build!: require python >= 3.11

.github/workflows/checks.yaml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       fail-fast: false
       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 routine for variations"
 license = {file = "LICENSE"}
 dependencies = [

src/variation/gnomad_vcf_to_protein_variation.py

@@ -457,7 +457,7 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
                 warnings=warnings,
                 service_meta_=ServiceMeta(
                     version=__version__,
-                    response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                    response_datetime=datetime.datetime.now(tz=datetime.UTC),
                 ),
             )
 
@@ -497,7 +497,7 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
                 warnings=warnings,
                 service_meta_=ServiceMeta(
                     version=__version__,
-                    response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                    response_datetime=datetime.datetime.now(tz=datetime.UTC),
                 ),
             )
 
@@ -516,7 +516,7 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
                 warnings=warnings,
                 service_meta_=ServiceMeta(
                     version=__version__,
-                    response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                    response_datetime=datetime.datetime.now(tz=datetime.UTC),
                 ),
             )
 
@@ -539,7 +539,7 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
                 warnings=warnings,
                 service_meta_=ServiceMeta(
                     version=__version__,
-                    response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                    response_datetime=datetime.datetime.now(tz=datetime.UTC),
                 ),
             )
 
@@ -590,6 +590,6 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
             warnings=warnings,
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         )

src/variation/main.py

@@ -235,7 +235,7 @@ def translate_identifier(
         aliases=aliases,
         service_meta_=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
     )
 
@@ -315,7 +315,7 @@ def vrs_python_translate_from(
         variation=vrs_variation,
         service_meta_=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
         vrs_python_meta_=VrsPythonMeta(
             version=pkg_resources.get_distribution("ga4gh.vrs").version
@@ -423,7 +423,7 @@ async def vrs_python_translate_to(request_body: TranslateToQuery) -> TranslateTo
         variations=variations,
         service_meta_=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
         vrs_python_meta_=VrsPythonMeta(
             version=pkg_resources.get_distribution("ga4gh.vrs").version
@@ -481,7 +481,7 @@ async def vrs_python_to_hgvs(request_body: TranslateToHGVSQuery) -> TranslateToS
         variations=variations,
         service_meta_=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
         vrs_python_meta_=VrsPythonMeta(
             version=pkg_resources.get_distribution("ga4gh.vrs").version
@@ -579,7 +579,7 @@ def parsed_to_cn_var(request_body: ParsedToCnVarQuery) -> ParsedToCnVarService:
             warnings=["Unhandled exception. See logs for more details."],
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         )
 
@@ -612,7 +612,7 @@ def parsed_to_cx_var(request_body: ParsedToCxVarQuery) -> ParsedToCxVarService:
             warnings=["Unhandled exception. See logs for more details."],
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         )
 
@@ -705,7 +705,7 @@ async def p_to_c(
         warnings=[w] if w else [],
         service_meta=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
     )
 
@@ -765,7 +765,7 @@ async def c_to_g(
         warnings=[w] if w else [],
         service_meta=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
     )
 
@@ -819,6 +819,6 @@ async def p_to_g(
         warnings=[w] if w else [],
         service_meta=ServiceMeta(
             version=__version__,
-            response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+            response_datetime=datetime.datetime.now(tz=datetime.UTC),
         ),
     )

src/variation/normalize.py

@@ -200,7 +200,7 @@ async def normalize(
             "warnings": warnings,
             "service_meta_": ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         }
 

src/variation/to_copy_number_variation.py

@@ -232,7 +232,7 @@ async def hgvs_to_copy_number_count(
             warnings=warnings,
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
             copy_number_count=cn_var,
         )
@@ -265,7 +265,7 @@ async def hgvs_to_copy_number_change(
             warnings=warnings,
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
             copy_number_change=cx_var,
         )
@@ -628,7 +628,7 @@ def parsed_to_copy_number(
             "warnings": warnings,
             "service_meta_": ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         }
 
@@ -738,6 +738,6 @@ def amplification_to_cx_var(
             warnings=warnings,
             service_meta_=ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
         )

src/variation/to_vrs.py

@@ -128,7 +128,7 @@ async def to_vrs(self, q: str) -> ToVRSService:
             "variations": variations,
             "service_meta_": ServiceMeta(
                 version=__version__,
-                response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
+                response_datetime=datetime.datetime.now(tz=datetime.UTC),
             ),
             "warnings": warnings,
         }