[ci] reorder install, run apt-get first #45
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: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3] | |
| #python-version: [3.9] | |
| defaults: | |
| run: | |
| # this is needed, because otherwise conda env is not available | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install system dependencies | |
| run: sudo apt-get update && sudo apt-get -y --no-install-recommends install -y ghostscript | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| python-version: ${{ matrix.python-version }} | |
| use-only-tar-bz2: true | |
| #mamba-version: "*" | |
| - name: Set directory names | |
| run: | | |
| echo "MODELDIR=$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: Cache conda | |
| uses: pat-s/[email protected] | |
| id: cache-conda | |
| env: | |
| cache-name: cache-conda | |
| cache-version: 5 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| 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: Install python dependencies | |
| run: | | |
| conda install -y -c conda-forge mamba | |
| mamba install -y -c https://cxc.cfa.harvard.edu/conda/ciao ciao sherpa ds9 ciao-contrib caldb_main | |
| mamba 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: Conda info | |
| run: conda info | |
| - name: Conda list | |
| run: conda list | |
| - name: Conda paths | |
| run: | | |
| 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: | | |
| 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: | | |
| pushd examples/sherpa; | |
| # install interpolation code first | |
| echo $CONDA_PREFIX/lib/python* | |
| ls /usr/include/numpy/ || true | |
| sudo ln -s $CONDA_PREFIX/lib/python${{ matrix.python-version }}/site-packages/numpy/core/include/numpy /usr/include/numpy | |
| ls /usr/include/numpy/; | |
| 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: | | |
| pushd examples/sherpa/chandra; | |
| echo "179.pi 0.5 8" > filenames.txt | |
| PYTHONPATH=../../../:$PYTHONPATH WITHAPEC=0 coverage run -p ../xagnfitter.py || exit 1; | |
| ls; | |
| popd; | |
| - name: Install | |
| run: | | |
| python -m pip install . --user | |
| wc -l examples/sherpa/.cover* examples/xspec/.cover* docker/testsrc/.cover* .cover* || true | |
| - name: Coverage report | |
| run: | | |
| python -m coverage combine examples/sherpa examples/xspec docker/testsrc . | |
| python -m coverage report | |
| coverage-lcov | |
| # make paths relative | |
| sed -i s,$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: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9, '3.10', 3.11, 3] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install system dependencies | |
| run: sudo apt-get update && sudo apt-get -y --no-install-recommends install -y ghostscript | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| python-version: ${{ matrix.python-version }} | |
| use-only-tar-bz2: true | |
| #mamba-version: "*" | |
| - name: Install mamba | |
| run: conda install -y -c conda-forge mamba | |
| - name: Install python dependencies | |
| run: | | |
| mamba install -y -c conda-forge ultranest coverage coveralls scipy "matplotlib>=3.5" h5py astropy requests cython tqdm coverage toml | |
| pip install git+https://github.com/JohannesBuchner/coverage-lcov | |
| sudo sed -i '/PDF/s/none/read|write/' /etc/ImageMagick-6/policy.xml | |
| - name: Set directory names | |
| run: | | |
| echo "MYCACHE=$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: 3 | |
| 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"; | |
| python -c 'import xspec' || true; | |
| - 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: | | |
| python3 setup.py install --user | |
| wc -l examples/sherpa/.cover* examples/xspec/.cover* docker/testsrc/.cover* .cover* || true | |
| - 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 |