Doc fixes

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

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:**
 

lib/galaxy/model/orm/util.py

@@ -8,12 +8,13 @@ def add_object_to_object_session(object, object_with_session):
     https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0
 
     This function preserves SQLAlchemy's pre-2.0 logic and should be used when:
+
     1. foo and bar are model instances, that are associated (via SQLAlchemy's relationship), AND
     2. bar is assigned to foo's bar relationship (e.g. foo.bar = bar), AND
     3. bar is in a session and foo is not, AND
     4. foo is implicitly added to bar's session upon assignment(2), as indicated
-      by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session
-      along the backref cascade path...'
+       by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session
+       along the backref cascade path...'
     """
     if object_with_session:
         session = get_object_session(object_with_session)

lib/galaxy/webapps/galaxy/api/common.py

@@ -149,10 +149,10 @@ def query_parameter_as_list(query):
     """Used as FastAPI dependable for query parameters that need to behave as a list of values separated by comma
     or as multiple instances of the same parameter.
 
-    **Important**: the `query` annotation provided must define the `alias` exactly as the name of the actual parameter name.
+    .. important:: the ``query`` annotation provided must define the ``alias`` exactly as the name of the actual parameter name.
+
+    Usage example::
 
-    Usage example:
-    ```python
         ValueQueryParam = Query(
             default=None,
             alias="value", # Important! this is the parameter name that will be displayed in the API docs
@@ -166,11 +166,11 @@ def query_parameter_as_list(query):
             values: Optional[List[str]] = Depends(query_parameter_as_list(ValueQueryParam)),
         ):
             ...
-    ```
 
     This will render in the API docs as a single string query parameter but will make the following requests equivalent:
-    - `api/my_route?value=val1,val2,val3`
-    - `api/my_route?value=val1&value=val2&value=val3`
+
+    - ``api/my_route?value=val1,val2,val3``
+    - ``api/my_route?value=val1&value=val2&value=val3``
     """
 
     def parse_elements(