Merge pull request #14488 from nsoranzo/release_22.05_fix_docs

[22.05] Doc fixes
galaxyproject · Aug 21, 2022 · 0ac10db · 0ac10db
2 parents b5a75ca + 4fcbe80
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diff --git a/doc/source/admin/config.rst b/doc/source/admin/config.rst
@@ -93,7 +93,7 @@ Configuration Basics
 ----------------------------
 
 - Edit ``config/galaxy.yml`` (copy it from ``config/galaxy.yml.sample`` if it does not exist) to make configuration
-  changes. This is a `YAML configuration file`_ and should contain one or two sections, one named ``gravity`` for
+  changes. This is a YAML configuration file and should contain one or two sections, one named ``gravity`` for
   process management via `Gravity`_ (optional) and one named ``galaxy`` for Galaxy (required).
 
     - The `gravity` section contain several important options about how to

diff --git a/doc/source/admin/config_logging.rst b/doc/source/admin/config_logging.rst
@@ -9,22 +9,19 @@ There are two ways in which you can configure logging for Galaxy servers:
 1. Basic/automatic configuration with control over log level and log destination (standard output or a named log file).
 2. More complex configuration using the Python :mod:`logging` module's :func:`logging.config.dictConfig` or :func:`logging.config.fileConfig`.
 
-By default, Galaxy logs all messages to standard output at the ``DEBUG`` logging level, unless the ``--daemon`` argument
-is passed to ``run.sh``, in which case, output is logged to a location configured in `gravity`_.
-
-Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing <scaling>` documentation.
-
 Basic Configuration
 ----------------------------
 
-Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs. The level
-is controlled by the ``log_level`` configuration option.
+Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs.
 
-If not set, Galaxy logs all messages at the ``DEBUG`` level (versions prior to 18.01 defaulted to ``INFO`` if unset, but
-the default config file shipped with ``log_level`` explicitly set to ``DEBUG`` for development purposes).
+The logging level is controlled by the ``log_level`` configuration option. By default, Galaxy logs all messages at the
+``DEBUG`` level.
 
-Galaxy logs all messages to standard output by default if running in the foreground. If running in the background, the
-log is written to a location configured in `gravity`_.
+Galaxy logs all messages to standard output by default if running in the foreground. If running in the background (e.g.
+by passing the ``--daemon`` argument to ``run.sh``), the log is written to a location configured in
+`gravity <https://github.com/galaxyproject/gravity/>`_.
+
+Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing <scaling>` documentation.
 
 **Setting the log level:**
 

diff --git a/doc/source/lib/galaxy.app_unittest_utils.rst b/doc/source/lib/galaxy.app_unittest_utils.rst
@@ -9,14 +9,6 @@ galaxy.app\_unittest\_utils package
 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
 -----------------------------------------------
 

diff --git a/doc/source/lib/galaxy.containers.rst b/doc/source/lib/galaxy.containers.rst
diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst
@@ -268,6 +268,14 @@ galaxy.datatypes.proteomics module
    :undoc-members:
    :show-inheritance:
 
+galaxy.datatypes.qiime2 module
+------------------------------
+
+.. automodule:: galaxy.datatypes.qiime2
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.datatypes.qualityscore module
 ------------------------------------
 

diff --git a/doc/source/lib/galaxy.files.rst b/doc/source/lib/galaxy.files.rst
@@ -14,3 +14,14 @@ Subpackages
 
    galaxy.files.sources
    galaxy.files.unittest_utils
+
+Submodules
+----------
+
+galaxy.files.uris module
+------------------------
+
+.. automodule:: galaxy.files.uris
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/lib/galaxy.job_metrics.instrumenters.rst b/doc/source/lib/galaxy.job_metrics.instrumenters.rst
@@ -17,14 +17,6 @@ galaxy.job\_metrics.instrumenters.cgroup module
    :undoc-members:
    :show-inheritance:
 
-galaxy.job\_metrics.instrumenters.collectl module
--------------------------------------------------
-
-.. automodule:: galaxy.job_metrics.instrumenters.collectl
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 galaxy.job\_metrics.instrumenters.core module
 ---------------------------------------------
 

diff --git a/doc/source/lib/galaxy.job_metrics.rst b/doc/source/lib/galaxy.job_metrics.rst
@@ -24,3 +24,11 @@ galaxy.job\_metrics.formatting module
    :members:
    :undoc-members:
    :show-inheritance:
+
+galaxy.job\_metrics.safety module
+---------------------------------
+
+.. automodule:: galaxy.job_metrics.safety
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst
@@ -273,6 +273,14 @@ galaxy.managers.metrics module
    :undoc-members:
    :show-inheritance:
 
+galaxy.managers.model\_stores module
+------------------------------------
+
+.. automodule:: galaxy.managers.model_stores
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 galaxy.managers.pages module
 ----------------------------
 

diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst
diff --git a/doc/source/lib/galaxy.model.migrate.triggers.rst b/doc/source/lib/galaxy.model.migrate.triggers.rst