TST fix tests for JAX-Galsim #1130
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| name: GalSim CI | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - runci | |
| - releases/* | |
| pull_request: | |
| branches: | |
| - main | |
| - runci | |
| - releases/* | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # First all python versions in basic linux | |
| os: [ ubuntu-latest ] | |
| py: [ 3.7, 3.8, 3.9, "3.10", 3.11, 3.12 ] | |
| CC: [ gcc ] | |
| CXX: [ g++ ] | |
| FFTW_DIR: [ "/usr/local/lib" ] | |
| # Add some other particular combinations to test | |
| include: | |
| # Just one in MacOS, since GitHub actions seems to have some kind of | |
| # system problem where seg faults happen randomly on their Mac machines. | |
| # Usually just restarting will fix it, but that's annoying, so minimize | |
| # that by only having one of these to fight with. | |
| - os: macos-latest | |
| py: "3.10" | |
| CC: cc | |
| CXX: c++ | |
| FFTW_DIR: "/opt/homebrew/lib/" | |
| # Check one with clang compiler | |
| - os: ubuntu-latest | |
| py: "3.10" | |
| CC: clang | |
| CXX: clang++ | |
| FFTW_DIR: "/usr/local/lib/" | |
| # And a pypy system. | |
| # As of 12/1/2022, this is broken for astropy. | |
| # pypy3 used to work, but that's Py 3.6, and GHA no longer supports it. | |
| # Maybe revisit at some point. Or maybe don't care too much about pypy... | |
| #- os: ubuntu-latest | |
| #py: pypy-3.7 | |
| #CC: gcc | |
| #CXX: g++ | |
| env: | |
| FFTW_DIR: ${{ matrix.FFTW_DIR }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # Need this for git commands to work right. | |
| # Also for codecov upload apparently. | |
| fetch-depth: 0 | |
| - name: Print github context properties | |
| run: | | |
| echo 'event: ${{ github.event_name }}' | |
| echo 'sha: ${{ github.sha }}' | |
| echo 'ref: ${{ github.ref }}' | |
| echo 'head_ref: ${{ github.head_ref }}' | |
| echo 'base_ref: ${{ github.base_ref }}' | |
| echo 'event.before: ${{ github.event.before }}' | |
| echo 'event.after: ${{ github.event.after }}' | |
| - name: Set up Python ${{ matrix.py }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.py }} | |
| - name: Set up ccache | |
| uses: hendrikmuhs/ccache-action@v1 | |
| with: | |
| key: ${{ matrix.os }}-${{ matrix.py }}-${{ matrix.CXX }} | |
| - name: Cache pip | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| $HOME/des_data | |
| $HOME/Library/Caches/Homebrew | |
| /usr/local/Cellar | |
| key: ${{ runner.os }}-${{ matrix.py }}-pip-${{ hashFiles('requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.py }}-pip- | |
| ${{ runner.os }}- | |
| - name: Install fftw, etc. on linux | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| echo ${{ matrix.os }} | |
| sudo -H apt update -y | |
| sudo -H apt install -y libfftw3-dev | |
| ls $FFTW_DIR | |
| # Easier if eigen is installed with apt-get, but on at least one system, check that | |
| # it gets downloaded and installed properly if it isn't installed. | |
| if ${{ matrix.py != 3.7 }}; then sudo -H apt install -y libeigen3-dev; fi | |
| # Need this for the mpeg tests | |
| sudo -H apt install -y ffmpeg | |
| - name: Install fftw, etc. on MacOS | |
| if: matrix.os == 'macos-latest' | |
| # brew sometimes exits with 1 if things are already installed. | |
| # continue-on-error should mean that this still counds as success for this step. | |
| # but it doesn't seem to work right. Still counts as an error, it just moves | |
| # on and finishes everything else before calling the whole job a failure. :( | |
| # So we still need the || true bits below. | |
| continue-on-error: true | |
| run: | | |
| echo ${{ matrix.os }} | |
| # brew update takes forever to run. Hopefully won't need to enable this too often. | |
| # Note: The || true bit here is because brew returns an error code if everything is | |
| # already installed, which is goofy. So || true means these always give | |
| # non-error values. If there really is an error, we should notice later | |
| # when trying to use whatever package failed to install. | |
| #brew update || true | |
| brew install fftw wget || true | |
| brew upgrade wget || true | |
| brew link --overwrite fftw gcc wget || true | |
| brew install eigen || true | |
| brew link --overwrite eigen || true | |
| ls $FFTW_DIR | |
| - name: Download des_data | |
| run: | | |
| ls -l $HOME | |
| if test -d $HOME/des_data; then ls -l $HOME/des_data; fi | |
| if ! test -d $HOME/des_data || ! test -f $HOME/des_data/DECam_00154912_01.fits.fz; then wget --no-check-certificate http://www.sas.upenn.edu/~mjarvis/des_data.tar.gz; tar xfz des_data.tar.gz -C $HOME; fi | |
| ln -s $HOME/des_data examples/des/ | |
| - name: Install basic dependencies | |
| run: | | |
| python -m pip install -U pip | |
| # Do these three first to clarify potential conflicts | |
| pip install -U numpy | |
| pip install -U "setuptools<72" | |
| pip install -U wheel | |
| # Standard dependencies | |
| pip install -U -r requirements.txt | |
| # Extra packages needed for testing | |
| pip install -U -r test_requirements.txt | |
| pip install -U nose coverage | |
| pip install -U matplotlib | |
| - name: Install astroplan | |
| # astroplan isn't yet numpy 2.0 compatible. So don't install that on 3.9+. | |
| # I'm also getting errors with starlink, which I think may be related to | |
| # numpy 2.0. | |
| if: (matrix.py == 3.8) || (matrix.py == 3.9) | |
| run: | | |
| pip install -U astroplan | |
| pip install -U starlink-pyast | |
| - name: Install CPython-only dependencies | |
| if: matrix.py != 'pypy-3.7' | |
| run: | | |
| # The only one left that doesn't seem to work right on pypy is starlink-pyast. | |
| # (This is now above in numpy 1.x versions.) | |
| #pip install -U starlink-pyast | |
| # And now pandas is acting up on pypy. | |
| # cf. https://github.com/pandas-dev/pandas/issues/44253 | |
| pip install -U pandas | |
| - name: List all installed packages for reference | |
| run: pip list | |
| - name: Build GalSim | |
| run: | | |
| # The prefix is required for recent MacOS, because of System Integrity Protection. | |
| # It's not necessary on Linux, but is harmless enough. | |
| FFTW_DIR=$FFTW_DIR pip install -vvv . | |
| - name: Check download_cosmos only if it changed. (And only on 1 runner) | |
| if: matrix.py == 3.7 && github.base_ref != '' | |
| run: | | |
| git status | |
| git --no-pager log --graph --pretty=oneline --abbrev-commit | head -50 | |
| echo git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only | |
| git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only | |
| if git --no-pager diff origin/${{ github.base_ref }}...${{ github.event.after }} --name-only | grep -Fxq 'galsim/download_cosmos.py'; then galsim_download_cosmos -s 23.5 -v1; fi | |
| - name: Run unit tests | |
| run: | | |
| cd tests | |
| coverage run -m pytest -v | |
| pytest -v run_examples.py | |
| cd .. # N.B. This seems to happen automatically if omitted. | |
| # Less confusing to include it explicitly. | |
| - name: Check shared library | |
| if: matrix.py == 3.8 | |
| run: | | |
| # On a few systems (arbitrarily py3.8, where we also chec mac and clang), | |
| # check the shared library creation and link. | |
| GALSIM_BUILD_SHARED=1 python setup.py install | |
| # These directories/files should now exist. | |
| echo "Look for the shared library:" | |
| test -d build/shared_clib | |
| ls build/shared_clib | |
| ls build/shared_clib/libgalsim.* | |
| # For now, use `python setup.py test` to test linking to the shared library. | |
| # We run some C++ tests there, and we use the shared library for linking. | |
| # Caveats: | |
| # 1. The C++ tests are not very comprehensive, so it won't catch all errors. | |
| # 2. Apparently setup.py test is deprecated. I'm getting warnings when I run | |
| # it that indicate it may go away at some point. So whenever that happens, | |
| # we'll have to revisit this test to find another way to build and run | |
| # the C++ tests. | |
| GALSIM_TEST_PY=0 python setup.py test | |
| - name: Upload coverage to codecov | |
| if: matrix.py != 'pypy-3.7' | |
| run: | | |
| cd tests | |
| pwd -P | |
| ls -la | |
| coverage combine || true # (Not necessary I think, but just in case.) | |
| coverage report | |
| ls -la | |
| #codecov # This didn't work. | |
| # cf. https://community.codecov.io/t/github-not-getting-codecov-report-after-switching-from-travis-to-github-actions-for-ci/ | |
| # The solution was to switch to the bash uploader line instead. | |
| bash <(curl -s https://codecov.io/bash) | |
| cd .. | |
| - name: Pre-cache cleanup | |
| continue-on-error: true | |
| run: | | |
| # This was helpful in Travis. Not sure how important it is in GHA. | |
| rm -rfv $HOME/.cache/pip/log | |
| rm -rfv $HOME/.cache/pip/http | |
| if ${{ runner.os == 'macOS' }}; then brew cleanup || true; fi |