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Continuous Integration, Documentation Build, and Dockerfile Fixes #2608

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merged 2 commits into from
Feb 9, 2024
Merged

Continuous Integration, Documentation Build, and Dockerfile Fixes #2608

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fddacbf
patch the environment file to pin Julia to 1.9.5 + git syntax fix
JacksonBurns Feb 8, 2024
51924d9
update Docker image with stable Julia version
JacksonBurns Feb 8, 2024
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4 changes: 4 additions & 0 deletions .github/workflows/CI.yml
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Expand Up @@ -62,6 +62,8 @@ jobs:
uses: actions/checkout@v3

# configures the mamba environment manager and builds the environment
- name: Patch Environment File
run: sed -i '' 's/ - conda-forge::julia>=1.8.5,!=1.9.0/ - conda-forge::julia=1.9.1/' environment.yml
- name: Setup Mambaforge Python 3.7
uses: conda-incubator/setup-miniconda@v2
with:
Expand Down Expand Up @@ -112,6 +114,8 @@ jobs:
uses: actions/checkout@v3

# configures the mamba environment manager and builds the environment
- name: Patch Environment File
run: sed -i 's/ - conda-forge::julia>=1.8.5,!=1.9.0/ - conda-forge::julia=1.9.1/' environment.yml
- name: Setup Mambaforge Python 3.7
uses: conda-incubator/setup-miniconda@v2
with:
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8 changes: 5 additions & 3 deletions .github/workflows/docs.yml
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Expand Up @@ -16,6 +16,8 @@ jobs:
shell: bash -l {0}
steps:
- uses: actions/checkout@v2
- name: Patch Environment File
run: sed -i 's/ - conda-forge::julia>=1.8.5,!=1.9.0/ - conda-forge::julia=1.9.1/' environment.yml
- name: Setup Mambaforge Python 3.7
uses: conda-incubator/setup-miniconda@v2
with:
Expand Down Expand Up @@ -59,8 +61,8 @@ jobs:
- name: Make documentation - to publish
if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
run: |
git config user.name github-actions
git config user.email github-actions@github.com
git config user.name "github-actions"
git config user.email "github-actions@github.com"
cd documentation
make html
- name: Check documentation links
Expand All @@ -72,4 +74,4 @@ jobs:
if: ${{ github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
run: |
touch build/html/.nojekyll
cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push official gh-pages
cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push origin gh-pages
6 changes: 5 additions & 1 deletion Dockerfile
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Expand Up @@ -42,8 +42,10 @@ WORKDIR /rmg
RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git

# build the conda environment
WORKDIR /rmg/RMG-Py
# patch the env file to a specific version of Julia that we know to be working on all platforms
RUN sed -i 's/ - conda-forge::julia>=1.8.5,!=1.9.0/ - conda-forge::julia=1.9.4/' environment.yml
# build the conda environment
RUN conda env create --file environment.yml && \
conda clean --all --yes

Expand All @@ -61,6 +63,8 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"

# 1. Build RMG
# 2. Install and link Julia dependencies for RMS
# setting this env variable fixes an issue with Julia precompilation on Windows
ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
RUN make && \
julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
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