infrastructure updates

* enable codecov * use github pages for docs * update gh actions
lab-cosmo · Mar 1, 2024 · f2bbd6b · f2bbd6b
1 parent 0def465
commit f2bbd6b
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Showing 9 changed files with 57 additions and 68 deletions.
diff --git a/.codecov.yml b/.codecov.yml
@@ -4,9 +4,9 @@ coverage:
   status:
     project:
       default:
-        target: 90%
+        target: 80%
     patch:
       default:
-        target: 90%
+        target: 80%
 
 comment: off
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,12 +10,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
       if: ${{ false }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
     - run: pip install tox
 
     - name: Test build integrity

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -11,11 +11,11 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: install dependencies
         run: |
@@ -27,25 +27,25 @@ jobs:
           # Use the CPU only version of torch when building/running the code
           PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
 
-      # - name: put documentation in the website
-      #   run: |
-      #     git clone https://github.com/$GITHUB_REPOSITORY --branch gh-pages gh-pages
-      #     rm -rf gh-pages/.git
-      #     cd gh-pages
+      - name: put documentation in the website
+        run: |
+          git clone https://oauth2:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY --branch gh-pages gh-pages
+          rm -rf gh-pages/.git
+          cd gh-pages
 
-      #     REF_KIND=$(echo $GITHUB_REF | cut -d / -f2)
-      #     if [[ "$REF_KIND" == "tags" ]]; then
-      #         TAG=${GITHUB_REF#refs/tags/}
-      #         mv ../docs/build/html $TAG
-      #     else
-      #         rm -rf latest
-      #         mv ../docs/build/html latest
-      #     fi
+          REF_KIND=$(echo $GITHUB_REF | cut -d / -f2)
+          if [[ "$REF_KIND" == "tags" ]]; then
+              TAG=${GITHUB_REF#refs/tags/}
+              mv ../docs/build/html $TAG
+          else
+              rm -rf latest
+              mv ../docs/build/html latest
+          fi
 
-      # - name: deploy to gh-pages
-      #   if: github.event_name == 'push'
-      #   uses: peaceiris/actions-gh-pages@v3
-      #   with:
-      #     github_token: ${{ secrets.GITHUB_TOKEN }}
-      #     publish_dir: ./gh-pages/
-      #     force_orphan: true
+      - name: deploy to gh-pages
+        if: github.event_name == 'push'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./gh-pages/
+          force_orphan: true
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -9,12 +9,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
     - run: pip install tox
 
     - name: Lint the code

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -15,32 +15,32 @@ jobs:
           # - os: ubuntu-22.04
           #   python-version: "3.8"
           - os: ubuntu-22.04
-            python-version: "3.11"
+            python-version: "3.12"
           # - os: macos-11
-          #   python-version: "3.8"
-          # - os: macos-11
-          #   python-version: "3.11"
-          # - os: windows-2019
-          #   python-version: "3.8"
+          #   python-version: "3.12"
           # - os: windows-2019
-          #   python-version: "3.11"
+          #   python-version: "3.12"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: pip install tox
+    - run: pip install tox coverage[toml]
 
     - name: run Python tests
-      run: tox -e tests
+      run: |
+        tox -e tests
+        coverage xml
       env:
         # Use the CPU only version of torch when building/running the code
         PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
 
-    - name: Upload codecoverage
-      uses: codecov/codecov-action@v3
+    - name: upload to codecov.io
+      uses: codecov/codecov-action@v4
       with:
-        files: ./tests/coverage.xml
+        fail_ci_if_error: true
+        files: tests/coverage.xml
+        token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,11 +8,8 @@ version: 2
 # Set the version of Python and other tools we need
 build:
   os: ubuntu-22.04
-  apt_packages:
-    - cmake
   tools:
-    python: "3.10"
-    rust: "1.64"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -28,5 +25,4 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        # The documentation runs "examples" to produce outputs via sphinx-gallery.
-        - examples
+        - metatensor
diff --git a/README.rst b/README.rst
@@ -7,7 +7,7 @@ Particle-mesh based calculation of Long Distance Equivariants.
 
 For details, tutorials, and examples, please have a look at our `documentation`_.
 
-.. _`documentation`: https://meshlode.readthedocs.io
+.. _`documentation`: https://lab-cosmo.github.io/MeshLODE/latest
 
 .. marker-installation
 
@@ -53,15 +53,14 @@ Thanks goes to all people that make MeshLODE possible:
 .. image:: https://contrib.rocks/image?repo=lab-cosmo/MeshLODE
    :target: https://github.com/lab-cosmo/MeshLODE/graphs/contributors
 
-.. |tests| image:: https://github.com/lab-cosmo/MeshLODE/workflows/Test/badge.svg
+.. |tests| image:: https://github.com/lab-cosmo/MeshLODE/workflows/Tests/badge.svg
    :alt: Github Actions Tests Job Status
-   :target: (https://github.com/lab-cosmo/MeshLODE/\
-                actions?query=workflow%3ATests)
+   :target: https://github.com/lab-cosmo/MeshLODE/actions?query=workflow%3ATests
 
-.. |codecov| image:: https://codecov.io/gh/lab-cosmo/meshlode/branch/main/graph/badge.svg?token=UZJPJG34SM
+.. |codecov| image:: https://codecov.io/gh/lab-cosmo/meshlode/branch/main/graph/badge.svg
    :alt: Code coverage
    :target: https://codecov.io/gh/lab-cosmo/meshlode/
 
 .. |docs| image:: https://img.shields.io/badge/documentation-latest-sucess
-   :alt: Python
-   :target: https://meshlode.readthedocs.io
+   :alt: Documentation
+   :target: https://lab-cosmo.github.io/MeshLODE/latest/
diff --git a/pyproject.toml b/pyproject.toml
@@ -54,6 +54,7 @@ repository = "https://github.com/lab-cosmo/MeshLODE"
 issues = "https://github.com/lab-cosmo/MeshLODE/issues"
 
 [tool.coverage.report]
+show_missing = true
 include = [
     "src/meshlode/*"
 ]

diff --git a/tox.ini b/tox.ini
@@ -12,6 +12,7 @@ lint_folders =
 
 [testenv]
 passenv = *
+test_options = --cov --cov-append --cov-report= --import-mode=append
 
 [testenv:build]
 description = Asserts package build integrity.
@@ -40,15 +41,11 @@ extras = metatensor
 
 commands =
     # Run unit tests
-    pytest --cov --import-mode=append {posargs}
+    pytest {[testenv]test_options} {posargs}
 
     # Run documentation tests
     pytest --doctest-modules --pyargs meshlode {posargs}
 
-# after executing the pytest assembles the coverage reports
-commands_post =
-    coverage xml
-
 [testenv:tests-min]
 description = Run the minimal core tests with pytest and {basepython}.
 usedevelop = true
@@ -59,11 +56,7 @@ deps =
 
 commands =
     # Run unit tests
-    pytest --cov --import-mode=append {posargs}
-
-# after executing the pytest assembles the coverage reports
-commands_post =
-    coverage xml
+    pytest {[testenv]test_options} {posargs}
 
 [testenv:lint]
 description = Run linters and type checks