Merge branch 'joezuntz:main' into main #23
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Continuous Integration | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| Download_Data: | |
| name: Download test data | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - uses: actions/cache@v3 | |
| name: Planck Data Cache | |
| id: cache-planck | |
| with: | |
| path: COM_Likelihood_Data-baseline_R3.00.tar.gz | |
| key: planck-2018-data | |
| enableCrossOsArchive: true | |
| - if: ${{ steps.cache-planck.outputs.cache-hit != 'true' }} | |
| name: Download Planck | |
| shell: bash -l {0} | |
| run: | | |
| URL="https://portal.nersc.gov/cfs/lsst/zuntz/planck/COM_Likelihood_Data-baseline_R3.00.tar.gz" | |
| FILENAME="COM_Likelihood_Data-baseline_R3.00.tar.gz" | |
| wget -O ${FILENAME} ${URL} | |
| - name: Cache WMAP data | |
| id: cache-wmap | |
| uses: actions/cache@v3 | |
| with: | |
| path: wmap_likelihood_full_v5.tar.gz | |
| key: wmap-9-data | |
| enableCrossOsArchive: true | |
| - if: ${{ steps.cache-wmap.outputs.cache-hit != 'true' }} | |
| name: Download WMAP data | |
| run: | | |
| wget https://lambda.gsfc.nasa.gov/data/map/dr5/dcp/likelihood/wmap_likelihood_full_v5.tar.gz | |
| - name: Cache ACT data | |
| id: cache-act | |
| uses: actions/cache@v3 | |
| with: | |
| path: ACT_dr6_likelihood_v1.1.tgz | |
| key: act-dr6-data | |
| enableCrossOsArchive: true | |
| - if: ${{ steps.cache-act.outputs.cache-hit != 'true' }} | |
| name: Download ACT data | |
| run: | | |
| wget https://lambda.gsfc.nasa.gov/data/suborbital/ACT/ACT_dr6/likelihood/data/ACT_dr6_likelihood_v1.1.tgz | |
| conda_test: | |
| name: Conda Test | |
| needs: Download_Data | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, macos-latest] | |
| pyversion: ["3.8", "3.9", "3.10", "3.11"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: cosmosis-env | |
| channels: conda-forge | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: ${{ matrix.pyversion }} | |
| - name: Install dependencies with conda | |
| shell: bash -l {0} | |
| run: mamba install -c conda-forge "cosmosis>=3.2" cosmosis-build-standard-library pytest | |
| - name: Get Cached Planck | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: COM_Likelihood_Data-baseline_R3.00.tar.gz | |
| key: planck-2018-data | |
| fail-on-cache-miss: true | |
| - name: Get Cached WMAP | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: wmap_likelihood_full_v5.tar.gz | |
| key: wmap-9-data | |
| fail-on-cache-miss: true | |
| - name: Get Cached ACT | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: ACT_dr6_likelihood_v1.1.tgz | |
| key: act-dr6-data | |
| fail-on-cache-miss: true | |
| - name: Extract data | |
| shell: bash -l {0} | |
| run: | | |
| # WMAP | |
| pushd likelihood/wmap9/data | |
| tar -zxvf ../../../wmap_likelihood_full_v5.tar.gz | |
| mv wmap_likelihood_v5/data/* . | |
| popd | |
| #Planck | |
| pushd likelihood/planck2018 | |
| tar -zxvf ../../COM_Likelihood_Data-baseline_R3.00.tar.gz | |
| popd | |
| # ACT | |
| mkdir likelihood/act-dr6-lens/data | |
| pushd likelihood/act-dr6-lens/data | |
| tar -zxvf ../../../ACT_dr6_likelihood_v1.1.tgz | |
| popd | |
| - name: Build standard library | |
| shell: bash -l {0} | |
| run: | | |
| source cosmosis-configure | |
| make | |
| - name: Install likelihood python dependencies from pip | |
| shell: bash -l {0} | |
| run: | | |
| pip install "act_dr6_lenslike>=1.0.2" | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: | | |
| source cosmosis-configure | |
| pytest -vv --durations=0 tests/test_cosmosis_standard_library.py | |
| - name: Run Demos | |
| shell: bash -l {0} | |
| run: | | |
| source cosmosis-configure | |
| pytest -vv --durations=0 tests/test_demos.py | |
| apt-get-test: | |
| runs-on: ubuntu-20.04 | |
| needs: Download_Data | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, "3.10", "3.11"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install apt dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev | |
| sudo ln -s `which gfortran-7` /usr/local/bin/gfortran | |
| sudo apt-get -y install libgsl-dev libfftw3-bin libfftw3-dev libfftw3-3 autotools-dev autoconf libcfitsio-dev | |
| - name: Get Cached Planck | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: COM_Likelihood_Data-baseline_R3.00.tar.gz | |
| key: planck-2018-data | |
| fail-on-cache-miss: true | |
| - name: Get Cached WMAP | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: wmap_likelihood_full_v5.tar.gz | |
| key: wmap-9-data | |
| fail-on-cache-miss: true | |
| - name: Get Cached ACT | |
| uses: actions/cache/restore@v3 | |
| with: | |
| path: ACT_dr6_likelihood_v1.1.tgz | |
| key: act-dr6-data | |
| fail-on-cache-miss: true | |
| - name: Extract data | |
| shell: bash -l {0} | |
| run: | | |
| # WMAP | |
| pushd likelihood/wmap9/data | |
| tar -zxvf ../../../wmap_likelihood_full_v5.tar.gz | |
| mv wmap_likelihood_v5/data/* . | |
| popd | |
| #Planck | |
| pushd likelihood/planck2018 | |
| tar -zxvf ../../COM_Likelihood_Data-baseline_R3.00.tar.gz | |
| popd | |
| # ACT | |
| mkdir likelihood/act-dr6-lens/data | |
| pushd likelihood/act-dr6-lens/data | |
| tar -zxvf ../../../ACT_dr6_likelihood_v1.1.tgz | |
| popd | |
| - uses: actions/cache@v2 | |
| name: Load pip cache | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/setup.py') }}-v2 | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel setuptools | |
| pip install "cosmosis>=3.2" "nautilus-sampler==0.6.*" | |
| pip install -v --no-cache-dir --no-binary=mpi4py,camb mpi4py camb | |
| pip install fitsio astropy fast-pt "Cython<3.0" jupyter | |
| - name: Install likelihood python dependencies | |
| run: | | |
| pip install "act_dr6_lenslike>=1.0.2" | |
| - name: Build | |
| run: | | |
| source .github/ci-setup.sh && make | |
| # I have seen some failures here | |
| - name: Check camb installation | |
| run: | | |
| source .github/ci-setup.sh | |
| python -c "import camb" | |
| - name: Test campaign commands | |
| shell: bash -l {0} | |
| run: | | |
| source .github/ci-setup.sh | |
| cosmosis-campaign -l examples/des-campaign.yml | tee output/campaign.log | |
| grep -e "mira-titan" campaign.log | |
| grep -e "fiducial" campaign.log | |
| cosmosis-campaign --run fiducial-test-only examples/des-campaign.yml | |
| cosmosis-campaign examples/des-campaign.yml --status fiducial-test-only > output/campaign.log | |
| grep -e "🟢 fiducial-test-only" output/campaign.log | |
| cosmosis-campaign examples/des-campaign.yml --status | |
| - name: ExampleNotebook | |
| shell: bash -l {0} | |
| run: | | |
| source cosmosis-configure | |
| rm -f output/pantheon.txt | |
| jupyter nbconvert --to notebook --execute "examples/example.ipynb" |