Merge pull request #81 from ab5424/restructure-testing

Restructure testing

.github/workflows/test.yml

@@ -21,30 +21,36 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.11"]
+        version:
+          - { python: "3.9", resolution: lowest-direct, extra: "tests,ovito,ase,pymatgen" }
+          - { python: "3.11", resolution: highest, extra: "tests,ovito,ase,pymatgen" }
+        # Add macOS without optional dependencies, running only on python 3.10
+        include:
+          - os: macos-latest
+            version: { python: "3.10", resolution: highest, extra: "tests,strict" }
 
     runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.version.python }}
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.version.python }}
           cache: pip
       - name: Install dependencies
         run: |
           pip install uv
-          uv pip install packaging -e .[strict,dev,ovito,ase,pymatgen] --system
+          uv pip install -e .[${{ matrix.version.extra }}] --resolution=${{ matrix.version.resolution }} --system
       # Fix ImportError: libEGL.so.1: ...
-      - if: runner.os == 'Linux'
+      - name: Install libegl1-mesa-dev on Linux
+        if: runner.os == 'Linux'
         run: |
           sudo apt update && sudo apt install -y libegl1-mesa-dev
       - name: pytest
         run: |
           pytest --cov=agility --cov-report=xml tests
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
-        if: matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest'
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

agility/analysis.py

@@ -13,13 +13,14 @@
 
 import numpy as np
 import pandas as pd
-from typing_extensions import Self
 
 from agility.minimiser import minimise_lmp
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
+    from typing_extensions import Self
+
 available_backends = Literal["ovito", "pymatgen", "babel", "pyiron", "ase", "lammps"]
 # https://github.com/pyiron/pylammpsmpi
 

pyproject.toml

@@ -8,7 +8,7 @@ version = "0.0.3"
 description = "Analysis tool for simulations of grain boundaries and interfaces"
 authors = [{name = "Alexander Bonkowski", email = "[email protected]"}]
 maintainers = [{name = "Alexander Bonkowski"}]
-dependencies = ["numpy", "pandas", "scipy", "seaborn"]
+dependencies = ["numpy>=1.25", "pandas>=2", "scipy>=1.12", "seaborn>=0.13"]
 requires-python = ">=3.9"
 readme = "README.md"
 license = {file = "LICENSE"}
@@ -39,23 +39,19 @@ strict = [
     "scipy==1.13.1",
     "seaborn==0.13.2",
 ]
-dev = [
-    "mypy",
-    "coverage",
-    "pre-commit",
-    "pytest-cov",
-    "pytest-split",
-    "pytest",
-    "ruff",
+tests = [
+    "pytest-cov>=5",
+    "pytest-split>=0.9",
+    "pytest>=8",
 ]
 ovito = [
-    "ovito",
+    "ovito>=3.8",
 ]
 ase = [
     "ase>=3.23",
 ]
 pymatgen = [
-    "pymatgen",
+    "pymatgen>=2024",
 ]
 
 [tool.setuptools.packages.find]

tests/analysis/test_analysis.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+from importlib.util import find_spec
 from pathlib import Path
 from unittest import TestCase
 
@@ -15,6 +16,7 @@
 TEST_FILES_DIR = Path(MODULE_DIR / ".." / ".." / "tests" / "files")
 
 
+@pytest.mark.skipif(not find_spec("ovito"), reason="ovito not installed")
 class TestGBStructure(TestCase):
     """Test the GBStructure class."""
 
@@ -62,6 +64,7 @@ def test_grain_segmentation(self) -> None:
         assert self.data.pipeline.compute().attributes["GrainSegmentation.grain_count"] == 6
 
 
+@pytest.mark.skipif(not find_spec("ovito"), reason="ovito not installed")
 class TestGBStructureOxide(TestCase):
     """Test the GBStructure class for an oxide."""
 

tests/plotting/test_plotting.py

@@ -2,10 +2,11 @@
 
 from __future__ import annotations
 
+from importlib.util import find_spec
 from pathlib import Path
 from unittest import TestCase
 
-from PySide6.QtGui import QImage
+import pytest
 
 from agility.analysis import GBStructure
 from agility.plotting import render_ovito
@@ -14,6 +15,7 @@
 TEST_FILES_DIR = Path(MODULE_DIR / ".." / ".." / "tests" / "files")
 
 
+@pytest.mark.skipif(not find_spec("ovito"), reason="ovito not installed")
 class TestPlotting(TestCase):
     """Test the Plotting class."""
 
@@ -26,6 +28,8 @@ def setUp(self) -> None:
     def test_render_ovito(self) -> None:
         """Test the render_ovito method."""
         image = render_ovito(self.data.pipeline)
+        from PySide6.QtGui import QImage
+
         assert isinstance(image, QImage)
         assert image.width() == 282
         assert image.height() == 262