Add GitHub workflows back

.github/codecov.yml

@@ -0,0 +1,11 @@
+# configuration for code coverage testing with codecov
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+codecov: 
+ token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/codechecks.yml

@@ -0,0 +1,17 @@
+# This workflow checks for compliance with the Google C++ style guide.
+name: Codechecks
+on: [push, pull_request]
+jobs:
+  clang-format:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          brew install clang-format
+      - name: Run clang-format
+        run: |
+          mkdir Release
+          cd Release
+          cmake ..
+          make codecheck

.github/workflows/documentation.yml

@@ -0,0 +1,30 @@
+# This workflow builds and deploys the html documentation for svZeroDSolver.
+name: Documentation
+on: [push, pull_request]
+permissions:
+  contents: write
+jobs:
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Make build directory
+        run: mkdir docs/build
+      - name: Build doxygen documentation
+        continue-on-error: false
+        uses: mattnotmitt/doxygen-action@edge
+        with:
+          working-directory: '.'
+          doxyfile-path: 'docs/Doxyfile'
+          enable-latex: true
+      - name: Save documentation
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: ./docs/build/html
+      - name: Deploy documentation
+        if: github.ref == 'refs/heads/master'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/build/html

.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

@@ -0,0 +1,170 @@
+# This workflow builds and tests svZeroDSolver. It is built and tested on
+# different versions of ubuntu and macOS.
+name: Build and test
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest, windows-latest]
+        version: [13] # GCC version
+      fail-fast: false
+    env:
+      GCC_V: ${{ matrix.version }}
+      CONDA_ENV: zerod
+      PYTHONPATH: ${{ github.workspace }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: ${{env.CONDA_ENV}}
+          python-version: "3.11.4"
+      - name: Install ubuntu dependencies
+        if: startsWith(matrix.os, 'ubuntu')
+        run: sudo apt update && sudo apt install build-essential cmake lcov
+
+      - name: Install dependencies to get correct version numbers (Ubuntu)
+        if: startsWith(matrix.os, 'ubuntu')
+        run: conda install -c conda-forge libstdcxx-ng=${GCC_V} gcc=${GCC_V}
+
+      - name: Install dependencies to get correct version numbers (MacOS)
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          brew install gcc@${GCC_V}
+          ln -s /usr/local/bin/gcc-${GCC_V} /usr/local/bin/gcc
+
+      - name: Install dependencies for windows
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          choco install mingw --no-progress
+          conda install -y -c conda-forge cmake graphviz python-graphviz pydot
+          pip install --upgrade cmake-setuptools
+
+      - name: Install POISX-like svZeroDSolver
+        if: ${{!startsWith(matrix.os, 'windows')}}
+        run: conda run pip install -e ".[dev]"
+
+      - name: Install Windows svZeroDSolver
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          $Env:CMAKE_GENERATOR = 'MinGW Makefiles'
+          Write-Host "→ Using CMAKE_GENERATOR = $Env:CMAKE_GENERATOR"
+          pip install --no-build-isolation -v .[dev]
+          pip show pysvzerod
+
+      - name: Install Networkx
+        run: |
+            conda run pip install networkx
+
+      - name: Test the build
+        run: |
+          cd tests
+          conda run pytest -v --durations=0 --ignore=test_dirgraph.py
+
+      - name: Build using CMake for POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
+        run: |
+          mkdir Release
+          cd Release
+          cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_DISTRIBUTION=ON ..
+          make -j2
+
+      - name: Build using CMake for Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          mkdir Release
+          cd Release
+          cmake -G "MinGW Makefiles" `
+                -DCMAKE_BUILD_TYPE=Release `
+                -DENABLE_DISTRIBUTION=ON `
+                ..
+          cmake --build . --parallel 2
+
+      - name: Test interface POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
+        run: |
+          cd tests/test_interface
+          mkdir build_tests
+          cd build_tests
+          cmake ../
+          make -j2
+          cd test_01
+          ./svZeroD_interface_test01 ../../../../Release ../../test_01/svzerod_3Dcoupling.json
+          cd ../test_02
+          ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
+
+      - name: Test interface Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          cd tests/test_interface
+          mkdir build_tests
+          cd build_tests
+          cmake -G "MinGW Makefiles" ..
+          cmake --build . --parallel 2
+          cd test_01
+          ./svZeroD_interface_test01.exe `
+            ../../../../Release `
+            ../../test_01/svzerod_3Dcoupling.json
+
+          cd ../test_02
+          ./svZeroD_interface_test02 `
+            ../../../../Release `
+            ../../test_02/svzerod_tuned.json
+
+      - name: Generate code coverage
+        if: startsWith(matrix.os, 'ubuntu-22.04')
+        run: |
+          cd Release
+          cmake -DENABLE_COVERAGE=ON ..
+          make -j2
+          cd ../tests
+          conda run pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
+          cd ../Release
+          make coverage
+
+      - name: Save coverage report
+        if: startsWith(matrix.os, 'ubuntu-22.04')
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage_report
+          path: Release/coverage
+
+      - name: Upload coverage reports to Codecov
+        if: startsWith(matrix.os, 'ubuntu-22.04')
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Build installer POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
+        run: |
+          cd Release
+          cpack
+          cp distribution/svZeroDSolver_* ..
+
+      - name: Install NSIS
+        if: startsWith(matrix.os, 'windows')
+        run: choco install nsis -y
+
+      - name: Build installer Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          # NSIS will be at C:\Program Files (x86)\NSIS\Bin
+          echo "C:\Program Files (x86)\NSIS\Bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+          cd Release
+          cpack -C Release
+          Copy-Item distribution\svZeroDSolver_* -Destination ..\
+
+      - name: Upload installer
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.os }} installer
+          path: svZeroDSolver_*
+          if-no-files-found: error

.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

CMakeLists.txt

@@ -65,10 +65,13 @@ endif()
 # -----------------------------------------------------------------------------
 # Eigen is a header-only C++ template library for linear algebra.
 #
+# Tell FetchContent not to re-check for updates once Eigen is downloaded
+set(FETCHCONTENT_UPDATES_DISCONNECTED TRUE)
+
 FetchContent_Declare(
   Eigen
   GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
-  GIT_TAG master
+  GIT_TAG 3.4.0
   GIT_SHALLOW TRUE
   GIT_PROGRESS TRUE)
 

applications/pysvzerod.cpp

@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
-// SPDX-License-Identifier: BSD-3-Clause
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
+// University of California, and others. SPDX-License-Identifier: BSD-3-Clause
 /**
  * @file pysvzerod.cpp
  * @brief Python interface for svZeroDSolver
@@ -65,9 +65,8 @@ PYBIND11_MODULE(pysvzerod, m) {
     py::module_ sys = py::module_::import("sys");
     auto argv = sys.attr("argv").cast<std::vector<std::string>>();
     if (argv.size() != 3) {
-      std::cout
-          << "Usage: svzerodsolver path/to/config.json path/to/output.csv"
-          << std::endl;
+      std::cout << "Usage: svzerodsolver path/to/config.json path/to/output.csv"
+                << std::endl;
       exit(1);
     }
     std::ifstream ifs(argv[1]);

applications/svzerodcalibrator.cpp

@@ -1,5 +1,5 @@
-// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
-// SPDX-License-Identifier: BSD-3-Clause
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
+// University of California, and others. SPDX-License-Identifier: BSD-3-Clause
 /**
  * @file svzerodcalibrator.cpp
  * @brief Main routine for svZeroDCalibrator
@@ -26,7 +26,8 @@ int main(int argc, char* argv[]) {
   std::ifstream input_file(input_file_name);
 
   if (!input_file.is_open()) {
-    std::cerr << "[svzerodcalibrator] Error: The input file '" << input_file_name << "' cannot be opened." << std::endl;
+    std::cerr << "[svzerodcalibrator] Error: The input file '"
+              << input_file_name << "' cannot be opened." << std::endl;
     return 1;
   }
 
@@ -36,16 +37,19 @@ int main(int argc, char* argv[]) {
   try {
     output_config = calibrate(config);
   } catch (const nlohmann::json::parse_error& e) {
-    std::cerr << "[svzerodcalibrator] Error: The input file '" << input_file_name
-    << "' does not have the parameters needed by the calibrate program." << std::endl;
+    std::cerr
+        << "[svzerodcalibrator] Error: The input file '" << input_file_name
+        << "' does not have the parameters needed by the calibrate program."
+        << std::endl;
     return 1;
   }
 
   // Write optimized simulation config
   std::ofstream out_file(output_file_name);
 
   if (!out_file.is_open()) {
-    std::cerr << "[svzerodcalibrator] Error: The output file '" << output_file_name << "' cannot be opened." << std::endl;
+    std::cerr << "[svzerodcalibrator] Error: The output file '"
+              << output_file_name << "' cannot be opened." << std::endl;
     return 1;
   }