Rewrite Jupyter Notebook examples as Python examples

.github/workflows/main.yml

@@ -280,9 +280,10 @@ jobs:
         path: interfaces/dotnet/coveragereport*
         retention-days: 5
     - name: Upload Coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         verbose: true
+        token: ${{secrets.CODECOV_TOKEN}}
         files: ./coverage.xml,./build/pycov.xml,./interfaces/dotnet/coverage.cobertura.xml
         fail_ci_if_error: true
 
@@ -315,21 +316,27 @@ jobs:
             libblas-dev liblapack-dev libhdf5-dev libfmt-dev libsundials-dev
       - name: Install conda dependencies
         run: |
-          mamba install -q doxygen=1.9.7 scons pip
+          mamba install -q doxygen=1.9.7 scons pip scikits.odes
       - name: Upgrade pip
         run: pip install -U pip setuptools wheel
       - name: Install Python dependencies
         run: |
           pip install ruamel.yaml scons numpy cython 'sphinx>=7.2,<8' \
             sphinxcontrib-matlabdomain sphinxcontrib-doxylink sphinxcontrib-bibtex \
             pydata-sphinx-theme==0.14.1 sphinx-argparse sphinx_design myst-nb \
-            sphinx-copybutton matplotlib pandas scipy pint
+            sphinx-copybutton matplotlib pandas scipy pint coolprop graphviz
           pip install "git+https://github.com/sphinx-gallery/sphinx-gallery.git@master"
           pip install "git+https://github.com/Cantera/sphinx-tags.git@main"
       - name: Build Cantera
         run: scons build -j2 debug=n optimize=y use_pch=n
       - name: Build documentation
-        run: scons sphinx doxygen logging=debug
+        run: |
+          scons sphinx doxygen logging=debug \
+            sphinx_options="-W --keep-going --warning-file=sphinx-warnings.txt"
+      - name: Show Sphinx warnings
+        run: |
+          cat sphinx-warnings.txt
+        if: failure()
       - name: Ensure 'scons help' options work
         run: |
           scons help --options
@@ -409,12 +416,19 @@ jobs:
         run: python3 -m pip install -U pip setuptools wheel
       - name: Install Python dependencies
         run: |
-            python3 -m pip install numpy ruamel.yaml pandas pyarrow matplotlib scipy pint graphviz
+            python3 -m pip install numpy ruamel.yaml pandas pyarrow matplotlib scipy \
+              pint graphviz CoolProp
             python3 -m pip install --pre --no-index --find-links dist cantera
       - name: Run the examples
-        # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part
+        # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part.
+        # Skip 1D_packed_bed.py due to difficulty installing scikits.odes.
+        # Skip continuous_reactor.py due to thermo warnings
+        # Increase figure limit to handle flame_speed_convergence_analysis.py.
         run: |
           ln -s libcantera_shared.so build/lib/libcantera_shared.so.3
+          rm samples/python/reactors/1D_packed_bed.py
+          rm samples/python/reactors/continuous_reactor.py
+          echo "figure.max_open_warning: 100" > matplotlibrc
           export LD_LIBRARY_PATH=build/lib
           find samples/python -type f -iname "*.py" \
           -exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +

AUTHORS

@@ -60,6 +60,7 @@ Ingmar Schoegl (@ischoegl), Louisiana State University
 Santosh Shanbhogue (@santoshshanbhogue), Massachusetts Institute of Technology
 Travis Sikes (@tsikes)
 Harsh Sinha (@sin-ha)
+Sai Krishna Sirumalla (@skrsna), Northeastern University
 David Sondak
 Raymond Speth (@speth), Massachusetts Institute of Technology
 Su Sun (@ssun30), Northeastern University