cicd: do cleanup to make checks happy

.github/workflows/checks.yaml

@@ -78,7 +78,7 @@ jobs:
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip
-          python3 -m pip install '.[docs]'
+          python3 -m pip install '.[docs,etl,pg]'
 
       - name: Attempt docs build
         working-directory: ./docs

docs/source/api/api/gene.etl.exceptions.rst → docs/source/api/api/gene.etl.update.rst

@@ -1,7 +1,7 @@
-gene.etl.exceptions
-===================
+gene.etl.update
+===============
 
-.. automodule:: gene.etl.exceptions
+.. automodule:: gene.etl.update
    :members:
    :undoc-members:
    :special-members: __init__

docs/source/api/index.rst

@@ -24,17 +24,19 @@ Database connections
    gene.database.dynamodb
    gene.database.postgresql
 
-Source ETL
-----------
+.. _data_updates_api:
+
+Data updates
+------------
 
 .. autosummary::
    :nosignatures:
    :toctree: api/
    :template: module_summary.rst
 
+   gene.etl.update
    gene.etl.base
    gene.etl.ensembl
    gene.etl.hgnc
    gene.etl.ncbi
-   gene.etl.exceptions
    gene.etl.merge

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
 -----------

docs/source/managing_data/loading_and_updating_data.rst

@@ -7,7 +7,7 @@ The Gene Normalizer defines a command line tool for data management. It includes
 
 .. note::
 
-    See the :ref:`ETL API documentation<etl-api>` for information on programmatic access to the data loader classes.
+    See the :ref:`data updates API documentation <data_updates_api>` for information on programmatic access to the data loader classes.
 
 
 .. click:: gene.cli:cli

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
 --------------

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:class:`QueryHandler class <gene.query.QueryHandler>`:
 
 .. 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
 ------
@@ -68,13 +68,4 @@ Gene symbols and aliases often contain only a handful of characters, raising a n
 Match types
 -----------
 
-The **best match** for a search string is determined by which fields in a gene record that it matches against. The Gene Normalizer will first try to match a search string against known concept IDs and gene symbols, then check for matches against previous or deprecated symbols, then aliases, etc. Matches are case-insensitive but must otherwise be exact.
-
-.. autoclass:: gene.schemas.MatchType
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-.. note::
-
-    The `FUZZY_MATCH` Match Type is not currently used by the Gene Normalizer.
+The **best match** for a search string is determined by which fields in a gene record that it matches against. The Gene Normalizer will first try to match a search string against known concept IDs and gene symbols, then check for matches against previous or deprecated symbols, then aliases, etc. Matches are case-insensitive but must otherwise be exact. See the :py:class:`MatchType enum description <gene.schemas.MatchType>` for further information.

src/gene/query.py

@@ -283,7 +283,10 @@ def _get_service_meta() -> ServiceMeta:
 
         :return: Service Meta
         """
-        return ServiceMeta(version=__version__, response_datetime=str(datetime.now()))
+        return ServiceMeta(
+            version=__version__,
+            response_datetime=str(datetime.datetime.now(tz=datetime.timezone.utc)),
+        )
 
     def search(
         self,

src/gene/schemas.py

@@ -51,7 +51,12 @@ class Chromosome(str, Enum):
 
 
 class MatchType(IntEnum):
-    """Define string constraints for use in Match Type attributes."""
+    """Define string constraints for use in Match Type attributes.
+
+    .. note::
+
+        The `FUZZY_MATCH` Match Type is not currently used by the Gene Normalizer.
+    """
 
     CONCEPT_ID = 100
     SYMBOL = 100