add cross-links to doc notebooks #106
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| 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 coveralls 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 coveralls 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 |