build!: require python >= 3.11 (#445)

* GenomicMedLab/software-templates#66

.github/workflows/checks.yaml

@@ -14,7 +14,7 @@ jobs:
       THERAPY_TEST: true
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
 

pyproject.toml

@@ -16,11 +16,11 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 description = "VICC normalization routines for therapeutics"
 license = {file = "LICENSE"}
 dependencies = [

src/therapy/database/dynamodb.py

@@ -608,7 +608,7 @@ def delete_source(self, src_name: SourceName) -> None:
                                 "concept_id": record["concept_id"],
                             }
                         )
-                    except ClientError as e:  # noqa: PERF203
+                    except ClientError as e:
                         raise DatabaseWriteError(e) from e
 
     def complete_write_transaction(self) -> None:

src/therapy/etl/wikidata.py

@@ -120,9 +120,7 @@ def _get_latest_version() -> str:
 
         :return: formatted string for the current date
         """
-        return datetime.datetime.now(tz=datetime.timezone.utc).strftime(
-            DATE_VERSION_PATTERN
-        )
+        return datetime.datetime.now(tz=datetime.UTC).strftime(DATE_VERSION_PATTERN)
 
     def _get_data_handler(self, data_path: Path | None = None) -> DataSource:
         """Construct data handler instance for source. Overwrites base class method

src/therapy/query.py

@@ -144,7 +144,7 @@ def _fetch_records(
                     raise KeyError(msg)
                 (response, src) = self._add_record(response, match, match_type)
                 matched_sources.add(src)
-            except ClientError as e:  # noqa: PERF203
+            except ClientError as e:
                 logger.error(e.response["Error"]["Message"])
 
         return response, matched_sources
@@ -339,7 +339,7 @@ def search(
         response = self._get_search_response(query_str, query_sources, infer)
 
         response["service_meta_"] = ServiceMeta(
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ).model_dump()
         return SearchService(**response)
 
@@ -358,7 +358,7 @@ def _add_merged_meta(self, response: NormalizationService) -> NormalizationServi
         for src in sources:
             try:
                 src_name = SourceName(PREFIX_LOOKUP[src])
-            except KeyError:  # noqa: PERF203
+            except KeyError:
                 # not an imported source
                 continue
             else:
@@ -522,7 +522,7 @@ def _prepare_normalized_response(self, query: str) -> dict[str, Any]:
             "match_type": MatchType.NO_MATCH,
             "warnings": self._emit_char_warnings(query),
             "service_meta_": ServiceMeta(
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc)
+                response_datetime=datetime.datetime.now(tz=datetime.UTC)
             ),
         }
 

tests/scripts/build_wikidata_data.py

@@ -30,7 +30,7 @@
         test_data.append(params)
 
 TEST_DATA_DIR = Path(__file__).resolve().parents[1] / "data" / "wikidata"
-date = datetime.datetime.now(tz=datetime.timezone.utc).strftime("%Y-%m-%d")
+date = datetime.datetime.now(tz=datetime.UTC).strftime("%Y-%m-%d")
 outfile_path = TEST_DATA_DIR / f"wikidata_{date}.json"
 with outfile_path.open("w+") as f:
     json.dump(test_data, f, indent=2)