str enum

Author: bpblanken

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "seqr-loading-pipeline"
 dynamic = ['version']
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 
 [tool.setuptools]
 include-package-data = true
@@ -19,7 +19,7 @@ namespaces = false
 
 [tool.mypy]
 packages = 'v03_pipeline'
-python_version = "3.10"
+python_version = "3.11"
 ignore_missing_imports = true
 strict = true
 
@@ -55,7 +55,7 @@ line-length = 88
 select = [
     "ALL"
 ]
-target-version = "py310"
+target-version = "py311"
 
 [tool.ruff.flake8-quotes]
 inline-quotes = "single"

v03_pipeline/__init__.py

@@ -2,4 +2,6 @@
 
 MAJOR_VERSION = 3
 
-__version__ = f'{MAJOR_VERSION}.{datetime.datetime.now(datetime.timezone.utc).strftime("%Y%m%d.%H%M%S")}'
+__version__ = (
+    f'{MAJOR_VERSION}.{datetime.datetime.now(datetime.UTC).strftime("%Y%m%d.%H%M%S")}'
+)

v03_pipeline/bin/pipeline_worker.py

@@ -44,7 +44,7 @@ def main():
                 )
                 for project_guid in lpr.projects_to_run
             ]
-            run_id = datetime.datetime.now(datetime.timezone.utc).strftime(
+            run_id = datetime.datetime.now(datetime.UTC).strftime(
                 '%Y%m%d-%H%M%S',
             )
             loading_run_task_params = {

v03_pipeline/lib/model/dataset_type.py

@@ -1,5 +1,5 @@
 from collections.abc import Callable
-from enum import Enum
+from enum import StrEnum
 
 import hail as hl
 
@@ -10,7 +10,7 @@
 ZERO = 0.0
 
 
-class DatasetType(str, Enum):
+class DatasetType(StrEnum):
     GCNV = 'GCNV'
     MITO = 'MITO'
     SNV_INDEL = 'SNV_INDEL'

v03_pipeline/lib/model/definitions.py

@@ -1,14 +1,14 @@
-from enum import Enum
+from enum import StrEnum
 
 import hail as hl
 
 
-class AccessControl(str, Enum):
+class AccessControl(StrEnum):
     PUBLIC = 'public'
     PRIVATE = 'private'
 
 
-class Sex(str, Enum):
+class Sex(StrEnum):
     FEMALE = 'F'
     MALE = 'M'
     UNKNOWN = 'U'
@@ -26,13 +26,13 @@ def imputed_sex_values(self) -> list[str]:
         }.get(self, [self.name])
 
 
-class PipelineVersion(str, Enum):
+class PipelineVersion(StrEnum):
     V02 = 'v02'
     V03 = 'v03'
     V3_1 = 'v3.1'
 
 
-class ReferenceGenome(str, Enum):
+class ReferenceGenome(StrEnum):
     GRCh37 = 'GRCh37'
     GRCh38 = 'GRCh38'
 
@@ -158,6 +158,6 @@ def allele_registry_gnomad_id(self) -> str:
         }[self]
 
 
-class SampleType(str, Enum):
+class SampleType(StrEnum):
     WES = 'WES'
     WGS = 'WGS'

v03_pipeline/lib/reference_datasets/reference_dataset.py

@@ -1,7 +1,7 @@
 import importlib
 import types
 from collections.abc import Callable
-from enum import Enum
+from enum import StrEnum
 from typing import Union
 
 import hail as hl
@@ -140,7 +140,7 @@ def get_ht(
         )
 
 
-class ReferenceDataset(BaseReferenceDataset, str, Enum):
+class ReferenceDataset(BaseReferenceDataset, StrEnum):
     clinvar = 'clinvar'
     dbnsfp = 'dbnsfp'
     exac = 'exac'
@@ -162,7 +162,7 @@ class ReferenceDataset(BaseReferenceDataset, str, Enum):
     mitomap = 'mitomap'
 
 
-class ReferenceDatasetQuery(BaseReferenceDataset, str, Enum):
+class ReferenceDatasetQuery(BaseReferenceDataset, StrEnum):
     clinvar_path_variants = 'clinvar_path_variants'
     high_af_variants = 'high_af_variants'
 

v03_pipeline/lib/tasks/validate_callset.py

@@ -135,7 +135,7 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable:
                     **self.param_kwargs,
                     **validation_dependencies,
                 )
-            except SeqrValidationError as e:  # noqa: PERF203
+            except SeqrValidationError as e:
                 validation_exceptions.append(e)
         if validation_exceptions:
             write_validation_errors_for_run_task = self.clone(