Revision of the manual #297
Workflow file for this run
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# ----------------------------------------------------------------------------- | |
# | |
# Copyright (c) 2017 Sam Cox, Roberto Sommariva | |
# | |
# This file is part of the AtChem2 software package. | |
# | |
# This file is covered by the MIT license which can be found in the file | |
# LICENSE.md at the top level of the AtChem2 distribution. | |
# | |
# ----------------------------------------------------------------------------- | |
# Workflow for continuous integration (CI) of AtChem2, | |
# using Github Actions and Codecov | |
# | |
# Acknowledgements: J. Allsopp | |
# ----------------------------------------------------- # | |
name: AtChem2 CI | |
# ------------------------------ EVENTS ------------------------------ # | |
# Controls when the workflow is activated | |
on: | |
# Triggers when a pull request is created or updated (only on the | |
# master branch) | |
pull_request: | |
branches: [ master ] | |
# Triggers when a push is made to the master branch (either by | |
# merging a pull request, or by direct commit) | |
push: | |
branches: [ master ] | |
# Run manually from the Actions tab | |
workflow_dispatch: | |
# ------------------------------ JOBS ------------------------------ # | |
# This workflow contains a single job called `ci_testing`, which | |
# compiles the AtChem2 model, runs the Testsuite, and checks the | |
# Testsuite code coverage using Codecov | |
jobs: | |
ci_testing: | |
# The job runs on both linux (ubuntu) and macos runner images, | |
# with three versions of gnu fortran -- the runner images are | |
# described here: https://github.com/actions/runner-images | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
os: [ubuntu-22.04, macos-11, macos-12] | |
fortran: [9, 10, 11] | |
exclude: #TODO: fortran9 does not work on macos12 | |
- os: macos-12 | |
fortran: 9 | |
fail-fast: false | |
# ------------------------------------------------------------- | |
# Sequence of tasks to be executed as part of the `ci_testing` job: | |
# 1. Checkout the repository | |
# 2. Install gfortran, AtChem2 dependencies | |
# 3. Compile AtChem2 | |
# 4. Run all tests (indent, style, unit, model) | |
# 5. Recompile AtChem2, run unit and model tests for Codecov | |
steps: | |
# ------------------------------------------------------------- | |
# (1) Checkout the repository under $GITHUB_WORKSPACE | |
- name: Checkout repo | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 | |
# ------------------------------------------------------------- | |
# (2) Install gfortran, if not supplied with the runner image, | |
# and the AtChem2 dependencies (CVODE, openlibm, numdiff, FRUIT) | |
# gfortran on macos-11 | |
- name: Install gfortran-9 (macos-11) | |
if: matrix.os == 'macos-11' && matrix.fortran == 9 | |
run: brew install gcc@${{ matrix.fortran }} | |
# gfortran on macos-12 | |
- name: Install gfortran-9 and gfortran-10 (macos-12) | |
if: matrix.os == 'macos-12' && (matrix.fortran == 9 || matrix.fortran == 10) | |
run: brew install gcc@${{ matrix.fortran }} | |
# AtChem2 dependencies | |
- name: Install CVODE | |
run: ./tools/install/install_cvode.sh $PWD $(which gfortran-${{ matrix.fortran }}) | |
- name: Install openlibm | |
run: ./tools/install/install_openlibm.sh $PWD | |
- name: Install numdiff | |
run: ./tools/install/install_numdiff.sh $PWD | |
- name: Install FRUIT | |
run: sudo ./tools/install/install_fruit.sh $PWD | |
# ------------------------------------------------------------- | |
# (3) Compile AtChem2 using the standard compilation flags | |
- name: Build AtChem2 | |
# Set $FORT_VERSION for use with the `Makefile`, which is | |
# called by the `build_atchem2.sh` script | |
env: | |
FORT_VERSION: ${{ matrix.fortran }} | |
run: | | |
cp tools/install/Makefile.skel Makefile | |
./build/build_atchem2.sh ./model/mechanism.fac ./model/configuration/ ./mcm/ | |
# macos only | |
if [ $RUNNER_OS != "Linux" ] ; then | |
install_name_tool -change libopenlibm.4.dylib $PWD/openlibm-0.8.1/libopenlibm.4.dylib atchem2 ; | |
install_name_tool -change @rpath/libsundials_cvode.2.dylib $PWD/cvode/lib/libsundials_cvode.dylib atchem2 ; | |
install_name_tool -change @rpath/libsundials_fnvecserial.2.dylib $PWD/cvode/lib/libsundials_fnvecserial.dylib atchem2 ; | |
install_name_tool -change @rpath/libsundials_nvecserial.2.dylib $PWD/cvode/lib/libsundials_nvecserial.dylib atchem2 ; | |
fi | |
# ------------------------------------------------------------- | |
# (4) Run all tests: indent, style, unit, model | |
- name: Indent and Style tests | |
run: | | |
make indenttest | |
make styletest | |
- name: Unit and Model tests | |
# Set $FORT_VERSION for use with the `Makefile` | |
env: | |
FORT_VERSION: ${{ matrix.fortran }} | |
run: | | |
export PATH=$PATH:$PWD/numdiff/bin | |
make unittests | |
make oldtests # NB: oldtests will eventually be merged into modeltests | |
#make modeltests # NB: modeltests are temporarily deactivated (pass on linux, fail on macos) | |
# ------------------------------------------------------------- | |
# (5) Recompile AtChem2 using the code coverage flags, then | |
# upload the gcov files to Codecov | |
- name: Unit and Model tests (x Codecov) | |
if: matrix.os == 'ubuntu-22.04' && matrix.fortran == 11 | |
# Set $FORT_VERSION for use with the `Makefile` | |
env: | |
FORT_VERSION: ${{ matrix.fortran }} | |
run: | | |
export PATH=$PATH:$PWD/numdiff/bin | |
make clean | |
make unittests CCOV=true | |
mv tests/unit_tests/*.gc* ./ # Needed to deal with gcc11 changing the way it handles gcda and gcna files | |
make modeltests CCOV=true # Run only the new model Testsuite | |
- name: Upload coverage reports to Codecov | |
if: matrix.os == 'ubuntu-22.04' && matrix.fortran == 11 | |
uses: codecov/codecov-action@v3 | |
with: | |
gcov: true |