Refactor GitHub Actions workflow for Python testing

Updated the GitHub Actions workflow to use a matrix for Python versions, added pytest-cov for coverage reporting, and improved linting and testing commands.

Author: ryan-odea

.github/workflows/python-app.yml

@@ -1,7 +1,6 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
+name: Test pySEQ
 
 on:
   push:
@@ -13,27 +12,37 @@ permissions:
   contents: read
 
 jobs:
-  build:
-
+  test:
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: ${{ matrix.python-version }}
+    
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        pip install flake8 pytest pytest-cov
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    
+    - name: Install pySEQ package
+      run: |
+        pip install -e .
+    
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        # exit-zero treats all errors as warnings
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    
     - name: Test with pytest
       run: |
-        pytest
+        pytest tests/ -v --cov=pySEQ --cov-report=term-missing