diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 043879a9..6f76f637 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,12 @@ jobs: pip install -e '.[tests]' - name: Run tests run: | - SPARSE_BACKEND=Numba pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n auto -vvv + if [ $(python -c 'import numpy as np; print(np.lib.NumpyVersion(np.__version__) >= "2.0.0a1")') = 'True' ]; then + pytest --pyargs sparse --doctest-modules --cov-report=xml:coverage_Numba.xml -n auto -vvv + else + pytest --pyargs sparse --cov-report=xml:coverage_Numba.xml -n auto -vvv + fi + python -c 'import finch' SPARSE_BACKEND=Finch pytest --pyargs sparse/tests --cov-report=xml:coverage_Finch.xml -n auto -vvv SPARSE_BACKEND=MLIR pytest --pyargs sparse/mlir_backend --cov-report=xml:coverage_MLIR.xml -n auto -vvv - uses: codecov/codecov-action@v5 @@ -126,6 +131,9 @@ jobs: SPARSE_BACKEND: ${{ matrix.backend }} run: | cd ${GITHUB_WORKSPACE}/array-api-tests + if [ "${SPARSE_BACKEND}" = "Finch" ]; then + python -c 'import finch' + fi pytest array_api_tests -v -c pytest.ini -n auto --max-examples=2 --derandomize --disable-deadline -o xfail_strict=True --xfails-file ${GITHUB_WORKSPACE}/ci/${{ matrix.backend }}-array-api-xfails.txt --skips-file ${GITHUB_WORKSPACE}/ci/${{ matrix.backend }}-array-api-skips.txt on: diff --git a/.gitignore b/.gitignore index ed0ea873..616295ce 100644 --- a/.gitignore +++ b/.gitignore @@ -49,6 +49,7 @@ coverage.xml test_results/ junit/ .hypothesis/ +coverage_*.xml # Translations *.mo @@ -85,4 +86,3 @@ docs/examples_ipynb/ # Pixi envs .pixi/ -pixi.lock diff --git a/ci/environment.yml b/ci/environment.yml index 96e2ccd6..8126d749 100644 --- a/ci/environment.yml +++ b/ci/environment.yml @@ -5,14 +5,14 @@ channels: dependencies: - python - pip - - numpy - - numba - - scipy - - dask - - pytest - - pytest-cov - - pytest-xdist - pip: - finch-tensor>=0.2.2 - finch-mlir>=0.0.2 - pytest-codspeed + - numpy + - numba + - scipy + - dask + - pytest + - pytest-cov + - pytest-xdist diff --git a/conftest.py b/conftest.py index 626ef477..4077b874 100644 --- a/conftest.py +++ b/conftest.py @@ -1,3 +1,7 @@ +import pathlib + +import sparse + import pytest @@ -7,8 +11,18 @@ def add_doctest_modules(doctest_namespace): import numpy as np - if sparse._BackendType.Numba != sparse._BACKEND: - pass # TODO: pytest.skip() skips Finch and MLIR tests - doctest_namespace["np"] = np doctest_namespace["sparse"] = sparse + + +def pytest_ignore_collect(collection_path: pathlib.Path, config: pytest.Config) -> bool | None: + if "numba_backend" in collection_path.parts and sparse._BackendType.Numba != sparse._BACKEND: + return True + + if "mlir_backend" in collection_path.parts and sparse._BackendType.MLIR != sparse._BACKEND: + return True + + if "finch_backend" in collection_path.parts and sparse._BackendType.Finch != sparse._BACKEND: + return True + + return None diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 00000000..a40c89aa --- /dev/null +++ b/pixi.lock @@ -0,0 +1,6199 @@ +version: 6 +environments: + default: + channels: + - 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sphinx>=6.0 ; extra == 'docs' + - sphinx-rtd-theme>=1.1.0 ; extra == 'docs' + - myst-parser>=2.0.0 ; extra == 'docs' + - python-socks ; extra == 'optional' + - wsaccel ; extra == 'optional' + - websockets ; extra == 'test' + requires_python: '>=3.8' diff --git a/pixi.toml b/pixi.toml index 3fd4b0b3..bc8bf999 100644 --- a/pixi.toml +++ b/pixi.toml @@ -12,12 +12,12 @@ numpy = ">=1.17" [dependencies] python = ">=3.10,<3.13" -[feature.extras.pypi-dependencies] +[feature.extra.pypi-dependencies] dask = { version = ">=2024", extras = ["array"] } scipy = ">=0.19" scikit-learn = "*" -[feature.docs.pypi-dependencies] +[feature.doc.pypi-dependencies] mkdocs-material = "*" mkdocstrings = { version = "*", extras = ["python"] } mkdocs-gen-files = "*" @@ -25,16 +25,15 @@ mkdocs-literate-nav = "*" mkdocs-section-index = "*" mkdocs-jupyter = "*" -[feature.tests.tasks] -test = "pytest --pyargs sparse -n auto" -test-mlir = { cmd = "pytest --pyargs sparse.mlir_backend -v" } +[feature.test.tasks] +test = "pytest -n auto --doctest-modules" +test-mlir = "pytest --pyargs sparse.mlir_backend -v" test-finch = { cmd = "pytest --pyargs sparse/tests -n auto -v", depends-on = ["precompile"] } -[feature.tests.dependencies] +[feature.test.pypi-dependencies] pytest = ">=3.5" pytest-cov = "*" pytest-xdist = "*" -pre-commit = "*" pytest-codspeed = "*" [feature.notebooks.pypi-dependencies] @@ -51,6 +50,7 @@ matrepr = "*" precompile = "python -c 'import finch'" [feature.finch.dependencies] +python = ">=3.10" juliaup = ">=1.17.10" [feature.finch.pypi-dependencies] @@ -63,16 +63,20 @@ SPARSE_BACKEND = "Finch" [feature.finch.target.osx-arm64.activation.env] PYTHONFAULTHANDLER = "${HOME}/faulthandler.log" +[feature.mlir.dependencies] +python = ">=3.10" + [feature.mlir.pypi-dependencies] scipy = ">=0.19" finch-mlir = ">=0.0.2" +"PyYAML" = "*" [feature.mlir.activation.env] SPARSE_BACKEND = "MLIR" [environments] -tests = ["tests", "extras"] -docs = ["docs", "extras"] -mlir-dev = {features = ["tests", "mlir"], no-default-feature = true} -finch-dev = {features = ["tests", "finch"], no-default-feature = true} -notebooks = ["extras", "mlir", "finch", "notebooks"] +test = ["test", "extra"] +doc = ["doc", "extra"] +mlir-dev = {features = ["test", "mlir"], no-default-feature = true} +finch-dev = {features = ["test", "finch"], no-default-feature = true} +notebooks = ["extra", "mlir", "finch", "notebooks"] diff --git a/pytest.ini b/pytest.ini index d8979e47..bf57a05d 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,5 +1,5 @@ [pytest] -addopts = --cov-report term-missing --cov-report html --cov-report=term:skip-covered --cov sparse --cov-config .coveragerc --junitxml=junit/test-results.xml +addopts = --cov-report term-missing --cov-report html --cov-report=term:skip-covered --cov sparse --cov-config .coveragerc filterwarnings = ignore::PendingDeprecationWarning testpaths = diff --git a/sparse/mlir_backend/tests/__init__.py b/sparse/mlir_backend/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/sparse/mlir_backend/tests/test_simple.py b/sparse/mlir_backend/tests/test_simple.py index d0d75510..967b5fb4 100644 --- a/sparse/mlir_backend/tests/test_simple.py +++ b/sparse/mlir_backend/tests/test_simple.py @@ -9,9 +9,6 @@ import numpy as np import scipy.sparse as sps -if sparse._BACKEND != sparse._BackendType.MLIR: - pytest.skip("skipping MLIR tests", allow_module_level=True) - parametrize_dtypes = pytest.mark.parametrize( "dtype", [ diff --git a/sparse/numba_backend/_common.py b/sparse/numba_backend/_common.py index 2d056f9a..69c33b3c 100644 --- a/sparse/numba_backend/_common.py +++ b/sparse/numba_backend/_common.py @@ -1176,13 +1176,13 @@ def _parse_einsum_input(operands): Examples -------- The operand list is simplified to reduce printing: - >>> np.random.seed(123) - >>> a = np.random.rand(4, 4) - >>> b = np.random.rand(4, 4, 4) - >>> _parse_einsum_input(("...a,...a->...", a, b)) - ('za,xza', 'xz', [a, b]) # may vary - >>> _parse_einsum_input((a, [Ellipsis, 0], b, [Ellipsis, 0])) - ('za,xza', 'xz', [a, b]) # may vary + >>> rng = np.random.default_rng(42) + >>> a = rng.random((4, 4)) + >>> b = rng.random((4, 4, 4)) + >>> _parse_einsum_input(("...a,...a->...", a, b)) # doctest: +SKIP + ('za,xza', 'xz', [a, b]) + >>> _parse_einsum_input((a, [Ellipsis, 0], b, [Ellipsis, 0])) # doctest: +SKIP + ('za,xza', 'xz', [a, b]) """ if len(operands) == 0: @@ -2061,7 +2061,7 @@ def asarray(obj, /, *, dtype=None, format="coo", copy=False, device=None): Examples -------- >>> x = np.eye(8, dtype="i8") - >>> sparse.asarray(x, format="COO") + >>> sparse.asarray(x, format="coo") """ diff --git a/sparse/numba_backend/_compressed/compressed.py b/sparse/numba_backend/_compressed/compressed.py index 85bce095..380f539b 100644 --- a/sparse/numba_backend/_compressed/compressed.py +++ b/sparse/numba_backend/_compressed/compressed.py @@ -819,7 +819,7 @@ def _prune(self): -------- >>> coords = np.array([[0, 1, 2, 3]]) >>> data = np.array([1, 0, 1, 2]) - >>> s = COO(coords, data).asformat("gcxs") + >>> s = COO(coords, data, shape=(4,)).asformat("gcxs") >>> s._prune() >>> s.nnz 3 diff --git a/sparse/numba_backend/_coo/common.py b/sparse/numba_backend/_coo/common.py index 9ef5f5a9..9b186dfc 100644 --- a/sparse/numba_backend/_coo/common.py +++ b/sparse/numba_backend/_coo/common.py @@ -901,7 +901,7 @@ def diagonalize(a, axis=0): >>> a = sparse.random((3, 3, 3, 3, 3), density=0.3) >>> a_diag = sparse.diagonalize(a, axis=2) >>> (sparse.diagonal(a_diag, axis1=2, axis2=5) == a.transpose([0, 1, 3, 4, 2])).all() - True + np.True_ Returns ------- @@ -944,7 +944,7 @@ def isposinf(x, out=None): -------- [`numpy.isposinf`][] : The NumPy equivalent """ - from .core import elemwise + from sparse import elemwise return elemwise(lambda x, out=None, dtype=None: np.isposinf(x, out=out), x, out=out) @@ -971,7 +971,7 @@ def isneginf(x, out=None): -------- [`numpy.isneginf`][] : The NumPy equivalent """ - from .core import elemwise + from sparse import elemwise return elemwise(lambda x, out=None, dtype=None: np.isneginf(x, out=out), x, out=out) @@ -1234,7 +1234,7 @@ def unique_values(x, /): >>> import sparse >>> x = sparse.COO.from_numpy([1, 0, 2, 1, 2, -3]) >>> sparse.unique_values(x) - array([-3, 0, 1, 2]) + array([-3, 0, 1, 2]) """ x = _validate_coo_input(x) @@ -1279,9 +1279,9 @@ def sort(x, /, *, axis=-1, descending=False, stable=False): >>> import sparse >>> x = sparse.COO.from_numpy([1, 0, 2, 0, 2, -3]) >>> sparse.sort(x).todense() - array([-3, 0, 0, 1, 2, 2]) + array([-3, 0, 0, 1, 2, 2]) >>> sparse.sort(x, descending=True).todense() - array([ 2, 2, 1, 0, 0, -3]) + array([ 2, 2, 1, 0, 0, -3]) """ from .._common import moveaxis diff --git a/sparse/numba_backend/_coo/core.py b/sparse/numba_backend/_coo/core.py index 2b4b5a82..2db83fde 100644 --- a/sparse/numba_backend/_coo/core.py +++ b/sparse/numba_backend/_coo/core.py @@ -156,7 +156,7 @@ class COO(SparseArray, NDArrayOperatorsMixin): # lgtm [py/missing-equals] >>> rows = [0, 1, 2, 3, 4] >>> cols = [0, 0, 0, 1, 1] >>> data = [10, 20, 30, 40, 50] - >>> z = COO((data, (rows, cols))) + >>> z = COO((data, (rows, cols)), shape=(5, 2)) >>> z.todense() # doctest: +NORMALIZE_WHITESPACE array([[10, 0], [20, 0], @@ -168,10 +168,10 @@ class COO(SparseArray, NDArrayOperatorsMixin): # lgtm [py/missing-equals] indices imply summation: >>> d = {(0, 0, 0): 1, (1, 2, 3): 2, (1, 1, 0): 3} - >>> COO(d) + >>> COO(d, shape=(2, 3, 4)) >>> L = [((0, 0), 1), ((1, 1), 2), ((0, 0), 3)] - >>> COO(L).todense() # doctest: +NORMALIZE_WHITESPACE + >>> COO(L, shape=(2, 2)).todense() # doctest: +NORMALIZE_WHITESPACE array([[4, 0], [0, 2]]) @@ -440,6 +440,7 @@ def from_scipy_sparse(cls, x, /, *, fill_value=None): Examples -------- + >>> import scipy.sparse >>> x = scipy.sparse.rand(6, 3, density=0.2) >>> s = COO.from_scipy_sparse(x) >>> np.array_equal(x.todense(), s.todense()) @@ -459,7 +460,7 @@ def from_scipy_sparse(cls, x, /, *, fill_value=None): ) @classmethod - def from_iter(cls, x, shape=None, fill_value=None, dtype=None): + def from_iter(cls, x, shape, fill_value=None, dtype=None): """ Converts an iterable in certain formats to a [`sparse.COO`][] array. See examples for details. @@ -468,7 +469,7 @@ def from_iter(cls, x, shape=None, fill_value=None, dtype=None): ---------- x : Iterable or Iterator The iterable to convert to [`sparse.COO`][]. - shape : tuple[int], optional + shape : tuple[int] The shape of the array. fill_value : scalar The fill value for this array. @@ -486,7 +487,7 @@ def from_iter(cls, x, shape=None, fill_value=None, dtype=None): Here, the first part represents the coordinate and the second part represents the value. >>> x = [((0, 0), 1), ((1, 1), 1)] - >>> s = COO.from_iter(x) + >>> s = COO.from_iter(x, shape=(2, 2)) >>> s.todense() array([[1, 0], [0, 1]]) @@ -494,7 +495,7 @@ def from_iter(cls, x, shape=None, fill_value=None, dtype=None): You can also have a similar format with a dictionary. >>> x = {(0, 0): 1, (1, 1): 1} - >>> s = COO.from_iter(x) + >>> s = COO.from_iter(x, shape=(2, 2)) >>> s.todense() array([[1, 0], [0, 1]]) @@ -502,7 +503,7 @@ def from_iter(cls, x, shape=None, fill_value=None, dtype=None): The third supported format is ``(data, (..., row, col))``. >>> x = ([1, 1], ([0, 1], [0, 1])) - >>> s = COO.from_iter(x) + >>> s = COO.from_iter(x, shape=(2, 2)) >>> s.todense() array([[1, 0], [0, 1]]) @@ -510,7 +511,7 @@ def from_iter(cls, x, shape=None, fill_value=None, dtype=None): You can also pass in a [`collections.abc.Iterator`][] object. >>> x = [((0, 0), 1), ((1, 1), 1)].__iter__() - >>> s = COO.from_iter(x) + >>> s = COO.from_iter(x, shape=(2, 2)) >>> s.todense() array([[1, 0], [0, 1]]) @@ -1293,7 +1294,7 @@ def _sort_indices(self): -------- >>> coords = np.array([[1, 2, 0]], dtype=np.uint8) >>> data = np.array([4, 1, 3], dtype=np.uint8) - >>> s = COO(coords, data) + >>> s = COO(coords, data, shape=(3,)) >>> s._sort_indices() >>> s.coords # doctest: +NORMALIZE_WHITESPACE array([[0, 1, 2]], dtype=uint8) @@ -1321,7 +1322,7 @@ def _sum_duplicates(self): -------- >>> coords = np.array([[0, 1, 1, 2]], dtype=np.uint8) >>> data = np.array([6, 5, 2, 2], dtype=np.uint8) - >>> s = COO(coords, data) + >>> s = COO(coords, data, shape=(3,)) >>> s._sum_duplicates() >>> s.coords # doctest: +NORMALIZE_WHITESPACE array([[0, 1, 2]], dtype=uint8) @@ -1354,7 +1355,7 @@ def _prune(self): -------- >>> coords = np.array([[0, 1, 2, 3]]) >>> data = np.array([1, 0, 1, 2]) - >>> s = COO(coords, data) + >>> s = COO(coords, data, shape=(4,)) >>> s._prune() >>> s.nnz 3 diff --git a/sparse/numba_backend/_coo/indexing.py b/sparse/numba_backend/_coo/indexing.py index 6760e98f..5373da06 100644 --- a/sparse/numba_backend/_coo/indexing.py +++ b/sparse/numba_backend/_coo/indexing.py @@ -524,9 +524,9 @@ def _get_mask_pairs(starts_old, stops_old, c, idx): # pragma: no cover -------- >>> c = np.array([1, 2, 1, 2, 1, 1, 2, 2]) >>> starts_old = numba.typed.List() - ... starts_old.append(4) + >>> starts_old.append(4) >>> stops_old = numba.typed.List() - ... stops_old.append(8) + >>> stops_old.append(8) >>> idx = np.array([1, 2, 1]) >>> _get_mask_pairs(starts_old, stops_old, c, idx) (ListType[int64]([4]), ListType[int64]([6]), 2) @@ -575,9 +575,9 @@ def _filter_pairs(starts, stops, coords, indices): # pragma: no cover -------- >>> import numpy as np >>> starts = numba.typed.List() - ... starts.append(2) + >>> starts.append(2) >>> stops = numba.typed.List() - ... stops.append(7) + >>> stops.append(7) >>> coords = np.array([[0, 1, 2, 3, 4, 5, 6, 7]]) >>> indices = np.array([[2, 8, 2]]) # Start, stop, step pairs >>> _filter_pairs(starts, stops, coords, indices) @@ -627,11 +627,11 @@ def _join_adjacent_pairs(starts_old, stops_old): # pragma: no cover Examples -------- >>> starts = numba.typed.List() - ... starts.append(2) - ... starts.append(5) + >>> starts.append(2) + >>> starts.append(5) >>> stops = numba.typed.List() - ... stops.append(5) - ... stops.append(7) + >>> stops.append(5) + >>> stops.append(7) >>> _join_adjacent_pairs(starts, stops) (ListType[int64]([2]), ListType[int64]([7])) """ diff --git a/sparse/numba_backend/_dok.py b/sparse/numba_backend/_dok.py index 9c4e601d..4cfed3bc 100644 --- a/sparse/numba_backend/_dok.py +++ b/sparse/numba_backend/_dok.py @@ -149,6 +149,7 @@ def from_scipy_sparse(cls, x, /, *, fill_value=None): Examples -------- + >>> import scipy.sparse >>> x = scipy.sparse.rand(6, 3, density=0.2) >>> s = DOK.from_scipy_sparse(x) >>> np.array_equal(x.todense(), s.todense()) diff --git a/sparse/numba_backend/_sparse_array.py b/sparse/numba_backend/_sparse_array.py index 7f47c6eb..13180521 100644 --- a/sparse/numba_backend/_sparse_array.py +++ b/sparse/numba_backend/_sparse_array.py @@ -691,7 +691,7 @@ def mean(self, axis=None, keepdims=False, dtype=None, out=None): mean along all axes. >>> s.mean() - 0.5 + np.float64(0.5) """ if axis is None: @@ -771,7 +771,7 @@ def var(self, axis=None, dtype=None, out=None, ddof=0, keepdims=False): variance along all axes. >>> s.var() - 0.5 + np.float64(0.5) """ axis = normalize_axis(axis, self.ndim) diff --git a/sparse/numba_backend/_utils.py b/sparse/numba_backend/_utils.py index 554cb250..ce5fc29d 100644 --- a/sparse/numba_backend/_utils.py +++ b/sparse/numba_backend/_utils.py @@ -267,19 +267,18 @@ def random( Examples -------- - >>> from sparse import random >>> from scipy import stats - >>> rvs = lambda x: stats.poisson(25, loc=10).rvs(x, random_state=np.random.RandomState(1)) - >>> s = random((2, 3, 4), density=0.25, random_state=np.random.RandomState(1), data_rvs=rvs) - >>> s.todense() # doctest: +NORMALIZE_WHITESPACE - array([[[ 0, 0, 0, 0], - [34, 0, 29, 30], + >>> rng = np.random.default_rng(42) + >>> rvs = lambda x: stats.poisson(25, loc=10).rvs(x, random_state=rng) + >>> s = sparse.random((2, 3, 4), density=0.25, random_state=rng, data_rvs=rvs) + >>> s.todense() + array([[[39, 0, 0, 0], + [28, 33, 0, 37], [ 0, 0, 0, 0]], - [[33, 0, 0, 34], - [34, 0, 0, 0], - [ 0, 0, 0, 0]]]) - + [[ 0, 0, 0, 0], + [ 0, 0, 34, 0], + [ 0, 0, 0, 36]]]) """ # Copied, in large part, from scipy.sparse.random # See https://github.com/scipy/scipy/blob/main/LICENSE.txt @@ -422,15 +421,15 @@ def equivalent(x, y, /, loose=False): Examples -------- >>> equivalent(1, 1) - True + np.True_ >>> equivalent(np.nan, np.nan + 1) - True + np.True_ >>> equivalent(1, 2) - False + np.False_ >>> equivalent(np.inf, np.inf) - True - >>> equivalent(np.PZERO, np.NZERO) - False + np.True_ + >>> equivalent(np.float64(0.0), np.float64(-0.0)) + np.False_ """ x = np.asarray(x) y = np.asarray(y) diff --git a/sparse/numba_backend/tests/__init__.py b/sparse/numba_backend/tests/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/sparse/numba_backend/tests/test_coo.py b/sparse/numba_backend/tests/test_coo.py index c929fff3..58df49d9 100644 --- a/sparse/numba_backend/tests/test_coo.py +++ b/sparse/numba_backend/tests/test_coo.py @@ -1025,11 +1025,14 @@ def test_invalid_attrs_error(): def test_invalid_iterable_error(): with pytest.raises(ValueError): x = [(3, 4, 5)] - COO.from_iter(x) + COO.from_iter(x, shape=(6,)) with pytest.raises(ValueError): x = [((2.3, 4.5), 3.2)] - COO.from_iter(x) + COO.from_iter(x, shape=(5,)) + + with pytest.raises(TypeError): + COO.from_iter({(1, 1): 1}) def test_prod_along_axis(): diff --git a/sparse/tests/__init__.py b/sparse/tests/__init__.py new file mode 100644 index 00000000..e69de29b