docs: fix a few warnings, remove anonymous entries from search results (#646)

* docs: cleanup search results and resolve indent warning
* silence warning

Author: jsstevenson

docs/source/appendices/design_decisions.rst

@@ -57,12 +57,13 @@ proposal was presented for instance and class GKS identifiers.
 As an example, the Github JSON Schema URL ($id) for the VRS 2.0.0 Allele is:
 
 .. code-block:: json
+   :force:
 
-  {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Allele",
-    ...
-  }
+   {
+     "$schema": "https://json-schema.org/draft/2020-12/schema",
+     "$id": "https://w3id.org/ga4gh/schema/vrs/2.0.0/json/Allele",
+     ...
+   }
 
 During the **release and versioning** discussion at the GA4GH Connect April 2023 meeting the proposal
 delved into the idea of including the major version number in the VRS identifier itself. Proponents of

docs/source/concepts/SystemicVariation/CopyNumberChange.rst

@@ -18,6 +18,7 @@ The `CopyChange` attribute uses a valueset derived from the
 
 * **gain** (`EFO:0030070 <http://www.ebi.ac.uk/efo/EFO_0030070>`_ - *copy number gain*):
   Assessment of genomic copy number gain.
+
     * **high-level gain** (`EFO:0030072 <http://www.ebi.ac.uk/efo/EFO_0030072>`_ - *high-level copy number gain*):
       Assessment of high-level genomic copy number gain.
     * **low-level gain** (`EFO:0030071 <http://www.ebi.ac.uk/efo/EFO_0030071>`_ - *low-level copy number gain*):
@@ -26,10 +27,12 @@ The `CopyChange` attribute uses a valueset derived from the
   Copy number assessment of regional base ploidy.
 * **loss** (`EFO:0030067 <http://www.ebi.ac.uk/efo/EFO_0030067>`_ - *copy number loss*):
   Assessment of genomic copy number loss.
+
     * **low-level loss** (`EFO:0030068 <http://www.ebi.ac.uk/efo/EFO_0030068>`_ -
       *low-level copy number loss*): Assessment of low-level genomic copy number loss.
     * **high-level loss** (`EFO:0020073 <http://www.ebi.ac.uk/efo/EFO_0020073>`_ -
       *high-level copy number loss*): Assessment of high-level genomic copy number loss.
+
         * **complete genomic loss** (`EFO:0030069 <http://www.ebi.ac.uk/efo/EFO_0030069>`_ -
           *complete genomic deletion*: Assessment of complete genomic deletion.
 

docs/source/conf.py

@@ -64,7 +64,7 @@ def _parse_release_as_version(rls):
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
+exclude_patterns = ["def"]
 
 # TODO directive output
 todo_include_todos = True