Added Ahmed changes to the pipeline for comment on pr from coverage

nomad-coe · Jun 6, 2024 · c0e6553 · c0e6553 · github-actions · Jun 6, 2024
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diff --git a/.github/workflows/actions.yaml b/.github/workflows/actions.yaml
@@ -1,47 +1,54 @@
 name: install-and-test
 on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
 jobs:
   install-and-test:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-        pip install coverage coveralls
-    - name: mypy
-      run: |
-        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_simulations tests
-    - name: Test with pytest
-      run: |
-        python -m coverage run -m pytest -sv tests
-    - name: Submit to coveralls
-      continue-on-error: true
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        coveralls --service=github
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Install dependencies
+        run: |
+          pip install uv
+          uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
+      - name: mypy
+        run: |
+          python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_simulations tests
+      - name: Build coverage file
+        run: |
+          pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests/ | tee pytest-coverage.txt
+      - name: Pytest coverage comment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml
   build-and-install:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Build the package
-      run: |
-        pip install --upgrade pip
-        pip install build
-        python -m build --sdist
-    - name: Install the package
-      run: |
-        pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Build the package
+        run: |
+          pip install --upgrade pip
+          pip install build
+          python -m build --sdist
+      - name: Install the package
+        run: |
+          pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
   ruff-linting:
       runs-on: ubuntu-latest
       steps:

diff --git a/pyproject.toml b/pyproject.toml
@@ -31,9 +31,9 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
     'mypy==1.0.1',
-    'pytest==3.10.0',
-    'pytest-timeout==1.4.2',
-    'pytest-cov==2.7.1',
+    'pytest',
+    'pytest-timeout',
+    'pytest-cov',
     'ruff',
     "structlog==22.3.0",
     "lxml_html_clean>=0.1.0",
File	Stmts	Miss	Cover	Missing
src/nomad_simulations
atoms_state.py	187	18	90%	215–218, 242, 297–298, 366–367, 369, 551, 563–564, 625–629, 644–648, 655
general.py	68	5	93%	84, 148, 258–259, 269
model_method.py	259	74	71%	161–164, 167–174, 265–266, 286, 307–326, 342–368, 371–388, 740, 751, 793–800, 846, 865, 945, 1004, 1079, 1191
model_system.py	257	19	93%	507–510, 558–565, 739–740, 965–969, 975–976, 984–985, 990, 1013
numerical_settings.py	260	62	76%	160, 230, 232–233, 236–239, 243–244, 251–254, 263–266, 270–273, 275–278, 283–286, 292–295, 466–493, 568, 603–606, 630, 633, 678, 680–683, 687, 691, 738, 742–763, 818–819, 886, 895–897, 900
outputs.py	89	6	93%	201–204, 244–247, 272, 274
physical_property.py	90	1	99%	216
variables.py	61	8	87%	110, 133, 153–154, 157, 179, 202, 222
src/nomad_simulations/properties
band_gap.py	48	2	96%	149–150
band_structure.py	107	20	81%	235–267, 280, 287, 323–324, 327
energies.py	21	2	90%	51, 79
fermi_surface.py	12	1	92%	52
hopping_matrix.py	24	2	92%	69, 104
permittivity.py	45	5	89%	110–118
spectral_profile.py	254	123	52%	67–70, 105–108, 209–314, 370–382, 407–410, 430, 435–438, 480–516, 540, 587–590, 606–607, 612–618
src/nomad_simulations/utils
utils.py	66	11	83%	75–84, 93–94, 99, 102
TOTAL	1857	359	81%