tests updated

Author: prathameshnium

.github/workflows/ci.yml

@@ -0,0 +1,101 @@
+name: PICA Continuous Integration
+
+on:
+  push:
+    branches: [ "main", "master" ]
+  pull_request:
+    branches: [ "main", "master" ]
+  schedule:
+    - cron: '30 1 * * 0'
+
+jobs:
+  test-and-analyze:
+    name: Test, Analyze & Build Paper
+    runs-on: ubuntu-22.04
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+
+    steps:
+    # ------------------------------------------------------------------------
+    # PHASE 1: SETUP
+    # ------------------------------------------------------------------------
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Install System Dependencies (Tkinter/XVFB)
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y python3-tk xvfb
+
+    - name: Install Python Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest flake8 pytest-cov
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install -e .
+
+    # ------------------------------------------------------------------------
+    # PHASE 2: LINT & STYLE CHECKS
+    # ------------------------------------------------------------------------
+    - name: Run Style & Syntax Check (Flake8)
+      run: |
+        echo "STEP 1: Checking for critical syntax errors..."
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        
+        echo "STEP 2: Checking for code style warnings..."
+        flake8 . --count --exit-zero --max-complexity=18 --max-line-length=127 --statistics
+
+    # ------------------------------------------------------------------------
+    # PHASE 3: SECURITY SCAN (CodeQL)
+    # ------------------------------------------------------------------------
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{ matrix.language }}"
+
+    # ------------------------------------------------------------------------
+    # PHASE 4: AUTOMATED TESTING & COVERAGE
+    # ------------------------------------------------------------------------
+    - name: Run All Tests and Generate Reports
+      run: |
+        echo "Running tests within a virtual display..."
+        xvfb-run --auto-servernum pytest --cov=. --cov-report=xml --junitxml=junit.xml -o junit_family=legacy tests/
+
+    - name: Upload Coverage Report to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        fail_ci_if_error: true
+
+    # ------------------------------------------------------------------------
+    # PHASE 5: BUILD JOSS PAPER DRAFT
+    # ------------------------------------------------------------------------
+    - name: Build JOSS Paper Draft PDF
+      uses: openjournals/openjournals-draft-action@master
+      with:
+        journal: joss
+        paper-path: paper/paper.md
+
+    - name: Upload JOSS Paper Artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: paper
+        path: paper/paper.pdf

.github/workflows/python-app.yml

@@ -12,7 +12,7 @@ permissions:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
     # 1. Check out your code
@@ -27,9 +27,8 @@ jobs:
     # 3. Install System Dependencies (Required for Tkinter/Matplotlib on Linux)
     - name: Install Tkinter System Libs
       run: |
-        sudo rm -f /etc/apt/sources.list.d/azure-cli.list
-        sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
-        sudo apt-get update && sudo apt-get install -y python3-tk
+        sudo apt-get update
+        sudo apt-get install -y python3-tk xvfb
 
     # 4. Install Your Python Dependencies
     - name: Install dependencies
@@ -54,4 +53,4 @@ jobs:
     # but since we mocked them, they should run fast!
     - name: automated test
       run: |
-        python -m pytest tests/
+        xvfb-run --auto-servernum python -m pytest tests/