diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index 1c5c1945329..d2d4bfb5094 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -33,4 +33,12 @@ galaxy.auth.providers.localdb module :undoc-members: :show-inheritance: +galaxy.auth.providers.pam_auth module +------------------------------------- + +.. automodule:: galaxy.auth.providers.pam_auth + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index e660f27b6e5..bd76357adaa 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -51,6 +51,14 @@ galaxy.datatypes.chrominfo module :undoc-members: :show-inheritance: +galaxy.datatypes.constructive_solid_geometry module +--------------------------------------------------- + +.. automodule:: galaxy.datatypes.constructive_solid_geometry + :members: + :undoc-members: + :show-inheritance: + galaxy.datatypes.coverage module -------------------------------- diff --git a/doc/source/lib/galaxy.dependencies.rst b/doc/source/lib/galaxy.dependencies.rst new file mode 100644 index 00000000000..16ce685cbc1 --- /dev/null +++ b/doc/source/lib/galaxy.dependencies.rst @@ -0,0 +1,8 @@ +galaxy.dependencies package +=========================== + +.. automodule:: galaxy.dependencies + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index 52a243b3272..6331aa38fdd 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -6,23 +6,3 @@ galaxy.eggs package :undoc-members: :show-inheritance: -Submodules ----------- - -galaxy.eggs.dist module ------------------------ - -.. automodule:: galaxy.eggs.dist - :members: - :undoc-members: - :show-inheritance: - -galaxy.eggs.scramble module ---------------------------- - -.. automodule:: galaxy.eggs.scramble - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index cdb20be1e44..cbeb6de8b49 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -49,7 +49,6 @@ galaxy.jobs.runners.local module :undoc-members: :show-inheritance: - galaxy.jobs.runners.pbs module ------------------------------ diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index b811fd86a1a..f15c406fbe4 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -15,6 +15,7 @@ Subpackages galaxy.auth galaxy.dataset_collections galaxy.datatypes + galaxy.dependencies galaxy.eggs galaxy.exceptions galaxy.external_services diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst index ef2282bb8d3..0ff68422749 100644 --- a/doc/source/lib/galaxy.tools.deps.resolvers.rst +++ b/doc/source/lib/galaxy.tools.deps.resolvers.rst @@ -57,4 +57,12 @@ galaxy.tools.deps.resolvers.tool_shed_packages module :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.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index 3eb2cbe0ed2..20724c76198 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -57,6 +57,14 @@ galaxy.web.framework.middleware.static module :undoc-members: :show-inheritance: +galaxy.web.framework.middleware.statsd module +--------------------------------------------- + +.. automodule:: galaxy.web.framework.middleware.statsd + :members: + :undoc-members: + :show-inheritance: + galaxy.web.framework.middleware.translogger module -------------------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index 5a59cc4af81..fa807bddd54 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -41,14 +41,6 @@ galaxy.webapps.galaxy.controllers.biostar module :undoc-members: :show-inheritance: -galaxy.webapps.galaxy.controllers.cloudlaunch module ----------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch - :members: - :undoc-members: - :show-inheritance: - galaxy.webapps.galaxy.controllers.data_manager module ----------------------------------------------------- @@ -209,14 +201,6 @@ galaxy.webapps.galaxy.controllers.tool_runner module :undoc-members: :show-inheritance: -galaxy.webapps.galaxy.controllers.ucsc_proxy module ---------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy - :members: - :undoc-members: - :show-inheritance: - galaxy.webapps.galaxy.controllers.user module --------------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index 122b8e286ba..e5aee394422 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -9,6 +9,14 @@ galaxy.webapps.reports.controllers package Submodules ---------- +galaxy.webapps.reports.controllers.home module +---------------------------------------------- + +.. automodule:: galaxy.webapps.reports.controllers.home + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.reports.controllers.jobs module ---------------------------------------------- diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 2e301191c77..ddb0cd65214 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -15,3 +15,15 @@ Subpackages galaxy.webapps.reports galaxy.webapps.tool_shed +Submodules +---------- + +galaxy.webapps.util module +-------------------------- + +.. automodule:: galaxy.webapps.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index ae4c3b45f24..16a54648a2a 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -25,6 +25,14 @@ galaxy.webapps.tool_shed.api.categories module :undoc-members: :show-inheritance: +galaxy.webapps.tool_shed.api.configuration module +------------------------------------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.configuration + :members: + :undoc-members: + :show-inheritance: + galaxy.webapps.tool_shed.api.groups module ------------------------------------------ diff --git a/doc/source/lib/modules.rst b/doc/source/lib/modules.rst index bb4749bc352..2f834b22134 100644 --- a/doc/source/lib/modules.rst +++ b/doc/source/lib/modules.rst @@ -9,7 +9,6 @@ lib galaxy_utils log_tempfile mimeparse - pkg_resources psyco_full pulsar tool_shed diff --git a/doc/source/lib/pkg_resources.rst b/doc/source/lib/pkg_resources.rst deleted file mode 100644 index e3082f69603..00000000000 --- a/doc/source/lib/pkg_resources.rst +++ /dev/null @@ -1,7 +0,0 @@ -pkg_resources module -==================== - -.. automodule:: pkg_resources - :members: - :undoc-members: - :show-inheritance: