docs: clean up autodoc pages and refs (#382)

Noticed some small stuff while reviewing the previous PR * fix autodoc to include inherited members * fix refs to autodoc API pages
cancervariants · Dec 24, 2024 · 251f3e7 · 251f3e7
1 parent 1ee3408
commit 251f3e7
Show file tree

Hide file tree

Showing 11 changed files with 20 additions and 12 deletions.
diff --git a/docs/source/_templates/module_summary_inherited.rst b/docs/source/_templates/module_summary_inherited.rst
@@ -0,0 +1,7 @@
+{{ fullname | underline }}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :special-members: __init__
+   :inherited-members:
diff --git a/docs/source/managing_data/dynamodb.rst b/docs/source/managing_data/dynamodb.rst
@@ -7,7 +7,7 @@ The Gene Normalizer can store and retrieve gene records from a `local DynamoDB <
 
 .. note::
 
-    See the :ref:`DynamoDB handler API reference<dynamodb_api>` for information on programmatic access.
+    See the :py:mod:`DynamoDB handler API reference<gene.database.dynamodb>` for information on programmatic access.
 
 Local setup
 -----------

diff --git a/docs/source/managing_data/postgresql.rst b/docs/source/managing_data/postgresql.rst
@@ -7,7 +7,7 @@ The Gene Normalizer can store and retrieve gene records from a `PostgreSQL <http
 
 .. note::
 
-    See the :ref:`PostgreSQL handler API reference<postgres_api>` for information on programmatic access.
+    See the :py:mod:`PostgreSQL handler API reference<gene.database.postgresql>` for information on programmatic access.
 
 Local setup
 --------------

diff --git a/docs/source/reference/api/etl/gene.etl.base.rst b/docs/source/reference/api/etl/gene.etl.base.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/api/etl/gene.etl.ensembl.rst b/docs/source/reference/api/etl/gene.etl.ensembl.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/api/etl/gene.etl.exceptions.rst b/docs/source/reference/api/etl/gene.etl.exceptions.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/api/etl/gene.etl.hgnc.rst b/docs/source/reference/api/etl/gene.etl.hgnc.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/api/etl/gene.etl.merge.rst b/docs/source/reference/api/etl/gene.etl.merge.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/api/etl/gene.etl.ncbi.rst b/docs/source/reference/api/etl/gene.etl.ncbi.rst
@@ -5,4 +5,4 @@
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config
+   :inherited-members:
diff --git a/docs/source/reference/index.rst b/docs/source/reference/index.rst
@@ -29,12 +29,12 @@ Database Modules
 .. _etl-api:
 
 ETL Modules
-----------
+-----------
 
 .. autosummary::
    :nosignatures:
    :toctree: api/etl
-   :template: module_summary.rst
+   :template: module_summary_inherited.rst
 
    gene.etl.base
    gene.etl.ensembl

diff --git a/docs/source/usage.rst b/docs/source/usage.rst
@@ -24,7 +24,7 @@ The individual endpoints are:
 Internal Python API
 -------------------
 
-Each search mode can be accessed directly within Python using the :ref:`query API<query-api>`:
+Each search mode can be accessed directly within Python using the :py:mod:`query API<gene.query>`:
 
 .. code-block:: pycon
 
@@ -58,7 +58,7 @@ Users hoping for a more explicit connection declaration may instead call a datab
     )
     q = QueryHandler(pg_db)
 
-See the API documentation for the :ref:`database <database_api>`, :ref:`DynamoDB <dynamodb_api>`, and :ref:`PostgreSQL <postgres_api>` modules for more details.
+See the API documentation for the :py:mod:`database <gene.database.database>`, :py:mod:`DynamoDB <gene.database.dynamodb>`, and :py:mod:`PostgreSQL <gene.database.postgresql>` modules for more details.
 
 Inputs
 ------
@@ -74,6 +74,7 @@ The **best match** for a search string is determined by which fields in a gene r
     :members:
     :undoc-members:
     :show-inheritance:
+    :noindex:
 
 .. note::