diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst deleted file mode 100644 index 45e1ae92fbb..00000000000 --- a/doc/source/lib/galaxy.dataset_collections.rst +++ /dev/null @@ -1,67 +0,0 @@ -galaxy\.dataset\_collections package -==================================== - -.. automodule:: galaxy.dataset_collections - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.dataset_collections.types - -Submodules ----------- - -galaxy\.dataset\_collections\.builder module --------------------------------------------- - -.. automodule:: galaxy.dataset_collections.builder - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.matching module ---------------------------------------------- - -.. automodule:: galaxy.dataset_collections.matching - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.registry module ---------------------------------------------- - -.. automodule:: galaxy.dataset_collections.registry - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.structure module ----------------------------------------------- - -.. automodule:: galaxy.dataset_collections.structure - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.subcollections module ---------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.subcollections - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.type\_description module ------------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.type_description - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst deleted file mode 100644 index 64fe380d319..00000000000 --- a/doc/source/lib/galaxy.dataset_collections.types.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.dataset\_collections\.types package -=========================================== - -.. automodule:: galaxy.dataset_collections.types - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.dataset\_collections\.types\.list module ------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.types.list - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.types\.paired module --------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.types.paired - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst deleted file mode 100644 index 8999b1f717f..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.collectl.rst +++ /dev/null @@ -1,44 +0,0 @@ -galaxy\.jobs\.metrics\.collectl package -======================================= - -.. automodule:: galaxy.jobs.metrics.collectl - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.jobs\.metrics\.collectl\.cli module -------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.cli - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.processes module -------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.processes - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.stats module ---------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.stats - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.subsystems module --------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.subsystems - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst deleted file mode 100644 index 21123c4ca4c..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst +++ /dev/null @@ -1,76 +0,0 @@ -galaxy\.jobs\.metrics\.instrumenters package -============================================ - -.. automodule:: galaxy.jobs.metrics.instrumenters - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.jobs\.metrics\.instrumenters\.cgroup module ---------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.cgroup - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.collectl module ------------------------------------------------------ - -.. automodule:: galaxy.jobs.metrics.instrumenters.collectl - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.core module -------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.core - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.cpuinfo module ----------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.env module ------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.env - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.hostname module ------------------------------------------------------ - -.. automodule:: galaxy.jobs.metrics.instrumenters.hostname - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.meminfo module ----------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.meminfo - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.uname module --------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.uname - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst deleted file mode 100644 index 9e651976e30..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.jobs\.metrics package -============================= - -.. automodule:: galaxy.jobs.metrics - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.jobs.metrics.collectl - galaxy.jobs.metrics.instrumenters - -Submodules ----------- - -galaxy\.jobs\.metrics\.formatting module ----------------------------------------- - -.. automodule:: galaxy.jobs.metrics.formatting - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst index 1d006d7c914..02818574534 100644 --- a/doc/source/lib/galaxy.tool_util.rst +++ b/doc/source/lib/galaxy.tool_util.rst @@ -35,6 +35,14 @@ galaxy.tool\_util.loader module :undoc-members: :show-inheritance: +galaxy.tool\_util.loader\_directory module +------------------------------------------ + +.. automodule:: galaxy.tool_util.loader_directory + :members: + :undoc-members: + :show-inheritance: + galaxy.tool\_util.output\_checker module ---------------------------------------- diff --git a/doc/source/lib/galaxy.tools.cwl.rst b/doc/source/lib/galaxy.tools.cwl.rst deleted file mode 100644 index 9b0875eb8fd..00000000000 --- a/doc/source/lib/galaxy.tools.cwl.rst +++ /dev/null @@ -1,60 +0,0 @@ -galaxy\.tools\.cwl package -========================== - -.. automodule:: galaxy.tools.cwl - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.cwl\.cwltool\_deps module ----------------------------------------- - -.. automodule:: galaxy.tools.cwl.cwltool_deps - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.parser module ---------------------------------- - -.. automodule:: galaxy.tools.cwl.parser - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.representation module ------------------------------------------ - -.. automodule:: galaxy.tools.cwl.representation - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.runtime\_actions module -------------------------------------------- - -.. automodule:: galaxy.tools.cwl.runtime_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.schema module ---------------------------------- - -.. automodule:: galaxy.tools.cwl.schema - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.util module -------------------------------- - -.. automodule:: galaxy.tools.cwl.util - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.container_resolvers.rst b/doc/source/lib/galaxy.tools.deps.container_resolvers.rst deleted file mode 100644 index 1c36a12f77e..00000000000 --- a/doc/source/lib/galaxy.tools.deps.container_resolvers.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.tools\.deps\.container\_resolvers package -================================================= - -.. automodule:: galaxy.tools.deps.container_resolvers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.container\_resolvers\.explicit module ----------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_resolvers.explicit - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.container\_resolvers\.mulled module --------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_resolvers.mulled - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.mulled.rst b/doc/source/lib/galaxy.tools.deps.mulled.rst deleted file mode 100644 index 9fc6df39628..00000000000 --- a/doc/source/lib/galaxy.tools.deps.mulled.rst +++ /dev/null @@ -1,60 +0,0 @@ -galaxy\.tools\.deps\.mulled package -=================================== - -.. automodule:: galaxy.tools.deps.mulled - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.mulled\.mulled\_build module -------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_channel module ----------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_channel - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_files module --------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_files - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_tool module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_tool - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_search module --------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_search - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.util module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.util - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst deleted file mode 100644 index 2c64033be73..00000000000 --- a/doc/source/lib/galaxy.tools.deps.resolvers.rst +++ /dev/null @@ -1,84 +0,0 @@ -galaxy\.tools\.deps\.resolvers package -====================================== - -.. automodule:: galaxy.tools.deps.resolvers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.resolvers\.brewed\_tool\_shed\_packages module -------------------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.conda module --------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.conda - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.galaxy\_packages module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.galaxy_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.homebrew module ------------------------------------------------ - -.. automodule:: galaxy.tools.deps.resolvers.homebrew - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.lmod module -------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.lmod - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.modules module ----------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.modules - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.resolver\_mixins module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.tool\_shed\_packages module ------------------------------------------------------------ - -.. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.unlinked\_tool\_shed\_packages module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.unlinked_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst deleted file mode 100644 index f9539e01adc..00000000000 --- a/doc/source/lib/galaxy.tools.deps.rst +++ /dev/null @@ -1,133 +0,0 @@ -galaxy\.tools\.deps package -=========================== - -.. automodule:: galaxy.tools.deps - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.tools.deps.container_resolvers - galaxy.tools.deps.mulled - galaxy.tools.deps.resolvers - -Submodules ----------- - -galaxy\.tools\.deps\.brew\_exts module --------------------------------------- - -.. automodule:: galaxy.tools.deps.brew_exts - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.brew\_util module --------------------------------------- - -.. automodule:: galaxy.tools.deps.brew_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.commands module ------------------------------------- - -.. automodule:: galaxy.tools.deps.commands - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.conda\_compat module ------------------------------------------ - -.. automodule:: galaxy.tools.deps.conda_compat - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.conda\_util module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.conda_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.container\_classes module ----------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_classes - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.containers module --------------------------------------- - -.. automodule:: galaxy.tools.deps.containers - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.dependencies module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.dependencies - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.docker\_util module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.docker_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.dockerfiles module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.dockerfiles - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.installable module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.installable - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.requirements module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.requirements - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.singularity\_util module ---------------------------------------------- - -.. automodule:: galaxy.tools.deps.singularity_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.views module ---------------------------------- - -.. automodule:: galaxy.tools.deps.views - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.locations.rst b/doc/source/lib/galaxy.tools.locations.rst deleted file mode 100644 index 719eed3e90d..00000000000 --- a/doc/source/lib/galaxy.tools.locations.rst +++ /dev/null @@ -1,36 +0,0 @@ -galaxy\.tools\.locations package -================================ - -.. automodule:: galaxy.tools.locations - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.locations\.dockstore module ------------------------------------------- - -.. automodule:: galaxy.tools.locations.dockstore - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.locations\.file module -------------------------------------- - -.. automodule:: galaxy.tools.locations.file - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.locations\.http module -------------------------------------- - -.. automodule:: galaxy.tools.locations.http - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst deleted file mode 100644 index 474be80027c..00000000000 --- a/doc/source/lib/galaxy.tools.parser.rst +++ /dev/null @@ -1,92 +0,0 @@ -galaxy\.tools\.parser package -============================= - -.. automodule:: galaxy.tools.parser - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.parser\.cwl module ---------------------------------- - -.. automodule:: galaxy.tools.parser.cwl - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.error\_level module ------------------------------------------- - -.. automodule:: galaxy.tools.parser.error_level - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.factory module -------------------------------------- - -.. automodule:: galaxy.tools.parser.factory - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.interface module ---------------------------------------- - -.. automodule:: galaxy.tools.parser.interface - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_actions module ---------------------------------------------- - -.. automodule:: galaxy.tools.parser.output_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_collection\_def module ------------------------------------------------------ - -.. automodule:: galaxy.tools.parser.output_collection_def - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_objects module ---------------------------------------------- - -.. automodule:: galaxy.tools.parser.output_objects - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.util module ----------------------------------- - -.. automodule:: galaxy.tools.parser.util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.xml module ---------------------------------- - -.. automodule:: galaxy.tools.parser.xml - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.yaml module ----------------------------------- - -.. automodule:: galaxy.tools.parser.yaml - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 2a8aa83ea90..e544594648a 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -92,14 +92,6 @@ galaxy.tools.lint\_util module :undoc-members: :show-inheritance: -galaxy.tools.loader\_directory module -------------------------------------- - -.. automodule:: galaxy.tools.loader_directory - :members: - :undoc-members: - :show-inheritance: - galaxy.tools.repositories module -------------------------------- diff --git a/doc/source/lib/galaxy.web.security.rst b/doc/source/lib/galaxy.web.security.rst deleted file mode 100644 index c321bda248b..00000000000 --- a/doc/source/lib/galaxy.web.security.rst +++ /dev/null @@ -1,8 +0,0 @@ -galaxy\.web\.security package -============================= - -.. automodule:: galaxy.web.security - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.web.stack.rst b/doc/source/lib/galaxy.web.stack.rst deleted file mode 100644 index c2c5c305c2e..00000000000 --- a/doc/source/lib/galaxy.web.stack.rst +++ /dev/null @@ -1,36 +0,0 @@ -galaxy\.web\.stack package -========================== - -.. automodule:: galaxy.web.stack - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.web\.stack\.handlers module ------------------------------------ - -.. automodule:: galaxy.web.stack.handlers - :members: - :undoc-members: - :show-inheritance: - -galaxy\.web\.stack\.message module ----------------------------------- - -.. automodule:: galaxy.web.stack.message - :members: - :undoc-members: - :show-inheritance: - -galaxy\.web\.stack\.transport module ------------------------------------- - -.. automodule:: galaxy.web.stack.transport - :members: - :undoc-members: - :show-inheritance: - -