Merge pull request #429 from bioimage-io/add_coverage

add coverage reporting

.github/workflows/build.yaml

@@ -85,6 +85,23 @@ jobs:
       run: pip install --no-deps -e .
     - name: pytest-spec-main
       run: pytest --disable-pytest-warnings
+    - if: matrix.python-version == '3.12' && github.event_name == 'pull_request'
+      uses: orgoro/[email protected]
+      with:
+        coverageFile: coverage.xml
+        token: ${{ secrets.GITHUB_TOKEN }}
+    - if: matrix.python-version == '3.12' && github.ref == 'refs/heads/main'
+      run: |
+        pip install genbadge[coverage]
+        genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
+        coverage html -d dist/coverage
+    - if: matrix.python-version == '3.12' && github.ref == 'refs/heads/main'
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage
+        retention-days: 1
+        path: dist
+
 
   test-tf:
     runs-on: ubuntu-latest
@@ -140,6 +157,10 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: coverage
+          path: dist
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'

.gitignore

@@ -1,3 +1,5 @@
+__pycache__/
+.coverage
 .env
 .idea/
 .tox/
@@ -6,6 +8,7 @@
 **/tmp
 build/
 cache
+coverage.xml
 dist/
 docs/
 typings/pooch/

README.md

@@ -4,6 +4,7 @@
 [![downloads](https://static.pepy.tech/badge/bioimageio.core)](https://pepy.tech/project/bioimageio.core)
 [![conda-forge downloads](https://img.shields.io/conda/dn/conda-forge/bioimageio.core.svg?label=conda-forge)](https://anaconda.org/conda-forge/bioimageio.core/)
 ![code style](https://img.shields.io/badge/code%20style-black-000000.svg)
+[![coverage](https://bioimage-io.github.io/core-bioimage-io-python/coverage/coverage-badge.svg)](https://bioimage-io.github.io/core-bioimage-io-python/coverage/index.html)
 
 # core-bioimage-io-python
 

dev/env-py38.yaml

@@ -25,6 +25,7 @@ dependencies:
   - pydantic-settings
   - pyright
   - pytest
+  - pytest-cov
   - pytest-xdist
   - python-dotenv
   - python=3.8 # changed

dev/env-tf.yaml

@@ -25,6 +25,7 @@ dependencies:
   - pydantic-settings
   - pyright
   - pytest
+  - pytest-cov
   - pytest-xdist
   - python-dotenv
   # - python=3.9  # removed

dev/env-wo-python.yaml

@@ -25,6 +25,7 @@ dependencies:
   - pydantic-settings
   - pyright
   - pytest
+  - pytest-cov
   - pytest-xdist
   - python-dotenv
   # - python=3.9  # removed

dev/env.yaml

@@ -25,6 +25,7 @@ dependencies:
   - pydantic-settings
   - pyright
   - pytest
+  - pytest-cov
   - pytest-xdist
   - python-dotenv
   - python=3.9

pyproject.toml

@@ -30,7 +30,7 @@ typeCheckingMode = "strict"
 useLibraryCodeForTypes = true
 
 [tool.pytest.ini_options]
-addopts = " -n auto --capture=no --doctest-modules --failed-first"
+addopts = "--cov=bioimageio --cov-report=xml -n auto --capture=no --doctest-modules --failed-first"
 
 [tool.ruff]
 line-length = 88

setup.py

@@ -61,6 +61,7 @@
             "pdoc",
             "psutil",  # parallel pytest with 'pytest -n auto'
             "pyright",
+            "pytest-cov",
             "pytest-xdist",  # parallel pytest
             "pytest",
             "torch>=1.6",