CHG: Updating user manual #6
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| name: Casal2 Linux Build | |
| on: | |
| push: | |
| branches: | |
| - master # age_length_redesign_202109 | |
| pull_request: | |
| branches: | |
| - master ## this will run actions on current branch, to change to main, needed for testing. all branches '*' | |
| ## taken from https://keithweaverca.medium.com/only-run-github-actions-on-specific-branches-694782fcc07 | |
| ## for a release idea linux is fairly easy | |
| ## for windows look at this example https://github.com/freenet/wininstaller-innosetup/actions/runs/768471071/workflow | |
| jobs: | |
| Compile-Casal2-Linux: | |
| # should run on linux based operating system | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 180 | |
| env: | |
| CC: gcc-12 | |
| CXX: g++-12 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2.2.2 | |
| with: | |
| python-version: '3.8' | |
| - name: Install python dependencies | |
| run: pip install pytz python-dateutil --user --upgrade pip | |
| - name: Install gcc | |
| uses: egor-tensin/setup-gcc@v1 | |
| with: | |
| version: 10 | |
| platform: x86 | |
| - name: Build third-party library - release | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty | |
| - name: Build third-party library - adolc | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty adolc | |
| - name: Build third-party library - betadiff | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty betadiff | |
| - name: Build third-party libraries - boost | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty boost | |
| - name: Build third-party libraries - google test and mock | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty googletest_googlemock | |
| - name: Build third-party libraries - parser | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh thirdparty parser | |
| - name: Build release library | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh library release | |
| - name: Build "Betadiff" library | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh library betadiff | |
| - name: Build "ADOL-C" library | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh library adolc | |
| - name: Build "Unit Test" library | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh library test | |
| - name: Build Frontend | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh frontend | |
| shell: bash | |
| - name: Build Linux Archive | |
| continue-on-error: true | |
| run: | | |
| cd BuildSystem | |
| export CASAL2_BUILD_THREADS=16 | |
| ./doBuild.sh archive true | |
| shell: bash | |
| - name: Archive Linux build | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Linux-build | |
| path: BuildSystem/Casal2 | |
| - name: Run Linux model runner | |
| continue-on-error: true | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.sh modelrunner | |
| - name: Archive modelrunner | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Linux-modelrunner | |
| path: TestModels/ | |
| - name: Run Unit Tests from frontend build | |
| run: | | |
| cd BuildSystem/Casal2 | |
| ./casal2 --unittest > unittests.log | |
| - name: Archive unittest output | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Linux-unittest | |
| path: BuildSystem/Casal2/unittests.log | |
| Base-R-Ubuntu: | |
| needs: Compile-Casal2-Linux | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| working-directory: R-libraries/casal2 | |
| extra-packages: | | |
| any::devtools | |
| any::bayesplot | |
| any::purrr | |
| any::DHARMa | |
| any::mvtnorm | |
| dependencies: '"hard"' | |
| - name: Install Casal2 base | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # https://github.com/settings/tokens | |
| run: Rscript -e 'devtools::install_github("https://github.com/NIWAFisheriesModelling/CASAL2", subdir="R-libraries/casal2", ref = "HEAD")' | |
| ## download model runs | |
| - name: Download TestModels artifact | |
| uses: actions/download-artifact@v1.0.0 | |
| with: | |
| # Artifact name | |
| name: Casal2-Linux-modelrunner # optional | |
| # Destination path | |
| path: CheckTestModels # optional | |
| ## now run an R script that will check R-library compatible with exe output | |
| - name: Run Casal2 R test suite | |
| run: Rscript -e 'source(file.path("R-libraries","run_rlibrary_tests.R"))' | |
| Compile-Casal2-Windows: | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| # https://github.com/actions/virtual-environments/blob/main/images/win/Windows2019-Readme.md | |
| runs-on: windows-2019 | |
| timeout-minutes: 180 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2.2.2 | |
| with: | |
| python-version: '3.8' | |
| - name: Install python dependencies | |
| run: python.exe -m pip install pytz python-dateutil --user --upgrade pip | |
| - name: Install gcc | |
| uses: bwoodsend/setup-winlibs-action@v1 | |
| with: | |
| # see https://github.com/marketplace/actions/setup-winlibs | |
| # and https://github.com/brechtsanders/winlibs_mingw/tags | |
| #tag: '10.3.0-12.0.0-9.0.0-r2' | |
| tag: '10.3.1-snapshot20211112-9.0.0-ucrt-r1' # previous tag as of 2022-03-31 | |
| #tag: '11.1.0-12.0.0-9.0.0-r1' # reference tag in documentation | |
| #tag: '11.2.1-snapshot20220219-9.0.0-ucrt-r1' # caused issues with Casal2 unit tests | |
| #tag: '12.0.1-snapshot20220123-9.0.0-msvcrt-r1' | |
| - name: Build third-party library - adolc | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat thirdparty adolc | |
| - name: Build third-party library - betadiff | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat thirdparty betadiff | |
| - name: Build third-party library - boost | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat thirdparty boost | |
| - name: Build third-party libraries - google test and mock | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat thirdparty googletest_googlemock | |
| - name: Build third-party libraries - parser | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat thirdparty parser | |
| - name: Build release library | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat library release | |
| - name: Build "Betadiff" library | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat library betadiff | |
| - name: Build "ADOL-C" library | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat library adolc | |
| - name: Build "Unit Test" library | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat library test | |
| - name: Build Frontend | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat frontend | |
| shell: bash | |
| - name: Build Windows Archive | |
| continue-on-error: true | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat archive true | |
| shell: bash | |
| - name: Archive Windows build | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Windows-build | |
| path: BuildSystem/Casal2 | |
| - name: Run Windows model runner | |
| continue-on-error: true | |
| run: | | |
| cd BuildSystem | |
| ./doBuild.bat modelrunner | |
| - name: Archive Windows modelrunner | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Windows-modelrunner | |
| path: TestModels/ | |
| - name: Run Unit Tests from frontend application | |
| continue-on-error: false | |
| run: | | |
| cd BuildSystem/Casal2 | |
| ./casal2 --unittest > unittests.log | |
| - name: Archive unittest output | |
| continue-on-error: true | |
| uses: actions/upload-artifact@v2.2.4 | |
| with: | |
| name: Casal2-Windows-unittest | |
| path: BuildSystem/Casal2/unittests.log |