Merge pull request #5 from SimVascular/master

Update from master

.github/workflows/gui.yml

@@ -0,0 +1,49 @@
+# This workflow uses Cypress for end-to-end testing of the 0D model GUI.
+
+name: GUI-tests
+
+on: [push, pull_request]
+
+jobs:
+  cypress-run:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        working-directory: tests/cypress
+        run: npm install
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'  # Use the Python version compatible with your Flask app
+
+      - name: Install Flask dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flask
+
+      - name: Start Flask Application
+        run: |
+          cd applications/svZeroDGUI
+          FLASK_APP=app.py flask run --host=0.0.0.0 --port=8902 &
+        env:
+          FLASK_ENV: development
+
+      - name: Run Cypress tests
+        uses: cypress-io/github-action@v5
+        with:
+          start: npm start
+          working-directory: tests/cypress

.github/workflows/test.yml

@@ -23,10 +23,13 @@ jobs:
           #alias conda="$CONDA/bin/conda"
           conda create -n zerod python=3.11.4
           conda run -n zerod pip install -e ".[dev]"
+      - name: Install Networkx
+        run: |
+            conda run -n zerod pip install networkx
       - name: Test the build
         run: |
           cd tests
-          conda run -n zerod pytest -v --durations=0
+          conda run -n zerod pytest -v --durations=0 --ignore=test_dirgraph.py
       - name: Build using CMake
         run: |
           mkdir Release
@@ -51,7 +54,7 @@ jobs:
           cmake -DENABLE_COVERAGE=ON ..
           make -j2
           cd ../tests
-          conda run -n zerod pytest -v --durations=0 --coverage
+          conda run -n zerod pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
           cd ../Release
           make coverage
       - name: Save coverage report

.github/workflows/test_visualization.yml

@@ -0,0 +1,40 @@
+name: Test Visualization Application
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r tests/requirements.txt
+
+      - name: Install Graphviz
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y graphviz
+
+      - name: Install Graphviz (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install graphviz
+
+      - name: Run tests
+        run: |
+          pytest tests/test_dirgraph.py

.gitignore

@@ -28,10 +28,13 @@ Release*/
 Debug*/
 externals/
 *.so
-build
+build*/
 
 # IDE
 .cproject
 .project
 .settings
 *.swp
+
+# Node modules (for directed graph visualization)
+node_modules/

CMakeLists.txt

@@ -177,6 +177,7 @@ add_executable(svzerodsolver applications/svzerodsolver.cpp
 )
 
 add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp
+  $<TARGET_OBJECTS:svzero_algebra_library> 
   $<TARGET_OBJECTS:svzero_optimize_library> 
   $<TARGET_OBJECTS:svzero_model_library> 
 )

applications/svZeroDGUI/app.py

@@ -0,0 +1,22 @@
+"""
+app.py
+
+This script sets up a basic Flask web server for serving static files and handling
+HTTP requests. It includes:
+
+- Initialization of the Flask application.
+- A route for serving the main HTML file (`index.html`) when accessing the root URL ('/').
+- Configuration to run the application with debugging enabled on port 8902.
+"""
+
+from flask import Flask, jsonify, request
+
+app = Flask(__name__)
+
+@app.route('/')
+def index():
+    return app.send_static_file('index.html')
+
+if __name__ == "__main__":
+    # Generate a random port number between 5000 and 9999
+    app.run(debug=True, port=8902)