ci: fix failing tests and build related to pKa-ANI dependencies

.github/workflows/python-package.yml

@@ -18,15 +18,20 @@ jobs:
         python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install uv and activate environment
+        uses: astral-sh/setup-uv@v7
+        with:
+          # Use uv venv to activate a venv ready to be used by later steps
+          activate-environment: "true"
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e '.[test]'
+        run: uv pip install -e '.[test,pkaani]'
+        env:
+          UV_TORCH_BACKEND: cpu
       - name: Lint with ruff
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -41,12 +46,12 @@ jobs:
       - name: Upload coverage results
         run: bash <(curl -s https://codecov.io/bash)
       - name: Store coverage text results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: coverage-text-my-${{ matrix.python-version }}
           path: coverage.txt
       - name: Store coverage HTML results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: coverage-html-${{ matrix.python-version }}
           path: htmlcov/*

tests/common.py

@@ -323,7 +323,6 @@ def run_pkaani_for_tests(input_pdb, compare_file, pH):
         for key, val in results.items():
             f.write(f"{key},{val}\n")
 
-
     compare = {}
     with open(compare_file) as f:
         for line in f.readlines()[1:]:
@@ -349,4 +348,3 @@ def run_pkaani_for_tests(input_pdb, compare_file, pH):
             raise RuntimeError(
                 f"pKa-ANI test error. pKa values changed more than 1e-3 for group {key}: new {results[key]} reference {compare[key]}"
             )
-

tests/pkaani_test.py

@@ -5,12 +5,18 @@
 import common
 import pytest
 
-PKAANI_TEST_DIR = Path("pkaani_tests")
+PKAANI_TEST_DIR = Path("tests/pkaani_tests")
+
 
 @pytest.mark.parametrize(
-    "input_pdb", 
-    [str(PKAANI_TEST_DIR / "1brs_clean.pdb"), str(PKAANI_TEST_DIR / "1zy8_clean.pdb"), str(PKAANI_TEST_DIR / "6oge_de.pdb"), "1FCC.pdb"
-    ], ids=str
+    "input_pdb",
+    [
+        str(PKAANI_TEST_DIR / "1brs_clean.pdb"),
+        str(PKAANI_TEST_DIR / "1zy8_clean.pdb"),
+        str(PKAANI_TEST_DIR / "6oge_de.pdb"),
+        "1FCC.pdb",
+    ],
+    ids=str,
 )
 def test_pkaani_apo(input_pdb, tmp_path):
     """PKAANI non-regression tests on biomolecules without ligands."""
@@ -28,9 +34,14 @@ def test_pkaani_apo(input_pdb, tmp_path):
 
 
 @pytest.mark.parametrize(
-    "input_pdb", 
-    [str(PKAANI_TEST_DIR / "1brs_clean.pdb"), str(PKAANI_TEST_DIR / "1zy8_clean.pdb"), str(PKAANI_TEST_DIR / "6oge_de.pdb"), "1FCC.pdb"
-    ], ids=str
+    "input_pdb",
+    [
+        str(PKAANI_TEST_DIR / "1brs_clean.pdb"),
+        str(PKAANI_TEST_DIR / "1zy8_clean.pdb"),
+        str(PKAANI_TEST_DIR / "6oge_de.pdb"),
+        "1FCC.pdb",
+    ],
+    ids=str,
 )
 def test_pkaani_pka(input_pdb):
     """PKAANI non-regression tests for pKa values on biomolecules without ligands."""