update for python 3.10.12, isort, black

Author: David Rickett

.github/workflows/python.yml

@@ -0,0 +1,51 @@
+name: test
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+concurrency:
+  group: test-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHONUNBUFFERED: "1"
+  FORCE_COLOR: "1"
+
+jobs:
+  run:
+    name: Python ${{ matrix.python-version }} Tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11.0-beta.5 - 3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Hatch
+        run: pip install --upgrade hatch
+
+      - name: Run tests
+        run: hatch run ci-report
+
+      - name: Upload coverage data
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-data
+          path: coverage.xml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: success() || failure()
+        with:
+          report_paths: unit_test.xml

Pipfile

@@ -0,0 +1,26 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+biopython = "*"
+numpy = "*"
+pydantic = "*"
+pydantic-numpy = "*"
+typer = "*"
+pytz = "*"
+
+[dev-packages]
+pytest = "*"
+mypy = "*"
+mypy-extensions = "*"
+isort = "*"
+black = "*"
+pytest-cov = "*"
+pytest-html = "*"
+pytest-mock = "*"
+pytest-xdist = "*"
+
+[requires]
+python_version = "3.10"

Pipfile.lock

@@ -6,7 +6,7 @@ build-backend = "hatchling.build"
 name = "easyhla"
 description = ''
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 license = "MIT"
 keywords = []
 authors = [
@@ -16,8 +16,6 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: Implementation :: CPython",
@@ -29,7 +27,7 @@ dependencies = [
   "pydantic-numpy",
   "typer",
   "pytz",
-  "numpy"
+  "numpy",
 ]
 
 dynamic = ["version"]
@@ -55,7 +53,7 @@ exclude = [
   "src/easyhla/check_date_modified.py",
   "tools",
   "tests/output",
-  "tests/input"
+  "tests/input",
 ]
 skip-excluded-dirs = true
 directory = "output"
@@ -70,7 +68,7 @@ dependencies = [
   "pydantic-numpy",
   "typer",
   "pytz",
-  "numpy"
+  "numpy",
 ]
 
 [tool.hatch.envs.test]
@@ -92,7 +90,8 @@ extra-dependencies = [
   "pytest-mock",
   "pytest-xdist",
   "black",
-  "mypy-extensions"
+  "mypy-extensions",
+  "isort",
 ]
 
 [tool.hatch.envs.test.scripts]
@@ -103,14 +102,13 @@ full-report = "pytest --junitxml=unit_test.xml --html=easyhla_test_report.html -
 no-cov = "cov --no-cov {args}"
 
 [[tool.hatch.envs.test.matrix]]
-python = ["38", "39", "310", "311"]
+python = ["310", "311"]
 
 [tool.pytest.ini_options]
+pythonpath = "src"
 minversion = "6.0"
 addopts = "-ra -n 4 --cov --cov-report xml --strict-markers -m 'not slow'"
-testpaths = [
-    "tests",
-]
+testpaths = ["tests"]
 markers = [
   "integration: Run integration tests",
   "slow: Run integration tests that take a really long time",
@@ -124,15 +122,11 @@ omit = [
   "src/easyhla/__about__.py",
   "tests/__init__.py",
   "src/easyhla/entrypoint.py",
-  "tools/*.py"
+  "tools/*.py",
 ]
 
 [tool.coverage.report]
-exclude_lines = [
-  "no cov",
-  "if __name__ == .__main__.:",
-  "if TYPE_CHECKING:",
-]
+exclude_lines = ["no cov", "if __name__ == .__main__.:", "if TYPE_CHECKING:"]
 
 [tool.pydocstyle]
 match = "src/**/*.py"

pyproject.toml

@@ -1,23 +1,23 @@
+import logging
 import os
 import re
-import logging
-import typer
-import numpy as np
-from pathlib import Path
 from datetime import datetime
-from typing import List, Optional, Dict, Tuple, Any, Final, Literal
-import Bio.SeqIO
 from enum import Enum
+from pathlib import Path
+from typing import Any, Dict, Final, List, Literal, Optional, Tuple
 
+import Bio.SeqIO
+import numpy as np
+import typer
 
 from .models import (
-    Exon,
     Alleles,
-    HLAStandard,
-    HLAStandardMatch,
+    Exon,
     HLACombinedStandardResult,
     HLAResult,
     HLAResultRow,
+    HLAStandard,
+    HLAStandardMatch,
 )
 
 

requirements.txt

@@ -1,6 +1,8 @@
-import typer
 import logging
 from pathlib import Path
+
+import typer
+
 from easyhla import EasyHLA, HLAType
 
 

src/easyhla/easyhla.py

@@ -1,9 +1,10 @@
-import numpy as np
 import re
-from pydantic import BaseModel
-from typing import Optional, Dict, List, Tuple, Set
-from pydantic_numpy.ndarray import NDArray
+from typing import Dict, List, Optional, Set, Tuple
 
+import numpy as np
+import pydantic_numpy.typing as pnd
+from pydantic import BaseModel
+from pydantic_numpy.model import NumpyModel
 
 ALLELES_MAX_REPORTABLE_STRING: int = 3900
 
@@ -140,14 +141,14 @@ def stringify(self) -> str:
         return alleles_all_str
 
 
-class HLASequence(BaseModel):
+class HLASequence(NumpyModel):
     exon: Exon
-    sequence: NDArray
+    sequence: pnd.NpNDArray
 
 
-class HLAStandard(BaseModel):
+class HLAStandard(NumpyModel):
     allele: str
-    sequence: NDArray
+    sequence: pnd.NpNDArray
 
     def __eq__(self, other):
         if type(self) != type(other):

src/easyhla/entrypoint.py

@@ -1,6 +1,7 @@
-from src.easyhla import EasyHLA
 from typing import Tuple
 
+from easyhla import EasyHLA
+
 
 def make_comparison(easyhla: EasyHLA, ref_seq: str, test_seq: str) -> str:
     """

src/easyhla/models.py

@@ -1,21 +1,23 @@
-import pytest
 import json
 import os
-import pytz
-import numpy as np
-from datetime import datetime
 from contextlib import nullcontext as does_not_raise
+from datetime import datetime
 from pathlib import Path
-from src.easyhla.easyhla import EasyHLA, DATE_FORMAT
-from src.easyhla.models import (
+from typing import Any, Dict, List, Optional, Tuple
+
+import numpy as np
+import pytest
+import pytz
+
+from easyhla.easyhla import DATE_FORMAT, EasyHLA
+from easyhla.models import (
+    Alleles,
+    HLACombinedStandardResult,
     HLAStandard,
     HLAStandardMatch,
-    HLACombinedStandardResult,
-    Alleles,
 )
-from typing import List, Optional, Dict, Tuple, Any
 
-from .conftest import make_comparison, compare_ref_vs_test
+from .conftest import compare_ref_vs_test, make_comparison
 
 
 @pytest.fixture(scope="module")