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JacksonBurnsJacksonBurns
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fix juliacall incompatibilities; see extended
 - CI updates: run CI on all platforms with and without RMS, split regression tests into separate job after that so that regression is only checked on one platform - installation updates: make RMG-Py actually `pip`-installable as `reactionmechanismgenerator` to avoid having to set the `PYTHONPATH` variable, which breaks `juliacall`, add a convenience script for installing RMS - code changes: fix some small bugs in the new optional-rms setup (one missed `requires_rms` and one incorrect rebase)
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‎.github/workflows/CI.yml‎

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@@ -49,21 +49,23 @@ env:
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# main with the name of the branch
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RMG_DATABASE_BRANCH: main
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jobs:
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build-and-test:
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9"]
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os: [macos-13, macos-latest, ubuntu-latest]
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include-rms: ["", "with RMS"]
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exclude:
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- os: macos-latest # needs Cantera 3 b/c x86 emulation breaks with Julia
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include-rms: 'with RMS'
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- os: macos-13 # GitHub's runners just aren't up to the task of installing Julia
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include-rms: 'with RMS'
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runs-on: ${{ matrix.os }}
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name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }}
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name: Python ${{ matrix.python-version }} ${{ matrix.os }} Build and Test ${{ matrix.include-rms }}
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# skip scheduled runs from forks
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if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
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env:
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# This is true only if this is a reference case for the regression testing:
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REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
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defaults:
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run:
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shell: bash -l {0}
@@ -83,73 +85,128 @@ jobs:
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miniforge-version: latest
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python-version: ${{ matrix.python-version }}
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activate-environment: rmg_env
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use-mamba: true
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auto-update-conda: true
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show-channel-urls: true
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channels: conda-forge,cantera,rmg
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conda-remove-defaults: "true"
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# list the environment for debugging purposes
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- name: mamba info
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- name: conda info
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run: |
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mamba info
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mamba list
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conda info
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conda list
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# Clone RMG-database
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- name: Clone RMG-database
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run: |
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cd ..
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git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
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# modify env variables as directed in the RMG installation instructions
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- name: Set Environment Variables
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run: |
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RUNNER_CWD=$(pwd)
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echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
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echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
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# RMG build step
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- name: make RMG
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run: |
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make clean
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make
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# Setup Juliaup
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- name: Set Julia paths
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run: |
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# echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
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# echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
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# echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
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# echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
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# echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
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# echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
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# echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
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# echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
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echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
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# echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
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- run: make install
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- name: Setup Juliaup
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if: matrix.include-rms == 'with RMS'
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uses: julia-actions/install-juliaup@v2
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with:
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channel: '1.9'
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- name: Check Julia version
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run: julia --version
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- name: Set some env vars
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if: matrix.include-rms == 'with RMS'
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run: |
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# https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-Python-and-required-Python-packages-installed
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echo "JULIA_CONDAPKG_BACKEND=Null" >> $GITHUB_ENV
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echo "JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python" >> $GITHUB_ENV
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# RMS installation and linking to Julia
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- name: Install and link Julia dependencies
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if: matrix.include-rms == 'with RMS'
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timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
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# JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
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run: . install_rms.sh
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127+
- name: Set some other env vars
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if: matrix.include-rms == 'with RMS'
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run: |
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mamba install conda-forge::pyjuliacall
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julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
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# ensure that juliacall in Python uses the correct julia executable and packages: https://github.com/JuliaPy/PyJuliaPkg?tab=readme-ov-file#which-julia-gets-used
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echo "PYTHON_JULIAPKG_EXE=$(which julia)" >> $GITHUB_ENV
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echo "PYTHON_JULIAPKG_PROJECT=$HOME/.julia/packages" >> $GITHUB_ENV
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- name: Install Q2DTor
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run: echo "" | make q2dtor
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# non-regression testing
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- name: Run Unit, Functional, and Database Tests
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# aggregate into one command so we only have to eat the collection time once
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run: make test-all
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regression-test:
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needs: build-and-test
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runs-on: ubuntu-latest
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name: Regression Test
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# skip scheduled runs from forks
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if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
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env:
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# This is true only if this is a reference case for the regression testing:
149+
REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Checkout RMG-Py
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uses: actions/checkout@v4
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- name: Setup Miniforge Python 3.9
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uses: conda-incubator/setup-miniconda@v3
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with:
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environment-file: environment.yml
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miniforge-variant: Miniforge3
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miniforge-version: latest
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python-version: 3.9
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activate-environment: rmg_env
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auto-update-conda: true
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show-channel-urls: true
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channels: conda-forge,cantera,rmg
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conda-remove-defaults: "true"
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# list the environment for debugging purposes
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- name: conda info
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run: |
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conda info
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conda list
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176+
# Clone RMG-database
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- name: Clone RMG-database
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run: |
179+
cd ..
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git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
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182+
# RMG build step
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- run: make install
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185+
- name: Setup Juliaup
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uses: julia-actions/install-juliaup@v2
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with:
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channel: '1.9'
189+
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- name: Set some env vars
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run: |
192+
# https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-Python-and-required-Python-packages-installed
193+
echo "JULIA_CONDAPKG_BACKEND=Null" >> $GITHUB_ENV
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echo "JULIA_PYTHONCALL_EXE=$CONDA_PREFIX/bin/python" >> $GITHUB_ENV
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# RMS installation and linking to Julia
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- name: Install and link Julia dependencies
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timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
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run: . install_rms.sh
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- name: Set some other env vars
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run: |
203+
# ensure that juliacall in Python uses the correct julia executable and packages: https://github.com/JuliaPy/PyJuliaPkg?tab=readme-ov-file#which-julia-gets-used
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echo "PYTHON_JULIAPKG_EXE=$(which julia)" >> $GITHUB_ENV
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echo "PYTHON_JULIAPKG_PROJECT=$HOME/.julia/packages" >> $GITHUB_ENV
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- name: Install Q2DTor
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run: echo "" | make q2dtor
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# Regression Testing - Test Execution
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- name: Regression Tests - Execution
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id: regression-execution
@@ -322,14 +379,14 @@ jobs:
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- name: Upload regression summary artifact
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# the annotate workflow uses this artifact to add a comment to the PR
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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if : ${{ github.event_name == 'pull_request' }}
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with:
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name: regression_summary
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path: summary.txt
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- name: Upload Comparison Results
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: regression_test_comparison_results
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path: |
@@ -339,7 +396,7 @@ jobs:
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- name: Code coverage install and run
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if: success() || ( failure() && steps.regression-execution.conclusion == 'success' )
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run: |
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mamba install -y -c conda-forge codecov
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conda install -y -c conda-forge codecov
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codecov
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build-and-push-docker:

‎.github/workflows/pure_python_ci.yml‎

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This file was deleted.

‎.gitignore‎

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@@ -4,13 +4,18 @@
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#
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################################################################################
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# build dir
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reactionmechanismgenerator.egg-info/
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# MacOS files
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.DS_Store
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# Compiled Python modules
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*.pyc
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*.so
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*.pyd
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# and intermediate source files
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*.c
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# Image files generated by RMG
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*.png

‎Makefile‎

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CC=gcc
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CXX=g++
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.PHONY : all minimal main solver check pycheck arkane clean install decython documentation test q2dtor
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.PHONY : all check clean install decython documentation test q2dtor
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all: pycheck main solver check
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minimal:
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python setup.py build_ext minimal --inplace --build-temp .
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main:
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python setup.py build_ext main --inplace --build-temp .
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solver:
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@ python utilities.py check-pydas
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python setup.py build_ext solver --inplace --build-temp .
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arkane:
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python setup.py build_ext arkane --inplace --build-temp .
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all: check install check
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check:
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@ python utilities.py check-dependencies
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pycheck:
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@ python utilities.py check-python
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@ python utilities.py check-pydas
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documentation:
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$(MAKE) -C documentation html
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install:
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@ python utilities.py check-pydas
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python setup.py install
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python -m pip install -vv --no-cache-dir -e .
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q2dtor:
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@ echo -e "\nInstalling Q2DTor...\n"

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