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test.yml
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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<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