Add surface mechanisms to flux diagram tool #4946
Workflow file for this run
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# CI.yml | |
# This file contains the script used by GitHub actions to execute the Continuous Integration (CI) | |
# for RMG-Py. This includes building RMG and its dependencies, executing the unit tests, | |
# functional tests, database tests, and regression tests. | |
# | |
# This will run automatically on any push to any branch, but will only run one instance of | |
# itself at a time per branch (to avoid spawning tons of runners, which prevents them from | |
# executing). | |
# | |
# In the regression testing section of the action the term "Stable" or "Reference" refers to | |
# the 'correct answers' to the regression tests, i.e. the way that the main branch executes | |
# them. These 'answers' are re-generated daily, or on any push to main, and retrieved whenever | |
# a push is made to a non-main branch. The new proposed changes are referred to as "Dynamic". | |
# | |
# | |
# Changelog: | |
# 2023-04 - Jackson Burns - Added this header, regression tests, cleanup of action in | |
# in general, and documentation throughout the file. | |
# 2023-05 - added Docker build steps | |
# 2023-05-12 - added changes to allow running on forks | |
# 2023-06-06 - added matrix build for libstdcxx-ng versions 12 and 13 on ubuntu. Only expect 12 to work. | |
# 2023-06-07 - updated regression testing. Now fails if significant changes are detected. | |
# 2023-06-15 - revert changes from 06-06, both now work | |
# 2023-06-27 - add option to run from RMG-database with GitHub resuable workflows | |
# 2023-07-17 - made it pass by default | |
# 2023-07-21 - upload the regression results summary as artifact (for use as a comment on PRs) | |
# 2023-07-31 - removed option to run from RMG-database with GitHub resuable workflows | |
# 2024-10-01 - deprecated Mambaforge with Miniforge3 for environment creation | |
name: Continuous Integration | |
on: | |
schedule: | |
# * is a special character in YAML so you have to quote this string | |
- cron: "0 8 * * *" | |
# runs on all branches on both RMG-Py and forks | |
push: | |
# runs on PRs against RMG-Py (and anywhere else, but we add this for RMG-Py) | |
pull_request: | |
# this prevents one PR from simultaneously running multiple runners, which will clog up the queue | |
# and prevent other PRs from running the CI | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
env: | |
# if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace | |
# main with the name of the branch | |
RMG_DATABASE_BRANCH: main | |
jobs: | |
build-osx: | |
runs-on: macos-13 | |
# skip scheduled runs from forks | |
if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout RMG-Py | |
uses: actions/checkout@v4 | |
# Step to create a custom condarc.yml before setting up conda | |
- name: Create custom conda config file | |
run: | | |
RUNNER_CWD=$(pwd) | |
echo "channels:" > $RUNNER_CWD/condarc.yml | |
echo " - conda-forge" >> $RUNNER_CWD/condarc.yml | |
echo " - rmg" >> $RUNNER_CWD/condarc.yml | |
echo " - cantera" >> $RUNNER_CWD/condarc.yml | |
echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml | |
# configures the mamba environment manager and builds the environment | |
- name: Setup Miniforge Python 3.7 | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
environment-file: environment.yml | |
miniforge-variant: Miniforge3 | |
miniforge-version: latest | |
python-version: 3.7 | |
condarc-file: condarc.yml | |
activate-environment: rmg_env | |
use-mamba: true | |
# list the environment for debugging purposes | |
- name: mamba info | |
run: | | |
mamba info | |
mamba list | |
# Clone RMG-database | |
- name: Clone RMG-database | |
run: | | |
cd .. | |
git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git | |
# modify env variables as directed in the RMG installation instructions | |
- name: Set Environment Variables | |
run: | | |
RUNNER_CWD=$(pwd) | |
echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV | |
echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH | |
# RMG build step | |
- name: make RMG | |
run: | | |
make clean | |
make | |
build-and-test-linux: | |
runs-on: ubuntu-latest | |
# skip scheduled runs from forks | |
if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} | |
env: | |
# This is true only if this is a reference case for the regression testing: | |
REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }} | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout RMG-Py | |
uses: actions/checkout@v4 | |
# Step to create a custom condarc.yml before setting up conda | |
- name: Create custom condarc.yml | |
run: | | |
RUNNER_CWD=$(pwd) | |
echo "channels:" > $RUNNER_CWD/condarc.yml | |
echo " - conda-forge" >> $RUNNER_CWD/condarc.yml | |
echo " - rmg" >> $RUNNER_CWD/condarc.yml | |
echo " - cantera" >> $RUNNER_CWD/condarc.yml | |
echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml | |
# configures the mamba environment manager and builds the environment | |
- name: Setup Miniforge Python 3.7 | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
environment-file: environment.yml | |
miniforge-variant: Miniforge3 | |
miniforge-version: latest | |
python-version: 3.7 | |
condarc-file: condarc.yml | |
activate-environment: rmg_env | |
use-mamba: true | |
# list the environment for debugging purposes | |
- name: mamba info | |
run: | | |
mamba info | |
mamba list | |
# Clone RMG-database | |
- name: Clone RMG-database | |
run: | | |
cd .. | |
git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git | |
# modify env variables as directed in the RMG installation instructions | |
- name: Set Environment Variables | |
run: | | |
RUNNER_CWD=$(pwd) | |
echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV | |
echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH | |
# RMG build step | |
- name: make RMG | |
run: | | |
make clean | |
make | |
# RMS installation and linking to Julia | |
- name: Install and link Julia dependencies | |
timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours). | |
run: | | |
python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" | |
julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' | |
- name: Install Q2DTor | |
run: echo "" | make q2dtor | |
# non-regression testing | |
- name: Run Unit, Functional, and Database Tests | |
# aggregate into one command so we only have to eat the collection time once | |
run: make test-all | |
# Regression Testing - Test Execution | |
- name: Regression Tests - Execution | |
id: regression-execution | |
timeout-minutes: 60 | |
run: | | |
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface; | |
do | |
if python-jl rmg.py test/regression/"$regr_test"/input.py; then | |
echo "$regr_test" "Executed Successfully" | |
else | |
echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY | |
export FAILED=Yes | |
fi | |
done | |
if [[ ${FAILED} ]]; then | |
echo "One or more regression tests could not be executed." | tee -a $GITHUB_STEP_SUMMARY | |
echo "Please download the failed results or check the above log to see why." | tee -a $GITHUB_STEP_SUMMARY | |
exit 1 | |
fi | |
# Upload Regression Results as Failed if above step failed | |
- name: Upload Failed Results | |
if: ${{ failure() && steps.regression-execution.conclusion == 'failure' }} | |
uses: actions/upload-artifact@v4 | |
with: | |
name: failed_regression_results | |
path: | | |
test/regression | |
# Upload Regression Results as Stable if Scheduled or Push to Main | |
- name: Upload Results as Reference | |
# upload the results for scheduled CI (on main) and pushes to main | |
if: ${{ env.REFERENCE_JOB == 'true' }} | |
uses: actions/upload-artifact@v4 | |
with: | |
name: stable_regression_results | |
path: | | |
test/regression | |
# Upload Regression Results as Dynamic if Push to non-main Branch | |
- name: Upload Results as Dynamic | |
if: ${{ env.REFERENCE_JOB == 'false' }} | |
uses: actions/upload-artifact@v4 | |
with: | |
name: dynamic_regression_results | |
path: | | |
test/regression | |
- name: mkdir stable_regression_results | |
if: ${{ env.REFERENCE_JOB == 'false' }} | |
run: mkdir stable_regression_results | |
# Retrieve Stable Results for reference | |
- name : Find ID of Reference Results | |
env: | |
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
# this will search for the last successful execution of CI on main | |
run: | | |
run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 15 --json databaseId,conclusion --jq 'map(select(.conclusion == "success")) | .[0].databaseId') | |
echo "CI_RUN_ID=$run_id" >> $GITHUB_ENV | |
- name: Retrieve Stable Regression Results | |
if: ${{ env.REFERENCE_JOB == 'false' }} | |
uses: actions/download-artifact@v4 | |
with: | |
# download stable regression results | |
run-id: ${{ env.CI_RUN_ID }} | |
repository: ReactionMechanismGenerator/RMG-Py | |
github-token: ${{ secrets.GITHUB_TOKEN }} | |
name: stable_regression_results | |
path: stable_regression_results | |
# Regression Testing - Actual Comparisons | |
- name: Regression Tests - Compare to Baseline | |
id: regression-comparison | |
if: ${{ env.REFERENCE_JOB == 'false' }} | |
env: | |
REFERENCE: stable_regression_results | |
run: | | |
exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout) | |
mkdir -p "test/regression-diff" | |
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface; | |
do | |
echo "" | |
echo "### Regression test $regr_test:" | |
# Memory Usage and Execution Time | |
echo -n 'Reference: ' | |
grep "Execution time" $REFERENCE/"$regr_test"/RMG.log | tail -1 | |
echo -n 'Current: ' | |
grep "Execution time" test/regression/"$regr_test"/RMG.log | tail -1 | |
echo -n 'Reference: ' | |
grep "Memory used:" $REFERENCE/"$regr_test"/RMG.log | tail -1 | |
echo -n 'Current: ' | |
grep "Memory used:" test/regression/"$regr_test"/RMG.log | tail -1 | |
echo "<details>" | |
# Compare the edge and core | |
if python-jl scripts/checkModels.py \ | |
"$regr_test-core" \ | |
$REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \ | |
$REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \ | |
test/regression/"$regr_test"/chemkin/chem_annotated.inp \ | |
test/regression/"$regr_test"/chemkin/species_dictionary.txt | |
then | |
echo "<summary>$regr_test Passed Core Comparison ✅</summary>" | |
else | |
echo "<summary>$regr_test Failed Core Comparison ❌</summary>" | |
cp "$regr_test-core.log" test/regression-diff/ | |
export FAILED=Yes | |
fi | |
echo "" # blank line so next block is interpreted as markdown | |
cat "$regr_test-core.log" | |
echo "</details>" | |
echo "<details>" | |
if python-jl scripts/checkModels.py \ | |
"$regr_test-edge" \ | |
$REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \ | |
$REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \ | |
test/regression/"$regr_test"/chemkin/chem_edge_annotated.inp \ | |
test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt | |
then | |
echo "<summary>$regr_test Passed Edge Comparison ✅</summary>" | |
else | |
echo "<summary>$regr_test Failed Edge Comparison ❌</summary>" | |
cp "$regr_test-edge.log" test/regression-diff/ | |
export FAILED=Yes | |
fi | |
echo "" # blank line so next block is interpreted as markdown | |
cat "$regr_test-edge.log" | |
echo "</details>" | |
# Check for Regression between Reference and Dynamic (skip superminimal) | |
if [ -f test/regression/"$regr_test"/regression_input.py ]; | |
then | |
echo "<details>" | |
if python-jl rmgpy/tools/regression.py \ | |
test/regression/"$regr_test"/regression_input.py \ | |
$REFERENCE/"$regr_test"/chemkin \ | |
test/regression/"$regr_test"/chemkin | |
then | |
echo "<summary>$regr_test Passed Observable Testing ✅</summary>" | |
else | |
echo "<summary>$regr_test Failed Observable Testing ❌</summary>" | |
export FAILED=Yes | |
fi | |
echo "</details>" | |
fi | |
echo "" | |
done | |
if [[ ${FAILED} ]]; then | |
echo "⚠️ One or more regression tests failed." | tee -a $GITHUB_STEP_SUMMARY >&2 | |
echo "Please download the failed results and run the tests locally or check the log to see why." | tee -a $GITHUB_STEP_SUMMARY >&2 | |
fi | |
- name: Prepare Results for PR Comment | |
if: ${{ env.REFERENCE_JOB == 'false' }} | |
env: | |
PR_NUMBER: ${{ github.event.number || github.event.after || github.event_name }} | |
run: | | |
echo $PR_NUMBER > summary.txt | |
echo "## Regression Testing Results" >> summary.txt | |
cat regression.stderr >> summary.txt | |
echo "<details>" >> summary.txt | |
echo "<summary>Detailed regression test results.</summary>" >> summary.txt | |
cat regression.stdout >> summary.txt | |
echo "</details>" >> summary.txt | |
echo "" >> summary.txt | |
echo "_beep boop this comment was written by a bot_ :robot:" >> summary.txt | |
cat summary.txt > $GITHUB_STEP_SUMMARY | |
- name: Upload regression summary artifact | |
# the annotate workflow uses this artifact to add a comment to the PR | |
uses: actions/upload-artifact@v3 | |
if : ${{ github.event_name == 'pull_request' }} | |
with: | |
name: regression_summary | |
path: summary.txt | |
- name: Upload Comparison Results | |
uses: actions/upload-artifact@v3 | |
with: | |
name: regression_test_comparison_results | |
path: | | |
test/regression-diff | |
# Install and Call codecov only if the tests were successful (permitting failures in the regression comparison tests) | |
- name: Code coverage install and run | |
if: success() || ( failure() && steps.regression-execution.conclusion == 'success' ) | |
run: | | |
mamba install -y -c conda-forge codecov | |
codecov | |
build-and-push-docker: | |
# after testing and on pushes to main, build and push docker image | |
# technically we could live without the 'needs' since _in theory_ | |
# nothing will ever be merged into main that fails the tests, but | |
# who knows ¯\_(ツ)_/¯ | |
# | |
# taken from https://github.com/docker/build-push-action | |
needs: build-and-test-linux | |
runs-on: ubuntu-latest | |
if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py' | |
steps: | |
- name: Set up QEMU | |
uses: docker/setup-qemu-action@v2 | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v2 | |
- name: Login to Docker Hub | |
uses: docker/login-action@v2 | |
with: | |
username: ${{ secrets.DOCKERHUB_USERNAME }} | |
password: ${{ secrets.DOCKERHUB_TOKEN }} | |
- name: Build and Push | |
uses: docker/build-push-action@v6 | |
with: | |
push: true | |
tags: reactionmechanismgenerator/rmg:latest |