diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml index 807123889..04ffd3eb5 100644 --- a/.github/workflows/test_and_build.yml +++ b/.github/workflows/test_and_build.yml @@ -88,6 +88,10 @@ jobs: matrix: os: ["ubuntu-latest", "macos-latest", "windows-latest"] slowtask: ["pytest_normal", "pytest_bizarro", "notebooks"] + env: + # Wheels on OS X come with an OpenMP that conflicts with OpenMP from conda-forge. + # Setting this is a workaround. + KMP_DUPLICATE_LIB_OK: ${{ contains(matrix.os, 'macos') && 'TRUE' || 'FALSE' }} steps: - name: Checkout uses: actions/checkout@v3 @@ -98,6 +102,9 @@ jobs: id: pyver with: # We should support major Python versions for at least 36-42 months + # We could probably support pypy if numba were optional + # 3.8.16 0_73_pypy + # 3.9.16 0_73_pypy contents: | 3.8 3.9 @@ -110,20 +117,22 @@ jobs: uses: ddradar/choose-random-action@v2.0.2 id: sourcetype with: - # Set weight to 0 to skip (such as if 'upstream' is known to not work). - # Have slightly higher weight for `conda-forge` for faster CI. + # Weights must be natural numbers, so set weights to very large to skip one + # (such as if 'upstream' is known to not work). contents: | conda-forge wheel source upstream weights: | - 2 1 1 1 - - name: Setup conda + 1 + - name: Setup mamba uses: conda-incubator/setup-miniconda@v2 + id: setup_mamba + continue-on-error: true with: miniforge-variant: Mambaforge miniforge-version: latest @@ -133,6 +142,18 @@ jobs: channel-priority: strict activate-environment: graphblas auto-activate-base: false + - name: Setup conda + uses: conda-incubator/setup-miniconda@v2 + id: setup_conda + if: steps.setup_mamba.outcome == 'failure' + continue-on-error: false + with: + auto-update-conda: true + python-version: ${{ steps.pyver.outputs.selected }} + channels: conda-forge,nodefaults + channel-priority: strict + activate-environment: graphblas + auto-activate-base: false - name: Update env run: | # Install dependencies based on the needs of the job. @@ -144,17 +165,17 @@ jobs: yamlver=$(python -c 'import random ; print(random.choice(["=5.4", "=6.0", ""]))') sparsever=$(python -c 'import random ; print(random.choice(["=0.12", "=0.13", "=0.14", ""]))') fmmver=$(python -c 'import random ; print(random.choice(["=1.4", ""]))') - if [[ ${{ steps.pyver.outputs.selected }} == "3.8" ]]; then + if [[ ${{ startsWith(steps.pyver.outputs.selected, '3.8') }} == true ]]; then npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", ""]))') spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", ""]))') pdver=$(python -c 'import random ; print(random.choice(["=1.2", "=1.3", "=1.4", "=1.5", ""]))') akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))') - elif [[ ${{ steps.pyver.outputs.selected }} == "3.9" ]]; then + elif [[ ${{ startsWith(steps.pyver.outputs.selected, '3.9') }} == true ]]; then npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", ""]))') spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", ""]))') pdver=$(python -c 'import random ; print(random.choice(["=1.2", "=1.3", "=1.4", "=1.5", ""]))') akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))') - elif [[ ${{ steps.pyver.outputs.selected }} == "3.10" ]]; then + elif [[ ${{ startsWith(steps.pyver.outputs.selected, '3.10') }} == true ]]; then npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", ""]))') spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", ""]))') pdver=$(python -c 'import random ; print(random.choice(["=1.3", "=1.4", "=1.5", ""]))') @@ -175,8 +196,15 @@ jobs: # We can have a tight coupling with python-suitesparse-graphblas. # That is, we don't need to support versions of it that are two years old. # But, it's still useful for us to test with different versions! + psg="" if [[ ${{ steps.sourcetype.outputs.selected}} == "conda-forge" ]] ; then - psgver=$(python -c 'import random ; print(random.choice(["=7.4.0", "=7.4.1", "=7.4.2", "=7.4.3.0", "=7.4.3.1", ""]))') + psgver=$(python -c 'import random ; print(random.choice(["=7.4.0", "=7.4.1", "=7.4.2", "=7.4.3.0", "=7.4.3.1", "=7.4.3.2", ""]))') + psg=python-suitesparse-graphblas${psgver} + elif [[ ${{ steps.sourcetype.outputs.selected}} == "wheel" ]] ; then + psgver=$(python -c 'import random ; print(random.choice(["==7.4.3.2", ""]))') + elif [[ ${{ steps.sourcetype.outputs.selected}} == "source" ]] ; then + # These should be exact versions + psgver=$(python -c 'import random ; print(random.choice(["==7.4.0.0", "==7.4.1.0", "==7.4.2.0", "==7.4.3.0", "==7.4.3.1", "==7.4.3.2", ""]))') else psgver="" fi @@ -187,23 +215,30 @@ jobs: fi echo "versions: np${npver} sp${spver} pd${pdver} ak${akver} nx${nxver} numba${numbaver} yaml${yamlver} sparse${sparsever} psgver${psgver}" - # Once we have wheels for all OSes, we can delete the last two lines. - mamba install packaging pytest coverage coveralls=3.3.1 pytest-randomly cffi donfig tomli pyyaml${yamlver} sparse${sparsever} \ - pandas${pdver} scipy${spver} numpy${npver} awkward${akver} networkx${nxver} numba${numbaver} fast_matrix_market${fmmver} \ + $(command -v mamba || command -v conda) install packaging pytest coverage coveralls=3.3.1 pytest-randomly cffi donfig tomli \ + pyyaml${yamlver} sparse${sparsever} pandas${pdver} scipy${spver} numpy${npver} awkward${akver} \ + networkx${nxver} numba${numbaver} fast_matrix_market${fmmver} ${psg} \ ${{ matrix.slowtask == 'pytest_bizarro' && 'black' || '' }} \ ${{ matrix.slowtask == 'notebooks' && 'matplotlib nbconvert jupyter "ipython>=7"' || '' }} \ ${{ steps.sourcetype.outputs.selected == 'upstream' && 'cython' || '' }} \ ${{ steps.sourcetype.outputs.selected != 'wheel' && '"graphblas>=7.4.0"' || '' }} \ - ${{ steps.sourcetype.outputs.selected == 'conda-forge' && 'python-suitesparse-graphblas' || '' }}${psgver} \ - ${{ matrix.os != 'ubuntu-latest' && '"graphblas>=7.4.0"' || '' }} \ - ${{ steps.sourcetype.outputs.selected == 'wheel' && matrix.os != 'ubuntu-latest' && 'python-suitesparse-graphblas' || '' }} + ${{ contains(steps.pyver.outputs.selected, 'pypy') && 'pypy' || '' }} - name: Build extension module run: | - # We only have wheels for Linux right now - if [[ ${{ steps.sourcetype.outputs.selected }} == "wheel" && ${{ matrix.os }} == "ubuntu-latest" ]]; then - pip install --no-deps suitesparse-graphblas + if [[ ${{ steps.sourcetype.outputs.selected }} == "wheel" ]]; then + # Add --pre if installing a pre-release + pip install --no-deps --only-binary ":all:" suitesparse-graphblas${psgver} + + # Add the below line to the conda install command above if installing from test.pypi.org + # ${{ steps.sourcetype.outputs.selected == 'wheel' && 'setuptools setuptools-git-versioning wheel cython' || '' }} \ + # pip install --no-deps --only-binary ":all:" --index-url https://test.pypi.org/simple/ "suitesparse-graphblas>=7.4.3" elif [[ ${{ steps.sourcetype.outputs.selected }} == "source" ]]; then - pip install --no-deps --no-binary=all suitesparse-graphblas + # Add --pre if installing a pre-release + pip install --no-deps --no-binary suitesparse-graphblas suitesparse-graphblas${psgver} + + # Add the below line to the conda install command above if installing from test.pypi.org + # ${{ steps.sourcetype.outputs.selected == 'source' && 'setuptools setuptools-git-versioning wheel cython' || '' }} \ + # pip install --no-deps --no-build-isolation --no-binary suitesparse-graphblas --index-url https://test.pypi.org/simple/ suitesparse-graphblas==7.4.3.3 elif [[ ${{ steps.sourcetype.outputs.selected }} == "upstream" ]]; then pip install --no-deps git+https://github.com/GraphBLAS/python-suitesparse-graphblas.git@main#egg=suitesparse-graphblas fi @@ -235,6 +270,7 @@ jobs: if [[ $H && $normal ]] ; then if [[ $macos ]] ; then echo " $vanilla" ; elif [[ $windows ]] ; then echo " $suitesparse" ; fi ; fi)$( \ if [[ $H && $bizarro ]] ; then if [[ $macos ]] ; then echo " $suitesparse" ; elif [[ $windows ]] ; then echo " $vanilla" ; fi ; fi) echo $args + pytest -v --pyargs suitesparse_graphblas coverage run -m pytest --color=yes --randomly -v $args \ ${{ matrix.slowtask == 'pytest_normal' && '--runslow' || '' }} - name: Unit tests (bizarro scalars) @@ -300,7 +336,9 @@ jobs: coverage run -a -m graphblas.core.automethods coverage run -a -m graphblas.core.infixmethods git diff --exit-code - - name: Coverage + - name: Coverage1 + id: coverageAttempt1 + continue-on-error: true env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} COVERALLS_FLAG_NAME: ${{ matrix.os }}/${{ matrix.slowtask }} @@ -309,6 +347,19 @@ jobs: coverage xml coverage report --show-missing coveralls --service=github + # Retry upload if first attempt failed. + # This happens somewhat randomly and for irregular reasons. + # Logic is a duplicate of previous step. + - name: Coverage2 + id: coverageAttempt2 + if: steps.coverageAttempt1.outcome == 'failure' + continue-on-error: false + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + COVERALLS_FLAG_NAME: ${{ matrix.os }}/${{ matrix.slowtask }} + COVERALLS_PARALLEL: true + run: | + coveralls --service=github - name: codecov uses: codecov/codecov-action@v3 - name: Notebooks Execution check diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8eb2bf10b..13caf89e4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -67,7 +67,7 @@ repos: # These versions need updated manually - flake8==6.0.0 - flake8-bugbear==23.3.23 - - flake8-simplify==0.19.3 + - flake8-simplify==0.20.0 - repo: https://github.com/asottile/yesqa rev: v1.4.0 hooks: diff --git a/graphblas/core/operator/base.py b/graphblas/core/operator/base.py index ef92b41a4..38a76cbcf 100644 --- a/graphblas/core/operator/base.py +++ b/graphblas/core/operator/base.py @@ -426,7 +426,7 @@ def _initialize(cls, include_in_ops=True): return # Read in the parse configs trim_from_front = cls._parse_config.get("trim_from_front", 0) - delete_exact = cls._parse_config.get("delete_exact", None) + delete_exact = cls._parse_config.get("delete_exact") num_underscores = cls._parse_config["num_underscores"] for re_str, return_prefix in [ diff --git a/graphblas/tests/test_numpyops.py b/graphblas/tests/test_numpyops.py index c528d4051..5b7e797f3 100644 --- a/graphblas/tests/test_numpyops.py +++ b/graphblas/tests/test_numpyops.py @@ -168,7 +168,10 @@ def test_npbinary(): compare_op = isclose else: np_result = getattr(np, binary_name)(np_left, np_right) - compare_op = npbinary.equal + if binary_name in {"arctan2"}: + compare_op = isclose + else: + compare_op = npbinary.equal except Exception: # pragma: no cover (debug) print(f"Error computing numpy result for {binary_name}") print(f"dtypes: ({gb_left.dtype}, {gb_right.dtype}) -> {gb_result.dtype}") @@ -184,11 +187,13 @@ def test_npbinary(): match(accum=gb.binary.lor) << gb_result.apply(npunary.isinf) compare = match.reduce(gb.monoid.land).new() if not compare: # pragma: no cover (debug) + print(compare_op) print(binary_name) print(compute(gb_left)) print(compute(gb_right)) print(compute(gb_result)) print(np_result) + print((np_result - compute(gb_result)).new().to_coo()[1]) assert compare diff --git a/graphblas/tests/test_ss_utils.py b/graphblas/tests/test_ss_utils.py index d21f41f03..12c8c6329 100644 --- a/graphblas/tests/test_ss_utils.py +++ b/graphblas/tests/test_ss_utils.py @@ -198,6 +198,11 @@ def test_about(): assert "library_name" in repr(about) +def test_openmp_enabled(): + # SuiteSparse:GraphBLAS without OpenMP enabled is very undesirable + assert gb.ss.about["openmp"] + + def test_global_config(): d = {} config = gb.ss.config diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh index cdd4adf16..54b02d1f9 100755 --- a/scripts/check_versions.sh +++ b/scripts/check_versions.sh @@ -13,4 +13,5 @@ conda search 'fast_matrix_market[channel=conda-forge]>=1.4.5' conda search 'numba[channel=conda-forge]>=0.56.4' conda search 'pyyaml[channel=conda-forge]>=6.0' conda search 'flake8-bugbear[channel=conda-forge]>=23.3.23' -conda search 'flake8-simplify[channel=conda-forge]>=0.19.3' +conda search 'flake8-simplify[channel=conda-forge]>=0.20.0' +# conda search 'python[channel=conda-forge]>=3.8 *pypy*' pFad - Phonifier reborn

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