Test #108
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '42 4 5,20 * *' | |
| jobs: | |
| Sherpa: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| #python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3] | |
| python-version: [3.11] | |
| defaults: | |
| run: | |
| # this is needed, because otherwise conda env is not available | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| run: sudo apt-get update && sudo apt-get -y --no-install-recommends install -y ghostscript | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: test | |
| cache-environment: false | |
| cache-downloads: true | |
| - name: Set directory names | |
| run: | | |
| echo "MODELDIR=$HOME/Downloads/models" >> $GITHUB_ENV | |
| - name: Cache models | |
| uses: pat-s/[email protected] | |
| id: cache-downloads | |
| with: | |
| path: ${{ env.MODELDIR }} | |
| key: cache-downloads | |
| - name: Download models (if necessary) | |
| run: | | |
| mkdir -p $MODELDIR | |
| pushd $MODELDIR | |
| wget -q -nc https://zenodo.org/record/1169181/files/uxclumpy-cutoff.fits https://zenodo.org/record/1169181/files/uxclumpy-cutoff-omni.fits; | |
| popd | |
| - name: Install python dependencies | |
| run: | | |
| micromamba create -y -n ciao --override-channels -c https://cxc.cfa.harvard.edu/conda/ciao -c conda-forge ciao sherpa ds9 ciao-contrib caldb_main astropy "matplotlib>=3.5" ultranest "coverage<7.0.0" coveralls==3.3.1 scipy h5py astropy requests cython tqdm coverage toml && | |
| # micromamba env create -y -n ciao -f .github/workflows/ciao-conda-env.yml && | |
| micromamba activate ciao && | |
| echo "--- Environment dump start ---" && | |
| env && | |
| echo "--- Environment dump end ---" && | |
| python -c 'from sherpa.astro import io; print(io.backend)' && | |
| pip install git+https://github.com/JohannesBuchner/coverage-lcov && | |
| sudo sed -i '/PDF/s/none/read|write/' /etc/ImageMagick-6/policy.xml && | |
| pip uninstall -y h5py && | |
| pip install --no-cache-dir h5py | |
| - name: Conda info | |
| run: | | |
| micromamba activate ciao | |
| micromamba info | |
| - name: Conda list | |
| run: | | |
| micromamba activate ciao | |
| micromamba list | |
| - name: Conda paths | |
| run: | | |
| micromamba activate ciao | |
| pwd | |
| echo $PATH | |
| ls $CONDA/bin/ | |
| which coverage | |
| - name: Conda download clean-up | |
| continue-on-error: true | |
| # we must keep below 5GB, otherwise caching fails | |
| # prefer keeping large files (ciao) | |
| run: | | |
| rm -rf ~/conda_pkgs_dir/*/ | |
| find ~/conda_pkgs_dir -type f -printf '%s\t%p\n' | sort -nr -k1,1 | | |
| { S=0; while read s l; do | |
| ((S+=s)); [[ $S -gt 6000000000 ]] && rm -v "$l"; | |
| done; } | |
| - name: Prepare testing | |
| run: | | |
| cp .coveragerc docker/testsrc | |
| cp .coveragerc examples/sherpa | |
| cp .coveragerc examples/xspec | |
| pushd docker/testsrc | |
| echo "backend: Agg" > matplotlibrc | |
| ls | |
| rm *.nh | |
| - name: Test helper scripts | |
| run: | | |
| micromamba activate ciao | |
| pushd docker/testsrc | |
| python -m coverage run -p ../../fixkeywords.py combined_src.pi combined_bkg.pi combined_src.rmf combined_src.arf | |
| python -m coverage run -p ../../gal.py combined_src.pi | |
| ls combined_src.pi.nh | |
| python -m coverage run -p ../../autobackgroundmodel/fitbkg.py combined_bkg.pi combined_src.pi || exit 1 | |
| python -m coverage run -p ../../autobackgroundmodel/fitbkg.py combined_bkg.pi || exit 1 | |
| python -m coverage run -p ../../autobackgroundmodel/fitbkg.py || true | |
| python -m coverage run -p ../../gal.py || true | |
| python -m coverage run -p ../../fixkeywords.py || true | |
| git checkout . | |
| popd | |
| - name: Test examples | |
| run: | | |
| micromamba activate ciao | |
| pushd examples/sherpa; | |
| # install interpolation code first | |
| echo $CONDA_PREFIX/lib/python*; | |
| ls /usr/include/numpy/ || true; | |
| for d in $CONDA_PREFIX/lib/python*/site-packages/numpy/core/include/numpy; do echo $d; sudo ln -f -v -s $d /usr/include/numpy; done; | |
| ls /usr/include/numpy/ || true; | |
| git clone https://github.com/JohannesBuchner/npyinterp.git; | |
| pushd npyinterp; make; popd; | |
| # run examples | |
| PYTHONPATH=../../:${PYTHONPATH}:npyinterp/ LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:npyinterp/ bash -v runall.sh || exit 1; | |
| popd; | |
| - name: Run XAGNFitter | |
| run: | | |
| micromamba activate ciao | |
| pushd examples/sherpa/chandra; | |
| echo "179.pi 0.5 8" > filenames.txt | |
| PYTHONPATH=../../../:$PYTHONPATH WITHAPEC=0 coverage run -p ../xagnfitter.py || exit 1; | |
| ls; | |
| popd; | |
| - name: Install | |
| run: | | |
| micromamba activate ciao | |
| python -m pip -y install . --user | |
| wc -l examples/sherpa/.cover* examples/xspec/.cover* docker/testsrc/.cover* .cover* || true | |
| - name: Coverage report | |
| run: | | |
| micromamba activate ciao | |
| python -m coverage combine examples/sherpa examples/xspec docker/testsrc . | |
| python -m coverage report | |
| coverage-lcov | |
| # make paths relative | |
| sed -i s,$PWD/,,g lcov.info | |
| - name: Coveralls | |
| uses: coverallsapp/github-action@master | |
| with: | |
| path-to-lcov: lcov.info | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: sherpa-${{ matrix.test_number }} | |
| parallel: true | |
| Xspec: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| #python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3] | |
| python-version: [3.9, 3.11] | |
| defaults: | |
| run: | |
| # this is needed, because otherwise conda env is not available | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| run: sudo apt-get update && sudo apt-get -y --no-install-recommends install -y ghostscript | |
| - name: Cache conda package downloads | |
| uses: actions/cache@v4 | |
| env: | |
| # Increase this value to reset cache if environment-test.yml has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-Xspec-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }} | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: test | |
| cache-environment: false | |
| cache-downloads: true | |
| - name: Set directory names | |
| run: | | |
| echo "MYCACHE=$HOME/Downloads/xspec" >> $GITHUB_ENV | |
| echo "MODELDIR=$HOME/Downloads/models" >> $GITHUB_ENV | |
| echo "PATH=$PATH:$HOME/.local/bin/" >> $GITHUB_ENV | |
| - name: Cache models | |
| uses: pat-s/[email protected] | |
| id: cache-downloads | |
| with: | |
| path: ${{ env.MODELDIR }} | |
| key: cache-downloads | |
| - name: Download models (if necessary) | |
| run: | | |
| mkdir -p $MODELDIR | |
| pushd $MODELDIR | |
| wget -q -nc https://zenodo.org/record/1169181/files/uxclumpy-cutoff.fits https://zenodo.org/record/1169181/files/uxclumpy-cutoff-omni.fits; | |
| popd | |
| - name: Cache xspec install | |
| uses: pat-s/[email protected] | |
| id: cache-xspec | |
| env: | |
| cache-name: cache-xspec-install | |
| cache-version: 4 | |
| with: | |
| path: ${{ env.MYCACHE }}/xspec-install | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ matrix.python-version }}-${{ env.cache-version }} | |
| restore-keys: | | |
| ${{ runner.os }}-build-${{ env.cache-name }}-${{ matrix.python-version }}-${{ env.cache-version }} | |
| ${{ runner.os }}-build-${{ env.cache-name }}-${{ matrix.python-version }} | |
| - name: Download and Install heasoft (if necessary) | |
| run: | | |
| mkdir -p $MYCACHE | |
| pushd $MYCACHE | |
| if ! ls -d $MYCACHE/xspec-install/x86_64-pc-linux-gnu-libc*/; then | |
| rm -rf heasoft*/; | |
| wget -O - 'https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/tarit/tarit.pl?mode=download&arch=src&src_pc_linux_ubuntu=Y&src_other_specify=&general=heasptools&general=heagen&xanadu=xspec' --header 'User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:84.0) Gecko/20100101 Firefox/84.0' --header 'Accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8' --header 'Accept-Language: en-US' --header 'DNT: 1' --header 'Connection: keep-alive' --header 'Referer: https://heasarc.gsfc.nasa.gov/lheasoft/download.html' --header 'Upgrade-Insecure-Requests: 1' --header 'Sec-GPC: 1' --progress=dot:giga | tar -xzf - | |
| ls heasoft*; | |
| ls; | |
| echo "compiling xspec"; | |
| sudo apt-get install -y gfortran build-essential cmake liblapack3 liblapack-dev libatlas3-base libatlas-base-dev libblas3 libblas-dev libreadline-dev; | |
| ls heasoft*; | |
| export XSPEC_BUILD_DIR=`ls -d heasoft-*/BUILD_DIR`; | |
| pushd $XSPEC_BUILD_DIR; | |
| mkdir -p $MYCACHE/xspec-install/; | |
| ./configure --prefix=$MYCACHE/xspec-install/ --with-components="Xspec" && make && make install | grep -v hd_install; | |
| ls $MYCACHE/xspec-install/x86_64-pc-linux-gnu-libc*/; | |
| popd; | |
| fi | |
| - name: Load heasoft | |
| run: | | |
| export HEADAS=`ls -d $MYCACHE/xspec-install/x86_64-pc-linux-gnu-libc*/`; | |
| echo "HEADAS=$HEADAS" >> $GITHUB_ENV | |
| ls $HEADAS; | |
| echo "loading xspec from " $HEADAS; | |
| source ${HEADAS}/headas-init.sh; | |
| echo "PYTHONPATH: $PYTHONPATH"; | |
| echo "PATH: $PATH"; | |
| echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV | |
| echo "PATH=$PATH" >> $GITHUB_ENV | |
| echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
| python -c 'import xspec' || true; | |
| - name: Install python dependencies | |
| run: | | |
| micromamba install -y -c conda-forge ultranest "coverage<7.0.0" coveralls==3.3.1 scipy "matplotlib>=3.5" h5py astropy requests cython tqdm coverage toml && | |
| pip install git+https://github.com/JohannesBuchner/coverage-lcov && | |
| sudo sed -i '/PDF/s/none/read|write/' /etc/ImageMagick-6/policy.xml | |
| - name: Check install | |
| run: | | |
| python -c "import numpy"; | |
| python -c "import xspec" | |
| - name: Prepare testing | |
| run: | | |
| cp .coveragerc docker/testsrc | |
| cp .coveragerc examples/sherpa | |
| cp .coveragerc examples/xspec | |
| pushd docker/testsrc | |
| echo "backend: Agg" > matplotlibrc | |
| ls | |
| rm *.nh | |
| - name: Test helper scripts | |
| run: | | |
| pushd docker/testsrc | |
| coverage run -p ../../fixkeywords.py combined_src.pi combined_bkg.pi combined_src.rmf combined_src.arf | |
| coverage run -p ../../gal.py combined_src.pi | |
| ls combined_src.pi.nh | |
| coverage run -p ../../autobackgroundmodel/fitbkg.py combined_bkg.pi combined_src.pi || exit 1 | |
| coverage run -p ../../autobackgroundmodel/fitbkg.py combined_bkg.pi || exit 1 | |
| coverage run -p ../../autobackgroundmodel/fitbkg.py || true | |
| coverage run -p ../../gal.py || true | |
| coverage run -p ../../fixkeywords.py || true | |
| git checkout . | |
| popd | |
| - name: Test examples | |
| run: | | |
| pushd examples/xspec; | |
| source ${HEADAS}/headas-init.sh | |
| PYTHONPATH=../../:$PYTHONPATH bash -v runall.sh || exit 1; | |
| ls; | |
| popd; | |
| - name: Install | |
| run: | | |
| python -m pip install . | |
| wc -l examples/sherpa/.cover* examples/xspec/.cover* docker/testsrc/.cover* .cover* || true | |
| - name: David Homan's workflow | |
| run: | | |
| python -m pip install natsort; | |
| pushd examples/xspec/bayesian-workflow/tutorials/; | |
| bash run_all.sh; | |
| popd; | |
| - name: Coverage report | |
| run: | | |
| coverage combine examples/sherpa examples/xspec docker/testsrc . | |
| coverage report | |
| coverage-lcov | |
| # make paths relative | |
| sed -i s,$PWD/,,g lcov.info | |
| - name: Coveralls | |
| uses: coverallsapp/github-action@master | |
| with: | |
| path-to-lcov: lcov.info | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| flag-name: xspec-${{ matrix.test_number }} | |
| parallel: true | |
| finish: | |
| needs: [Sherpa, Xspec] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| parallel-finished: true |