Use GitHub actions for continuous-integration (#28)

This change replaces GitLab CI/CD config with its GitHub actions
counterpart.

.github/workflows/check-packaging.yml

@@ -0,0 +1,20 @@
+name: Check packaging
+on:
+  pull_request:
+  push:
+    branches:
+    - main
+jobs:
+  check-packaging:
+    name: Build and check the distribution package
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Install test dependencies
+      run: |
+        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install tox-gh-actions
+    - name: Run tox
+      run: |
+        tox -e check-packaging

.github/workflows/lint.yml

@@ -0,0 +1,20 @@
+name: Static code analysis
+on:
+  pull_request:
+  push:
+    branches:
+    - main
+jobs:
+  lint:
+    name: Perform static analysis of the code
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Install test dependencies
+      run: |
+        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install tox-gh-actions
+    - name: Run tox
+      run: |
+        tox -e lint

.github/workflows/publish-sdist.yml

@@ -0,0 +1,23 @@
+name: Publish source tarball to PyPi
+on:
+  push:
+    tags:
+    - '*'
+jobs:
+  build-n-publish:
+    name: Build and publish the release on PyPI
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Build a source tarball
+      run: |
+        python setup.py sdist
+    - name: Publish distribution package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/test.yml

@@ -0,0 +1,32 @@
+name: Test the contribution
+on:
+  pull_request:
+  push:
+    branches:
+    - main
+env:
+  apt_options: -o Acquire::Retries=3
+  PETSC_DIR: /usr/lib/petscdir/petsc3.15/x86_64-linux-gnu-real
+jobs:
+  test:
+    name: Build and test the contribution
+    runs-on: ubuntu-latest
+    steps:
+    - name: Setup MPI
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: openmpi
+    - name: Checkout repository
+      uses: actions/checkout@v3
+    - name: Install system packages
+      run: |
+        sudo apt-get ${{env.apt_options}} update -y
+        sudo apt-get ${{env.apt_options}} install python3-petsc4py python3-mpi4py libopenmpi-dev libpetsc-real3.15-dev
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install tox-gh-actions
+    - name: Run tox
+      run: tox
+      env:
+        PYTHONPATH: ${{env.PETSC_DIR}}/lib/python3/dist-packages

.pre-commit-config.yaml

@@ -1,5 +1,3 @@
-default_language_version:
-  python: python3.11
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.3.0

setup.py

@@ -21,6 +21,7 @@
     "h5py",
     "networkx",
     "morphio",
+    "mpi4py",
     "vascpy",
     "matplotlib",
     "seaborn",

tox.ini

@@ -41,24 +41,18 @@ commands =
     twine check {envtmpdir}/dist/*
 
 [testenv:lint]
+skip_install = true
 allowlist_externals = bash
 deps =
+    codespell
     pre-commit
     pylint
     pylint-exit
 commands =
+    codespell --config .codespellrc -i 3 -x .codespellignorelines -w {[base]files} README.md CHANGELOG.md docs/source
     pre-commit run --all-files --show-diff-on-failure
     bash -c "pylint -j {env:PYLINT_NPROCS:1} {[base]files} || pylint-exit $?"
 
-[testenv:format]
-skip_install = true
-deps =
-    codespell
-    pre-commit
-commands =
-    codespell --config .codespellrc -i 3 -x .codespellignorelines -w {[base]files} README.md CHANGELOG.md docs/source
-    pre-commit run --all-files
-
 [testenv:docs]
 changedir = docs
 extras = docs