Merge branch 'main' into dependabot/pip/requirements/scikit-learn-1.5.0

.github/workflows/CI.yaml

@@ -20,7 +20,6 @@ jobs:
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
-        environment-file: .github/workflows/envs/environment.yml
         channels: conda-forge
         activate-environment: test
         show-channel-urls: true
@@ -29,10 +28,13 @@ jobs:
     - name: Check and Conditionally Install PyMOL
       shell: bash -l {0}
       run: |
+        PYMOL_VER=3.0.0
         PYTHON_VER=${{ matrix.python-version }}
         PYTHON_VER=${PYTHON_VER//./}  # Remove the dot from the Python version
-        if mamba search -c conda-forge pymol-open-source=3.0.0 | grep -q "py${PYTHON_VER}"; then
-          mamba install -c conda-forge pymol-open-source=3.0.0
+        if mamba search -c conda-forge pymol-open-source==${PYMOL_VER} | grep -q "py${PYTHON_VER}"; then
+           mamba install -c conda-forge pymol-open-source==${PYMOL_VER} --file requirements/requirements-test.txt
+        else
+           mamba install -c conda-forge --file requirements/requirements-test.txt
         fi
     - name: Install package
       shell: bash -l {0}
@@ -42,5 +44,4 @@ jobs:
       shell: bash -l {0}
       run: |
         which python
-        python -m pip install pytest
-        pytest
+        python -m pytest

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
       - id: requirements-txt-fixer
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.2.2
+    rev: v0.4.10
     hooks:
       # Run the linter.
       - id: ruff

requirements/requirements-test.txt

@@ -2,3 +2,4 @@ matplotlib==3.8.4
 nglview==3.1.2
 numpy==1.26.4
 scikit-learn==1.5.0
+pytest==8.2.2

tests/conftest.py

@@ -37,7 +37,7 @@ def water_data(request):
     return np.loadtxt(request.param), request.param.split("/")[-1].split(".")[0]
 
 
-@pytest.fixture(autouse=True)
+@pytest.fixture()
 def _pymol_skip():
     pytest.importorskip("pymol")
 

tests/test_hydrogen_orientation.py

@@ -1,5 +1,4 @@
-"""Unit and regression test for the ConservedWaterSearch package.
-"""
+"""Unit and regression test for the ConservedWaterSearch package."""
 
 # Import package, test suite, and other packages as needed
 import numpy as np

tests/test_utils.py

@@ -98,6 +98,7 @@ def test_read_results(water_results):
         assert waterH2[0] == []
 
 
+@pytest.mark.usefixtures("_pymol_skip")
 def test_visualise_pymol():
     # Create a temporary file using with for writing and reading
     with tempfile.NamedTemporaryFile(mode="w+", suffix=".pse", delete=True) as f:
@@ -117,6 +118,7 @@ def test_visualise_pymol():
         )
 
 
+@pytest.mark.usefixtures("_pymol_skip")
 def test_visualise_pymol2():
     # Create a temporary file using with for writing and reading
     with tempfile.NamedTemporaryFile(mode="w+", suffix=".pdb", delete=True) as f:
@@ -133,6 +135,7 @@ def test_visualise_pymol2():
 
 
 # Visualise pymol tests
+@pytest.mark.usefixtures("_pymol_skip")
 @pytest.mark.parametrize(
     ("output_file", "align_file"),
     [