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Rerun make updaterst

Browse Source 
First rm doc/source/lib/*, then rerun sphinx. Cleans out obsolete files.
This commit is contained in:
Sergey Golitsynskiy
2019-07-06 10:10:56 +02:00
parent 410f31f271
commit b5f19e8466
16 changed files with 8 additions and 788 deletions
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doc/source/lib/galaxy.dataset_collections.rst
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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:
doc/source/lib/galaxy.dataset_collections.types.rst
-28
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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:
doc/source/lib/galaxy.jobs.metrics.collectl.rst
-44
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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:
doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
-76
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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:
doc/source/lib/galaxy.jobs.metrics.rst
-28
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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:
doc/source/lib/galaxy.tool_util.rst
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@@ -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
----------------------------------------
doc/source/lib/galaxy.tools.cwl.rst
-60
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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:
doc/source/lib/galaxy.tools.deps.container_resolvers.rst
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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:
doc/source/lib/galaxy.tools.deps.mulled.rst
-60
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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:
doc/source/lib/galaxy.tools.deps.resolvers.rst
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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:
doc/source/lib/galaxy.tools.deps.rst
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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:
doc/source/lib/galaxy.tools.locations.rst
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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:
doc/source/lib/galaxy.tools.parser.rst
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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:
doc/source/lib/galaxy.tools.rst
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@@ -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
--------------------------------
doc/source/lib/galaxy.web.security.rst
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galaxy\.web\.security package
=============================
.. automodule:: galaxy.web.security
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.web.stack.rst
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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: