaxy.tool\_util.verify package +================================ + +.. automodule:: galaxy.tool_util.verify + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_util.verify.asserts + +Submodules +---------- + +galaxy.tool\_util.verify.interactor module +------------------------------------------ + +.. automodule:: galaxy.tool_util.verify.interactor + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.script module +-------------------------------------- + +.. automodule:: galaxy.tool_util.verify.script + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.verify.test\_data module +------------------------------------------ + +.. automodule:: galaxy.tool_util.verify.test_data + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst deleted file mode 100644 index f79ce27f18b..00000000000 --- a/doc/source/lib/galaxy.tools.linters.rst +++ /dev/null @@ -1,92 +0,0 @@ -galaxy.tools.linters package -============================ - -.. automodule:: galaxy.tools.linters - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.tools.linters.citations module -------------------------------------- - -.. automodule:: galaxy.tools.linters.citations - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.command module ------------------------------------ - -.. automodule:: galaxy.tools.linters.command - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.cwl module -------------------------------- - -.. automodule:: galaxy.tools.linters.cwl - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.general module ------------------------------------ - -.. automodule:: galaxy.tools.linters.general - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.help module --------------------------------- - -.. automodule:: galaxy.tools.linters.help - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.inputs module ----------------------------------- - -.. automodule:: galaxy.tools.linters.inputs - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.outputs module ------------------------------------ - -.. automodule:: galaxy.tools.linters.outputs - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.stdio module ---------------------------------- - -.. automodule:: galaxy.tools.linters.stdio - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.tests module ---------------------------------- - -.. automodule:: galaxy.tools.linters.tests - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.linters.xml\_order module --------------------------------------- - -.. automodule:: galaxy.tools.linters.xml_order - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index e544594648a..ad6b25686dc 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -18,12 +18,10 @@ Subpackages galaxy.tools.expressions galaxy.tools.filters galaxy.tools.imp_exp - galaxy.tools.linters galaxy.tools.parameters galaxy.tools.search galaxy.tools.toolbox galaxy.tools.util - galaxy.tools.verify Submodules ---------- @@ -76,22 +74,6 @@ galaxy.tools.execute module :undoc-members: :show-inheritance: -galaxy.tools.lint module ------------------------- - -.. automodule:: galaxy.tools.lint - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.lint\_util module ------------------------------- - -.. automodule:: galaxy.tools.lint_util - :members: - :undoc-members: - :show-inheritance: - galaxy.tools.repositories module -------------------------------- diff --git a/doc/source/lib/galaxy.tools.verify.asserts.rst b/doc/source/lib/galaxy.tools.verify.asserts.rst deleted file mode 100644 index 66b69426efb..00000000000 --- a/doc/source/lib/galaxy.tools.verify.asserts.rst +++ /dev/null @@ -1,52 +0,0 @@ -galaxy.tools.verify.asserts package -=================================== - -.. automodule:: galaxy.tools.verify.asserts - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.tools.verify.asserts.archive module ------------------------------------------- - -.. automodule:: galaxy.tools.verify.asserts.archive - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.asserts.hdf5 module ---------------------------------------- - -.. automodule:: galaxy.tools.verify.asserts.hdf5 - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.asserts.tabular module ------------------------------------------- - -.. automodule:: galaxy.tools.verify.asserts.tabular - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.asserts.text module ---------------------------------------- - -.. automodule:: galaxy.tools.verify.asserts.text - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.asserts.xml module --------------------------------------- - -.. automodule:: galaxy.tools.verify.asserts.xml - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.verify.rst b/doc/source/lib/galaxy.tools.verify.rst deleted file mode 100644 index 4daf18a03de..00000000000 --- a/doc/source/lib/galaxy.tools.verify.rst +++ /dev/null @@ -1,43 +0,0 @@ -galaxy.tools.verify package -=========================== - -.. automodule:: galaxy.tools.verify - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.tools.verify.asserts - -Submodules ----------- - -galaxy.tools.verify.interactor module -------------------------------------- - -.. automodule:: galaxy.tools.verify.interactor - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.script module ---------------------------------- - -.. automodule:: galaxy.tools.verify.script - :members: - :undoc-members: - :show-inheritance: - -galaxy.tools.verify.test\_data module -------------------------------------- - -.. automodule:: galaxy.tools.verify.test_data - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 792c0dfabb9..06cfeee6814 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -14,6 +14,7 @@ Subpackages galaxy.util.logging galaxy.util.pastescript galaxy.util.path + galaxy.util.tool_shed Submodules ---------- diff --git a/doc/source/lib/galaxy.util.tool_shed.rst b/doc/source/lib/galaxy.util.tool_shed.rst new file mode 100644 index 00000000000..42b92b9bc7e --- /dev/null +++ b/doc/source/lib/galaxy.util.tool_shed.rst @@ -0,0 +1,36 @@ +galaxy.util.tool\_shed package +============================== + +.. automodule:: galaxy.util.tool_shed + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.util.tool\_shed.common\_util module +------------------------------------------ + +.. automodule:: galaxy.util.tool_shed.common_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.tool\_shed.encoding\_util module +-------------------------------------------- + +.. automodule:: galaxy.util.tool_shed.encoding_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.tool\_shed.xml\_util module +--------------------------------------- + +.. automodule:: galaxy.util.tool_shed.xml_util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst deleted file mode 100644 index f81bd29947a..00000000000 --- a/doc/source/lib/galaxy.web.base.rst +++ /dev/null @@ -1,20 +0,0 @@ -galaxy.web.base package -======================= - -.. automodule:: galaxy.web.base - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.web.base.controller module ---------------------------------- - -.. automodule:: galaxy.web.base.controller - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index dc3fd75cfd6..8bf2e29cc68 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -11,7 +11,6 @@ Subpackages .. toctree:: - galaxy.web.base galaxy.web.framework galaxy.web.proxy diff --git a/doc/source/lib/galaxy.webapps.base.rst b/doc/source/lib/galaxy.webapps.base.rst new file mode 100644 index 00000000000..57a5db43038 --- /dev/null +++ b/doc/source/lib/galaxy.webapps.base.rst @@ -0,0 +1,20 @@ +galaxy.webapps.base package +=========================== + +.. automodule:: galaxy.webapps.base + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.base.controller module +------------------------------------- + +.. automodule:: galaxy.webapps.base.controller + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index f5e0f2027ef..5256155b1ed 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -25,12 +25,4 @@ galaxy.webapps.galaxy.buildapp module :undoc-members: :show-inheritance: -galaxy.webapps.galaxy.config\_watchers module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.config_watchers - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 0ca4f9f0d3a..bcf4c1e750f 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -11,6 +11,7 @@ Subpackages .. toctree:: + galaxy.webapps.base galaxy.webapps.galaxy galaxy.webapps.reports galaxy.webapps.tool_shed 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 3faeb2ab908..90e8d042ed1 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -6,6 +6,13 @@ galaxy.webapps.tool\_shed.model.migrate package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.tool_shed.model.migrate.versions + Submodules ---------- diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.versions.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.versions.rst new file mode 100644 index 00000000000..dd416885749 --- /dev/null +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.versions.rst @@ -0,0 +1,220 @@ +galaxy.webapps.tool\_shed.model.migrate.versions package +======================================================== + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.webapps.tool\_shed.model.migrate.versions.0001\_initial\_tables module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0001_initial_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0002\_add\_tool\_suite\_column module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0002_add_tool_suite_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0003\_review\_and\_review\_association\_tables module +------------------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0003_review_and_review_association_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0004\_repository\_tables module +-------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0004_repository_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0005\_drop\_tool\_related\_tables module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0005_drop_tool_related_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0006\_add\_email\_alerts\_column module +---------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0006_add_email_alerts_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0007\_add\_long\_description\_times\_downloaded\_columns module +---------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0007_add_long_description_times_downloaded_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0008\_add\_repository\_metadata\_table module +---------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0008_add_repository_metadata_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0009\_add\_malicious\_column module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0009_add_malicious_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0010\_add\_new\_repo\_alert\_column module +------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0010_add_new_repo_alert_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0011\_add\_tool\_versions\_column module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0011_add_tool_versions_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0012\_add\_downloadable\_column module +--------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0012_add_downloadable_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0013\_add\_review\_tables module +--------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0013_add_review_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0014\_add\_deprecated\_column module +------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0014_add_deprecated_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0015\_add\_api\_keys\_table module +----------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0015_add_api_keys_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0016\_add\_do\_not\_test\_tools\_functionally\_correct\_errors\_columns module +------------------------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0017\_add\_galaxy\_utility\_columns\_to\_repository\_metadata\_table module +---------------------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0018\_add\_repository\_metadata\_flag\_columns module +------------------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0018_add_repository_metadata_flag_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0019\_add\_skip\_tool\_test\_table\_and\_test\_install\_error\_column module +----------------------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0020\_add\_repository\_type\_column module +------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0020_add_repository_type_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0021\_change\_repository\_type\_value module +--------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0021_change_repository_type_value + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0022\_add\_repository\_admin\_roles module +------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0022_add_repository_admin_roles + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0023\_add\_repository\_url\_and\_hompeage\_url module +------------------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0023_add_repository_url_and_hompeage_url + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0024\_password\_reset module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0024_password_reset + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0025\_session\_timeout module +------------------------------------------------------------------------------ + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0025_session_timeout + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.tool\_shed.model.migrate.versions.0026\_add\_numeric\_revision\_column module +-------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.model.migrate.versions.0026_add_numeric_revision_column + :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 12d29998abc..578387dfd5f 100644 --- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -6,6 +6,13 @@ tool\_shed.galaxy\_install.migrate package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + tool_shed.galaxy_install.migrate.versions + Submodules ---------- diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.versions.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.versions.rst new file mode 100644 index 00000000000..f1db6f74f58 --- /dev/null +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.versions.rst @@ -0,0 +1,108 @@ +tool\_shed.galaxy\_install.migrate.versions package +=================================================== + +.. automodule:: tool_shed.galaxy_install.migrate.versions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +tool\_shed.galaxy\_install.migrate.versions.0001\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0001_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0002\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0002_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0003\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0003_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0004\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0004_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0005\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0005_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0006\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0006_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0007\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0007_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0008\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0008_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0009\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0009_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0010\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0010_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0011\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0011_tools + :members: + :undoc-members: + :show-inheritance: + +tool\_shed.galaxy\_install.migrate.versions.0012\_tools module +-------------------------------------------------------------- + +.. automodule:: tool_shed.galaxy_install.migrate.versions.0012_tools + :members: + :undoc-members: + :show-inheritance: + +