Update CI

.github/workflows/CI.yml

@@ -1,4 +1,4 @@
-# All CI tasks (linting, testing, building) are maintained in this workflow file
+# All CI tasks (testing, building) are maintained in this workflow file
 # and their inter-dependencies controlled with job-level `if` and `needs` until
 # GitHub Actions allows for them to be factored out into separate, inter-dependent
 # workflow files.
@@ -7,89 +7,37 @@
 name: CI
 on: [push, pull_request, release]    # runs on all branches
 env:
-  PYTHON_VERSION: 3.9
+  PYTHON_VERSION: 3.12
 
 jobs:
-
-  lint:
-
-    runs-on: ubuntu-latest
-
-    steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ env.PYTHON_VERSION }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8
-
-    - name: Lint
-      run: flake8 . --exclude biopeaks/images,biopeaks/tests/testdata,biopeaks/resources.py --max-complexity=10 --ignore E303,C901,E203,W503,E501,W504,E129,W605,E371,E731
-
-
   test:
-
-    needs: lint
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest]
+    runs-on: ubuntu-latest
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
           python-version: ${{ env.PYTHON_VERSION }}
 
     - name: Install and configure Poetry
       uses: snok/install-poetry@v1
       with:
-        virtualenvs-create: true
-        virtualenvs-in-project: true
-
-    - name: Load cached venv
-      id: cached-pip-wheels
-      uses: actions/cache@v2
-      with:
-        path: ~/.cache
-        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-
-    - name: Install dependencies
-      run: |
-        poetry install --no-interaction --no-root
+        virtualenvs-create: false
 
     - name: Install biopeaks
-      run: poetry install --no-interaction
+      run: poetry install --no-interaction --without build
 
-    - name: Test on Windows
-      if: matrix.os == 'windows-latest'
-      shell: bash -l {0}
-      run: |
-        source $VENV
-        pytest -v
+    - name: Install system dependencies for headless testing
+      run: sudo ./.devcontainer/install_system_dependencies.sh
 
-    - name: Test on Ubuntu
-      if: matrix.os == 'ubuntu-latest'
-      run: |    # run coverage only on Ubuntu
-        source $VENV
-        sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 \
-                                libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
-                                libxcb-xinerama0 libxcb-xfixes0 libegl1 libopengl0
-        xvfb-run pytest -v --cov-config=.coveragerc --cov-report=xml --cov=biopeaks
+    - name: Test and collect coverage
+      run: pytest -v --cov-config=.coveragerc --cov-report=xml --cov=biopeaks
 
     - name: Upload coverage report
-      if: matrix.os == 'ubuntu-latest'
-      uses: codecov/codecov-action@v2
+      uses: codecov/codecov-action@v4
       with:
         file: ./coverage.xml
 
@@ -102,10 +50,10 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ env.PYTHON_VERSION }}
 
@@ -117,7 +65,7 @@ jobs:
 
     - name: Load cached venv
       id: cached-pip-wheelsy
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: ~/.cache
         key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
@@ -138,10 +86,10 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ env.PYTHON_VERSION }}
 
@@ -153,7 +101,7 @@ jobs:
 
     - name: Load cached venv
       id: cached-pip-wheels
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       with:
         path: ~/.cache
         key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
@@ -172,7 +120,7 @@ jobs:
         --icon=biopeaks\\images\\python_icon.ico biopeaks\\__main__.py
 
     - name: Upload executable
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: biopeaks_windows
         path: dist/biopeaks.exe
@@ -187,7 +135,7 @@ jobs:
     steps:
 
     - name: Download executable
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: biopeaks_windows