fix coverage reporting

- fix #287
- must install as editable for --cov=gromacs to work
- consolidated pytest-cov/coverage configuration in pyproject.toml
- updated codecov plugin to v5

Author: orbeckst

.coveragerc

@@ -102,21 +102,33 @@ jobs:
          micromamba info
          micromamba list
          cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu)
-         micromamba list | grep gromacs | grep ${{ matrix.gromacs-version }}
          micromamba list | grep python | grep ${{ matrix.python-version }}
 
     - name: Install package (with no dependencies)
       run: |
-        python -m pip install --no-deps .
+        python -m pip install --no-deps -e .
 
     - name: Run tests
+      run: >-
+        pytest -v
+        --disable-pytest-warnings
+        --durations=20
+        --low-performance
+        --cov-config=pyproject.toml
+        --cov="./gromacs"
+        --cov-report=xml
+        --cov-report=term
+        --color=yes
+        ./tests
+
+    - name: Coverage report
       run: |
-        pytest -v --disable-pytest-warnings --durations=20 --low-performance --cov=gromacs --cov-report=xml --color=yes ./tests
+        coverage report --show-missing
 
     - name: Codecov
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-        file: ./coverage.xml
+        files: ./coverage.xml
         fail_ci_if_error: false

.github/workflows/ci.yaml

@@ -9,6 +9,7 @@ build/
 .idea/
 .cache/
 .coverage
+coverage.xml
 .pytest_cache/
 dist
 gromacs.log

.gitignore

@@ -10,7 +10,8 @@ dependencies:
 - pocl
 - setuptools
 # dev tools
-- codecov
 - pytest 
 - pytest-cov 
-- pytest-pep8 
+- pytest-pep8
+- coverage
+- codecov

ci/conda-envs/test_env.yaml

@@ -10,9 +10,10 @@ coverage:
         target: 100%
       package:
         paths: ["gromacs/"]
+        target: auto
     patch:
       default: false
-      test:
+      tests:
         paths: ["tests/"]
         target: 100%
         threshold: 0%

codecov.yml

@@ -89,6 +89,23 @@ file = "gromacs/_version.py"
 extend-exclude = "tests/(test_core|fileformats/test_convert)\\.py"
 
 
+[tool.coverage.run]
+branch = true
+omit = [
+    "doc/sphinx/source/conf.py"
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "def __repr__",
+    "def _repr_html_",
+    "def __str__",
+    "raise AssertionError",
+    "raise NotImplementedError",
+    "if __name__ == .__main__.:"
+]
+
 [tool.pytest.ini_options]
 filterwarnings = [
 	       "ignore::gromacs.AutoCorrectionWarning",