Update GalaxySDShape naming scheme and create support for sigma fitting with shapeHSM products #3175
Workflow file for this run
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| name: Build and Check | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| pull_request: | |
| branches: | |
| - '*' | |
| env: | |
| CONDA_ENV: numcosmo_developer | |
| CACHE_VERSION: 0 | |
| jobs: | |
| build-gcc-ubuntu: | |
| name: (ubuntu, apt, pip) | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v6 | |
| with: | |
| python-version: '3.12' | |
| - name: Install pre-requisites | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install gobject-introspection gir1.2-glib-2.0 gir1.2-glib-2.0-dev libgirepository-2.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-dev libcfitsio-dev libfyaml-dev libnlopt-dev libhdf5-dev libopenmpi-dev libcairo2-dev uncrustify | |
| pip install meson ninja pytest pytest-lazy-fixtures numpy scipy pygobject typer matplotlib --break-system-packages | |
| - name: Ensure clear Jupyter Notebooks | |
| uses: ResearchSoftwareActions/[email protected] | |
| - name: Configure NumCosmo | |
| run: meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate -Ddocumentation=false --prefix=/usr || (cat build/meson-logs/meson-log.txt && exit 1) | |
| - name: Building NumCosmo | |
| run: meson compile -C build | |
| - name: Checking indentation | |
| run: | | |
| uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/*.c numcosmo/*.h | |
| uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/math/*.c numcosmo/math/*.h | |
| uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/model/*.c numcosmo/model/*.h | |
| uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/xcor/*.c numcosmo/xcor/*.h | |
| - name: Test python examples | |
| run: | | |
| source build/numcosmo_export.sh | |
| cd examples | |
| python example_simple.py | |
| python example_cbe.py | |
| - name: Test example compilation using non-installed library | |
| run: | | |
| source build/numcosmo_export.sh | |
| cd examples | |
| gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags) | |
| gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca -lnumcosmo -lgsl -lm $(pkg-config glib-2.0 gobject-2.0 --libs --cflags) | |
| ./example_simple | |
| ./example_ca | |
| - name: Check NumCosmo | |
| run: meson test -v -C build --num-processes=2 || (cat build/meson-logs/testlog.txt && exit 1) | |
| - name: Create a NumCosmo tarball | |
| run: meson dist -C build --no-tests | |
| - name: Upload a Build Artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: release | |
| path: build/meson-dist/numcosmo-*.tar.xz | |
| - name: Test example compilation using installed library | |
| run: | | |
| meson install -C build --destdir=install_tmp | |
| sudo cp -a build/install_tmp/* / | |
| cd examples | |
| gcc -D_GNU_SOURCE -Wall example_simple.c -o example_simple $(pkg-config numcosmo --libs --cflags) | |
| gcc -D_GNU_SOURCE -Wall example_ca.c -o example_ca $(pkg-config numcosmo --libs --cflags) | |
| ./example_simple | |
| ./example_ca | |
| build-gcc-macos: | |
| name: (macos, brew, pip) | |
| runs-on: macos-latest | |
| env: | |
| CC: gcc-14 | |
| FC: gfortran-14 | |
| F77: gfortran-14 | |
| F90: gfortran-14 | |
| LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib | |
| LD_LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib | |
| DYLD_LIBRARY_PATH: /usr/local/lib:/opt/homebrew/Cellar/gmp/6.3.0/lib | |
| CPATH: /usr/local/include | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Brew install pre-requisites | |
| run: | | |
| brew uninstall --ignore-dependencies --force [email protected] | |
| brew install python3 gobject-introspection pygobject3 numpy scipy python-matplotlib meson ninja gsl gmp mpfr fftw cfitsio libfyaml nlopt gfortran glib openblas | |
| - name: Pip install pre-requisites | |
| run: | | |
| python3 -m pip install pytest pytest-lazy-fixtures typer pydantic --break-system-packages | |
| - name: Ensure clear Jupyter Notebooks | |
| uses: ResearchSoftwareActions/[email protected] | |
| - name: Fix libfyaml.pc | |
| run: | | |
| pc=$(pkg-config --variable=pcfiledir libfyaml)/libfyaml.pc | |
| sed -i '' 's/none required//g' "$pc" || true | |
| - name: Dump pkg-config info (cfitsio + libfyaml) | |
| run: | | |
| set -x | |
| echo "which pkg-config:" | |
| which pkg-config || true | |
| echo "version:" | |
| pkg-config --version || true | |
| echo "env:" | |
| echo "PKG_CONFIG_PATH=$PKG_CONFIG_PATH" | |
| echo "PKG_CONFIG_LIBDIR=$PKG_CONFIG_LIBDIR" | |
| echo "---- cfitsio ----" | |
| pkg-config --libs cfitsio || true | |
| pkg-config --cflags cfitsio || true | |
| pkg-config --variable=pcfiledir cfitsio || true | |
| pkg-config --debug --libs cfitsio || true | |
| echo "---- libfyaml ----" | |
| pkg-config --libs libfyaml || true | |
| pkg-config --cflags libfyaml || true | |
| pkg-config --variable=pcfiledir libfyaml || true | |
| pkg-config --debug --libs libfyaml || true | |
| - name: Configure NumCosmo | |
| run: | | |
| meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate -Dmpi=disabled --prefix=/usr || (cat build/meson-logs/meson-log.txt && exit 1) | |
| - name: Building NumCosmo | |
| run: | | |
| meson compile -C build | |
| - name: Test python examples | |
| run: | | |
| source build/numcosmo_export.sh | |
| cd examples | |
| python3 example_simple.py | |
| python3 example_cbe.py | |
| cd .. | |
| pytest -xvs tests/python --run-sphere-map -m sphere_map | |
| - name: Check NumCosmo | |
| run: | | |
| meson test -v -C build --num-processes=2 || (cat build/meson-logs/testlog.txt && exit 1) | |
| build-miniforge: | |
| name: (${{ matrix.os }}, py${{ matrix.python-version }}, ${{ matrix.mpi }}, Miniforge) | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| matrix: | |
| os: ["ubuntu", "macos"] | |
| python-version: ["3.12"] | |
| mpi: ["openmpi", "mpich"] | |
| exclude: | |
| - os: "macos" | |
| mpi: "openmpi" | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup miniforge | |
| uses: conda-incubator/setup-miniconda@v4 | |
| with: | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: ${{ env.CONDA_ENV }} | |
| - name: Cache date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| - name: Cache Conda env | |
| uses: actions/cache/restore@v4 | |
| id: cache | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ matrix.mpi }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }} | |
| - name: Update environment | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| conda env update -q -v -n ${{ env.CONDA_ENV }} -f environment.yml | |
| which python | |
| conda list | |
| conda remove -q -v -n numcosmo_developer openmpi | |
| conda install -q -v -n numcosmo_developer ${{ matrix.mpi }} | |
| conda install -q -v -n numcosmo_developer libfabric-devel | |
| conda list | |
| - name: Save conda-forge cache | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| id: cache-primes-save | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: ${{ steps.cache.outputs.cache-primary-key }} | |
| - name: Setting up NumCosmo | |
| run: | | |
| conda activate numcosmo_developer | |
| meson setup build -Dbuildtype=release -Dnumcosmo_py=true -Dfftw-planner=estimate --libdir=$CONDA_PREFIX/lib --prefix=$CONDA_PREFIX || (cat build/meson-logs/meson-log.txt && exit 1) | |
| - name: Building NumCosmo | |
| run: | | |
| meson compile -C build | |
| - name: Installing NumCosmo | |
| run: | | |
| meson install -C build | |
| cd examples | |
| python example_simple.py | |
| python example_cbe.py | |
| numcosmo generate planck18 test_exp_gen.yaml --data-type TT | |
| - name: Running black check | |
| run: | | |
| black --check numcosmo_py | |
| - name: Running flake8 | |
| run: | | |
| flake8 numcosmo_py | |
| - name: Running mypy | |
| run: | | |
| mypy --exclude '.*meson.*|numcosmo_py/generate_stubs\.py' -p numcosmo_py | |
| #- name: Checking indentation | |
| # run: | | |
| # uncrustify -c numcosmo_uncrustify.cfg --check -q numcosmo/*.c numcosmo/*.h | |
| #- name: Running pylint | |
| # run: | | |
| # pylint --rcfile .pylintrc numcosmo_py | |
| - name: Check NumCosmo | |
| run: meson test -v -C build --num-processes=2 || (cat build/meson-logs/testlog.txt && exit 1) | |
| build-miniforge-coverage: | |
| name: Cov-${{ matrix.suites }} (py${{ matrix.python-version }}, openmpi) | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| matrix: | |
| os: ["ubuntu"] | |
| python-version: ["3.12"] | |
| suites: ["python", "c", "stats-dist", "fit-esmcmc", "powspec", "data-cluster-wl", "py-powspec", "py-xcor"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup miniforge | |
| uses: conda-incubator/setup-miniconda@v4 | |
| with: | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: ${{ env.CONDA_ENV }} | |
| - name: Cache date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| - name: Cache Conda env | |
| uses: actions/cache/restore@v4 | |
| id: cache | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-v${{ env.CACHE_VERSION }} | |
| - name: Update environment | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| conda env update -q -v -n ${{ env.CONDA_ENV }} -f environment.yml | |
| conda list | |
| - name: Save conda-forge cache | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| id: cache-primes-save | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: ${{ steps.cache.outputs.cache-primary-key }} | |
| - name: Setting up NumCosmo | |
| run: | | |
| conda activate numcosmo_developer | |
| meson setup build -Dbuildtype=debug -Db_coverage=true -Dnumcosmo_py=true -Dfftw-planner=estimate -Dnumcosmo_debug=disabled --libdir=$CONDA_PREFIX/lib --prefix=$CONDA_PREFIX || (cat build/meson-logs/meson-log.txt && exit 1) | |
| - name: Building NumCosmo | |
| run: | | |
| meson compile -C build | |
| - name: Check and coverage | |
| # First run to generate the coverage base | |
| # Second run to generate the coverage for the tests | |
| # Third run to merge the coverage base and the coverage for the tests | |
| run: | | |
| lcov --config-file .lcovrc --no-external --capture --initial --directory build --directory numcosmo --directory tests --base-directory $(pwd)/build --output-file numcosmo-coverage-base.info | |
| meson test -v -C build --timeout-multiplier 0 --num-processes=2 --suite=${{ matrix.suites }} || (cat build/meson-logs/testlog.txt && exit 1) | |
| lcov --config-file .lcovrc --no-external --capture --directory build --directory numcosmo --directory tests --base-directory $(pwd)/build --output-file numcosmo-coverage-tests.info | |
| lcov --config-file .lcovrc --add-tracefile numcosmo-coverage-base.info --add-tracefile numcosmo-coverage-tests.info --output-file numcosmo-coverage-full.info | |
| lcov --config-file .lcovrc --remove numcosmo-coverage-full.info '*/class/*' '*/levmar/*' '*/libcuba/*' '*/plc/*' '*/sundials/*' '*/toeplitz/*' '*/tools/*' --output-file numcosmo-coverage.info | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| disable_search: true | |
| fail_ci_if_error: true | |
| files: ./numcosmo-coverage.info,./build/coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| #- name: Generate coverage | |
| # # For some reason, gcovr is ignoring the configured gcovr.cfg file | |
| # # ninja coverage -C build -v -d stats -d explain | |
| # run: | | |
| # gcovr --root . --object-directory build --config gcovr.cfg --xml-pretty -o build/meson-logs/coverage.xml | |
| #- name: Coveralls | |
| # uses: coverallsapp/github-action@v2 | |
| # with: | |
| # files: ./numcosmo-coverage.info | |
| # format: lcov | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |