add packages required by faw diag to python3 base yaml (#578) #2
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| # This file builds and runs a lightweight version of the MDTF test suite. | |
| # Note that the tests assess functionality of the diagnostics, | |
| # and do not evaluate data or scientific content. | |
| name: MDTF_test | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| build: | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13] | |
| json-file: ["tests/github_actions_test_ubuntu_set1.jsonc","tests/github_actions_test_macos_set1.jsonc"] | |
| json-file-set2: ["tests/github_actions_test_ubuntu_set2.jsonc", "tests/github_actions_test_macos_set2.jsonc"] | |
| json-file-set3: ["tests/github_actions_test_ubuntu_set3.jsonc", "tests/github_actions_test_macos_set3.jsonc"] | |
| # if experimental is true, other jobs to run if one fails | |
| experimental: [false] | |
| exclude: | |
| - os: ubuntu-latest | |
| json-file: "tests/github_actions_test_macos_set1.jsonc" | |
| - os: ubuntu-latest | |
| json-file-set2: "tests/github_actions_test_macos_set2.jsonc" | |
| - os: ubuntu-latest | |
| json-file-set3: "tests/github_actions_test_macos_set3.jsonc" | |
| - os: macos-12 | |
| json-file: "tests/github_actions_test_ubuntu_set1.jsonc" | |
| - os: macos-12 | |
| json-file-set2: "tests/github_actions_test_ubuntu_set2.jsonc" | |
| - os: macos-12 | |
| json-file-set3: "tests/github_actions_test_ubuntu_set3.jsonc" | |
| - os: macos-13 | |
| json-file: "tests/github_actions_test_ubuntu_set1.jsonc" | |
| - os: macos-13 | |
| json-file-set2: "tests/github_actions_test_ubuntu_set2.jsonc" | |
| - os: macos-13 | |
| json-file-set3: "tests/github_actions_test_ubuntu_set3.jsonc" | |
| max-parallel: 3 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| #- name: Download Miniconda 3 | |
| # uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # miniconda-version: "latest" | |
| # python-version: 3.11.0 | |
| # channels: conda-forge | |
| #- name: Conda info | |
| # shell: bash -el {0} | |
| # run: conda info | |
| # Set up Micromamba | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| init-shell: bash | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - name: Install XQuartz if macOS | |
| if: ${{ matrix.os == 'macos-12' || matrix.os == 'macos-13'}} | |
| run: | | |
| echo "Installing XQuartz" | |
| brew install --cask xquartz | |
| echo "CONDA_ROOT=$(echo /Users/runner/micromamba)" >> $GITHUB_ENV | |
| echo "MICROMAMBA_EXE=$(echo /Users/runner/micromamba-bin/micromamba)" >> $GITHUB_ENV | |
| echo "CONDA_ENV_DIR=$(echo /Users/runner/micromamba/envs)" >> $GITHUB_ENV | |
| - name: Set environment variables | |
| run: | | |
| echo "POD_OUTPUT=$(echo $PWD/../wkdir)" >> $GITHUB_ENV | |
| - name: Set conda vars | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: | | |
| echo "MICROMAMBA_EXE=$(echo /home/runner/micromamba-bin/micromamba)" >> $GITHUB_ENV | |
| echo "CONDA_ROOT=$(echo /home/runner/micromamba)" >> $GITHUB_ENV | |
| echo "CONDA_ENV_DIR=$(echo /home/runner/micromamba/envs)" >> $GITHUB_ENV | |
| - name: Install Conda Environments | |
| run: | | |
| echo "Installing Conda Environments" | |
| echo "conda root ${CONDA_ROOT}" | |
| echo "env dir ${CONDA_ENV_DIR}" | |
| # MDTF-specific setup: install all conda envs | |
| ./src/conda/micromamba_env_setup.sh --all --micromamba_root ${CONDA_ROOT} --micromamba_exe ${MICROMAMBA_EXE} --env_dir ${CONDA_ENV_DIR} | |
| echo "Creating the _MDTF_synthetic_data environment" | |
| micromamba create -y -f ./src/conda/_env_synthetic_data.yml | |
| - name: Generate Model Data | |
| run: | | |
| cd ../ | |
| micromamba activate _MDTF_synthetic_data | |
| pip install mdtf-test-data | |
| mkdir mdtf_test_data ; cd mdtf_test_data | |
| # generate the data and run unit tests | |
| mdtf_synthetic.py -c GFDL --startyear 1 --nyears 10 --unittest | |
| mdtf_synthetic.py -c NCAR --startyear 1975 --nyears 7 | |
| mdtf_synthetic.py -c CMIP --startyear 1990 --nyears 20 | |
| cd ../ | |
| mkdir wkdir | |
| ## make input data directories | |
| mkdir -p inputdata/obs_data | |
| - name: Get Observational Data for Set 1 | |
| run: | | |
| echo "${PWD}" | |
| cd ../ | |
| echo "Available Space" | |
| df -h | |
| # attempt FTP data fetch | |
| # allow 20 min for transfer before timeout; Github actions allows 6 hours for individual | |
| # jobs, but we don't want to max out resources that are shared by the NOAA-GFDL repos. | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/convective_transition_diag_obs_data.tar --output convective_transition_diag_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/EOF_500hPa_obs_data.tar --output EOF_500hPa_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/Wheeler_Kiladis_obs_data.tar --output Wheeler_Kiladis_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/MJO_teleconnection_obs_data.tar --output MJO_teleconnection_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/MJO_suite_obs_data.tar --output MJO_suite_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/precip_diurnal_cycle_obs_data.tar --output precip_diurnal_cycle_obs_data.tar | |
| echo "Untarring set 1 NCAR/CESM standard test files" | |
| tar -xvf convective_transition_diag_obs_data.tar | |
| tar -xvf EOF_500hPa_obs_data.tar | |
| tar -xvf precip_diurnal_cycle_obs_data.tar | |
| tar -xvf MJO_teleconnection_obs_data.tar | |
| tar -xvf MJO_suite_obs_data.tar | |
| tar -xvf Wheeler_Kiladis_obs_data.tar | |
| # clean up tarballs | |
| rm -f *.tar | |
| - name: Run diagnostic tests set 1 | |
| run: | | |
| echo "POD_OUTPUT is: " | |
| echo "${POD_OUTPUT}" | |
| micromamba activate _MDTF_base | |
| # trivial check that install script worked | |
| ./mdtf_framework.py --version | |
| # run the test PODs | |
| ./mdtf -v -f ${{matrix.json-file}} | |
| # Debug POD log(s) | |
| # cat ${POD_OUTPUT}/MDTF_NCAR.Synthetic_1975_1981/Wheeler_Kiladis/Wheeler_Kiladis.log | |
| - name: Get observational data for set 2 | |
| run: | | |
| echo "${PWD}" | |
| # remove data from previous run | |
| # Actions moves you to the root repo directory in every step, so need to cd again | |
| cd ../inputdata/obs_data | |
| echo "deleting obs data from set 1" | |
| rm -rf * | |
| cd ../../ | |
| echo "Available Space" | |
| df -h | |
| # attempt FTP data fetch | |
| # allow 20 min for transfer before timeout; Github actions allows 6 hours for individual | |
| # jobs, but we don't want to max out resources that are shared by the NOAA-GFDL repos. | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/MJO_prop_amp_obs_data.tar --output MJO_prop_amp_obs_data.tar | |
| echo "Untarring set 2 GFDL standard test files" | |
| tar -xvf MJO_prop_amp_obs_data.tar | |
| # clean up tarballs | |
| rm -f *.tar | |
| - name: Run diagnostic tests set 2 | |
| run: | | |
| micromamba activate _MDTF_base | |
| # run the test PODs | |
| ./mdtf -v -f ${{matrix.json-file-set2}} | |
| # Uncomment the following line for debugging | |
| #cat ../wkdir/MDTF_GFDL.Synthetic_1_10/MJO_prop_amp/MJO_prop_amp.log | |
| - name: Get observational data for set 3 | |
| run: | | |
| echo "${PWD}" | |
| # remove data from previous run | |
| # Actions moves you to the root repo directory in every step, so need to cd again | |
| cd ../inputdata/obs_data | |
| echo "deleting obs data from set 2" | |
| rm -rf * | |
| cd ../../ | |
| echo "Available Space" | |
| df -h | |
| # attempt FTP data fetch | |
| # allow 20 min for transfer before timeout; Github actions allows 6 hours for individual | |
| # jobs, but we don't want to max out resources that are shared by the NOAA-GFDL repos. | |
| #curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/temp_extremes_distshape_obs_data.tar --output temp_extremes_distshape_obs_data.tar | |
| #curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/tropical_pacific_sea_level_obs_data.tar.gz --output tropical_pacific_sea_level_obs_data.tar.gz | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/mixed_layer_depth_obs_data.tar --output mixed_layer_depth_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/ocn_surf_flux_diag_obs_data.tar --output ocn_surf_flux_diag_obs_data.tar | |
| # curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/albedofb_obs_data.tar --output albedofb_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/seaice_suite_obs_data.tar --output seaice_suite_obs_data.tar | |
| curl --verbose --ipv4 --connect-timeout 8 --max-time 1200 --retry 128 --ftp-ssl --ftp-pasv -u "anonymous:anonymous" ftp://ftp.gfdl.noaa.gov/perm/oar.gfdl.mdtf/stc_eddy_heat_fluxes_obs_data.tar --output stc_eddy_heat_fluxes_obs_data.tar | |
| echo "Untarring set 3 CMIP standard test files" | |
| #tar -xvf temp_extremes_distshape_obs_data.tar | |
| #tar -zxvf tropical_pacific_sea_level_obs_data.tar.gz | |
| tar -xvf mixed_layer_depth_obs_data.tar | |
| tar -xvf ocn_surf_flux_diag_obs_data.tar | |
| # tar -xvf albedofb_obs_data.tar | |
| tar -xvf seaice_suite_obs_data.tar | |
| tar -xvf stc_eddy_heat_fluxes_obs_data.tar | |
| # clean up tarballs | |
| rm -f *.tar | |
| rm -f *.tar.gz | |
| - name: Run CMIP diagnostic tests set 3 | |
| run: | | |
| micromamba activate _MDTF_base | |
| # run the test PODs | |
| ./mdtf -v -f ${{matrix.json-file-set3}} | |
| - name: Run unit tests | |
| run: | | |
| micromamba activate _MDTF_base | |
| python -m unittest discover |