From 17110b25273ffe7357335a056fe506724a0a89df Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:16:06 -0400 Subject: [PATCH 01/10] added read methods for graphblas --- pyproject.toml | 1 + src/binsparse/_io/api.py | 9 ++-- src/binsparse/_io/methods.py | 89 ++++++++++++++++++++++++++---------- tests/test_basic.py | 13 ++++++ 4 files changed, 85 insertions(+), 27 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5807306..c207fb4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,6 +46,7 @@ doc = [ # For better type hints "h5py", "zarr", + "python-graphblas[default]", ] test = [ "pytest", diff --git a/src/binsparse/_io/api.py b/src/binsparse/_io/api.py index 0e33318..be5a05b 100644 --- a/src/binsparse/_io/api.py +++ b/src/binsparse/_io/api.py @@ -1,6 +1,7 @@ from collections.abc import Mapping from types import MappingProxyType +import graphblas as gb from scipy import sparse from binsparse._io.methods import ( @@ -15,7 +16,7 @@ from binsparse._types import GroupTypes -def read(group: GroupTypes) -> sparse.spmatrix: +def read(group: GroupTypes, struct: str | None = "scipy") -> gb.Matrix | sparse.spmatrix: """Read a sparse matrix from a store. Parameters @@ -25,11 +26,11 @@ def read(group: GroupTypes) -> sparse.spmatrix: """ metadata = read_attr(group, "binsparse") if metadata["format"] == "CSR": - return read_csr(group) + return read_csr(group, struct=struct) elif metadata["format"] == "CSC": - return read_csc(group) + return read_csc(group, struct=struct) elif metadata["format"] == "COO": - return read_coo(group) + return read_coo(group, struct=struct) else: raise NotImplementedError(f"no implementation for format {metadata['format']}") diff --git a/src/binsparse/_io/methods.py b/src/binsparse/_io/methods.py index a537a9c..0f39c4a 100644 --- a/src/binsparse/_io/methods.py +++ b/src/binsparse/_io/methods.py @@ -1,6 +1,7 @@ from collections.abc import Mapping from types import MappingProxyType +import graphblas as gb import numpy as np from scipy import sparse @@ -59,7 +60,7 @@ def write_csr(store: GroupTypes, key: str, x: sparse.csr_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_csr(group: GroupTypes) -> sparse.csr_matrix: +def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: """Read a CSR matrix from a store. Parameters @@ -67,6 +68,9 @@ def read_csr(group: GroupTypes) -> sparse.csr_matrix: group A Zarr or h5py group. + struct + The structure to return the data in. Either "scipy" or "graphblas" + Returns ------- x @@ -76,14 +80,25 @@ def read_csr(group: GroupTypes) -> sparse.csr_matrix: assert metadata["format"] == "CSR" shape = tuple(metadata["shape"]) - return sparse.csr_matrix( - ( - group["values"][()], + if struct.lower() == "scipy": + return sparse.csr_matrix( + ( + group["values"][()], + group["indices_1"][()], + group["pointers_to_1"][()], + ), + shape=shape, + ) + elif struct.lower() == "graphblas": + return gb.Matrix.from_csr( group["indices_1"][()], group["pointers_to_1"][()], - ), - shape=shape, - ) + group["values"][()], + nrows=shape[0], + ncols=shape[1], + ) + else: + raise NotImplementedError(f"no implementation for returning data using {struct}") def write_csc(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwargs: Mapping = MappingProxyType({})): @@ -116,7 +131,7 @@ def write_csc(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_csc(group: GroupTypes) -> sparse.csc_matrix: +def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: """Read a CSC matrix from a store. Parameters @@ -124,6 +139,9 @@ def read_csc(group: GroupTypes) -> sparse.csc_matrix: group A Zarr or h5py group. + struct + The structure to return the data in. Either "scipy" or "graphblas" + Returns ------- x @@ -133,14 +151,25 @@ def read_csc(group: GroupTypes) -> sparse.csc_matrix: assert metadata["format"] == "CSC" shape = tuple(metadata["shape"]) - return sparse.csc_matrix( - ( - group["values"][()], + if struct.lower() == "scipy": + return sparse.csc_matrix( + ( + group["values"][()], + group["indices_1"][()], + group["pointers_to_1"][()], + ), + shape=shape, + ) + elif struct.lower() == "graphblas": + return gb.Matrix.from_csc( group["indices_1"][()], group["pointers_to_1"][()], - ), - shape=shape, - ) + group["values"][()], + nrows=shape[0], + ncols=shape[1], + ) + else: + raise NotImplementedError(f"no implementation for returning data using {struct}") def write_coo(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwargs: Mapping = MappingProxyType({})): @@ -173,7 +202,7 @@ def write_coo(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_coo(group: GroupTypes): +def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: """Read a COO matrix from a store. Parameters @@ -181,6 +210,9 @@ def read_coo(group: GroupTypes): group A Zarr or h5py group. + struct + The structure to return the data in. Either "scipy" or "graphblas" + Returns ------- x @@ -190,13 +222,24 @@ def read_coo(group: GroupTypes): assert metadata["format"] == "COO" shape = tuple(metadata["shape"]) - return sparse.coo_matrix( - ( - group["values"][()], + if struct.lower() == "scipy": + return sparse.coo_matrix( ( - group["indices_0"][()], - group["indices_1"][()], + group["values"][()], + ( + group["indices_0"][()], + group["indices_1"][()], + ), ), - ), - shape=shape, - ) + shape=shape, + ) + elif struct.lower() == "graphblas": + return gb.Matrix.from_coo( + group["indices_0"][()], + group["indices_1"][()], + group["values"][()], + nrows=shape[0], + ncols=shape[1], + ) + else: + raise NotImplementedError(f"no implementation for returning data using {struct}") diff --git a/tests/test_basic.py b/tests/test_basic.py index 7059e9a..3700ae2 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -1,3 +1,4 @@ +import graphblas as gb import h5py import pytest import zarr @@ -45,3 +46,15 @@ def test_metadata(store, fmt): for k, v in metadata["data_types"].items(): assert v in _DTYPE_STR_REGISTRY.values(), f"unrecognized dtype for '{k}': {v}" + + +@pytest.fixture(params=["scipy", "graphblas"]) +@pytest.mark.parametrize("fmt", ["csr", "csc", "coo"]) +def test_structure(request, store, fmt): + struct = request.param + orig = sparse.random(100, 100, density=0.1, format=fmt) + binsparse.write(store, "X", orig) + if struct == "graphblas": + orig = gb.io.from_scipy_sparse(orig) + from_disk = binsparse.read(store["X"], struct=struct) + assert_equal(orig, from_disk) From 460f109fdb4ac67ab002303c4ce3a7b0bb7647d0 Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:24:00 -0400 Subject: [PATCH 02/10] removing shape --- src/binsparse/_io/methods.py | 7 +------ tests/test_basic.py | 8 +++----- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/src/binsparse/_io/methods.py b/src/binsparse/_io/methods.py index 0f39c4a..f54ff35 100644 --- a/src/binsparse/_io/methods.py +++ b/src/binsparse/_io/methods.py @@ -80,6 +80,7 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: assert metadata["format"] == "CSR" shape = tuple(metadata["shape"]) + print(shape) if struct.lower() == "scipy": return sparse.csr_matrix( ( @@ -94,8 +95,6 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: group["indices_1"][()], group["pointers_to_1"][()], group["values"][()], - nrows=shape[0], - ncols=shape[1], ) else: raise NotImplementedError(f"no implementation for returning data using {struct}") @@ -165,8 +164,6 @@ def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: group["indices_1"][()], group["pointers_to_1"][()], group["values"][()], - nrows=shape[0], - ncols=shape[1], ) else: raise NotImplementedError(f"no implementation for returning data using {struct}") @@ -238,8 +235,6 @@ def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: group["indices_0"][()], group["indices_1"][()], group["values"][()], - nrows=shape[0], - ncols=shape[1], ) else: raise NotImplementedError(f"no implementation for returning data using {struct}") diff --git a/tests/test_basic.py b/tests/test_basic.py index 3700ae2..9869491 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -48,13 +48,11 @@ def test_metadata(store, fmt): assert v in _DTYPE_STR_REGISTRY.values(), f"unrecognized dtype for '{k}': {v}" -@pytest.fixture(params=["scipy", "graphblas"]) @pytest.mark.parametrize("fmt", ["csr", "csc", "coo"]) -def test_structure(request, store, fmt): - struct = request.param +def test_graphblas_structure(store, fmt): + struct = "graphblas" orig = sparse.random(100, 100, density=0.1, format=fmt) binsparse.write(store, "X", orig) - if struct == "graphblas": - orig = gb.io.from_scipy_sparse(orig) + orig = gb.io.from_scipy_sparse(orig) from_disk = binsparse.read(store["X"], struct=struct) assert_equal(orig, from_disk) From ea30efa61c4fad816b7243dea0b34dca4782f98d Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:36:26 -0400 Subject: [PATCH 03/10] added better testing for equality in graphblas --- src/binsparse/_testing.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/binsparse/_testing.py b/src/binsparse/_testing.py index d01da6b..926aeae 100644 --- a/src/binsparse/_testing.py +++ b/src/binsparse/_testing.py @@ -1,10 +1,11 @@ from functools import singledispatch +import graphblas as gb import numpy as np from scipy import sparse -def assert_equal(a: sparse.spmatrix, b): +def assert_equal(a: gb.Matrix | sparse.spmatrix, b): assert type(a) == type(b), f"types differ: {type(a)} != {type(b)}" assert a.shape == b.shape, f"shapes differ: {a.shape} != {b.shape}" _assert_equal(a, b) @@ -26,3 +27,9 @@ def _(a, b): def _(a, b): for attr in ["row", "col", "data"]: np.testing.assert_equal(getattr(a, attr), getattr(b, attr)) + + +@_assert_equal.register(gb.Matrix) +def _(a, b): + equal = a.isequal(b) + assert equal, "GraphBLAS matrices are not equal" From 898d1b91081c4d1eb710b7f0b3a90334a5461552 Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:43:35 -0400 Subject: [PATCH 04/10] swapping axes to fix errors --- src/binsparse/_io/methods.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/binsparse/_io/methods.py b/src/binsparse/_io/methods.py index f54ff35..ef2c8fc 100644 --- a/src/binsparse/_io/methods.py +++ b/src/binsparse/_io/methods.py @@ -80,7 +80,6 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: assert metadata["format"] == "CSR" shape = tuple(metadata["shape"]) - print(shape) if struct.lower() == "scipy": return sparse.csr_matrix( ( @@ -92,8 +91,8 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: ) elif struct.lower() == "graphblas": return gb.Matrix.from_csr( - group["indices_1"][()], group["pointers_to_1"][()], + group["indices_1"][()], group["values"][()], ) else: @@ -161,8 +160,8 @@ def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: ) elif struct.lower() == "graphblas": return gb.Matrix.from_csc( - group["indices_1"][()], group["pointers_to_1"][()], + group["indices_1"][()], group["values"][()], ) else: From 65b6bf32e2cefa224ae3872a0659af5a47f050a2 Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:52:11 -0400 Subject: [PATCH 05/10] added graphblas to basic usage --- docs/notebooks/basic-usage.ipynb | 148 ++++++++++++++++++++++++++++++- 1 file changed, 147 insertions(+), 1 deletion(-) diff --git a/docs/notebooks/basic-usage.ipynb b/docs/notebooks/basic-usage.ipynb index 4371b71..088b17d 100644 --- a/docs/notebooks/basic-usage.ipynb +++ b/docs/notebooks/basic-usage.ipynb @@ -53,6 +53,152 @@ "binsparse.write(z, \"csr\", csr)\n", "binsparse.read(z[\"csr\"])" ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + "\"M_0\" nvals nrows ncols dtype format\n", + "gb.Matrix 10000 1000 100 FP64 csr" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "z = zarr.group()\n", + "\n", + "binsparse.write(z, \"csr\", csr)\n", + "binsparse.read(z[\"csr\"], struct=\"graphblas\")" + ] } ], "metadata": { @@ -71,7 +217,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.6" }, "vscode": { "interpreter": { From 3b5ec7a54c03ea4e9f4bad28f41ebd341dc280ad Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:53:33 -0400 Subject: [PATCH 06/10] updated dependencies in pyproject.toml --- Pipfile | 12 ++ Pipfile.lock | 382 +++++++++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- 3 files changed, 395 insertions(+), 1 deletion(-) create mode 100644 Pipfile create mode 100644 Pipfile.lock diff --git a/Pipfile b/Pipfile new file mode 100644 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"scipy", "numpy", + "python-graphblas[default]", # for debug logging (referenced from the issue template) "session-info", ] @@ -46,7 +47,6 @@ doc = [ # For better type hints "h5py", "zarr", - "python-graphblas[default]", ] test = [ "pytest", From 4a1781cc21d8cff6cc16c1873b24197012a89504 Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:54:35 -0400 Subject: [PATCH 07/10] removing Pipfile --- Pipfile | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 Pipfile diff --git a/Pipfile b/Pipfile deleted file mode 100644 index 219e907..0000000 --- a/Pipfile +++ /dev/null @@ -1,12 +0,0 @@ -[[source]] -url = "https://pypi.org/simple" -verify_ssl = true -name = "pypi" - -[packages] - -[dev-packages] -ipykernel = "*" - -[requires] -python_version = "3.10" From 5f5be018375bad13dfd1499b327e7452fefdb82e Mon Sep 17 00:00:00 2001 From: taddyb Date: Tue, 12 Mar 2024 07:55:05 -0400 Subject: [PATCH 08/10] removing lock --- Pipfile.lock | 382 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"docutils>=0.8,!=0.18.*,!=0.19.*", "sphinx>=4", "sphinx-book-theme>=1.0.0", + "matplotlib", "myst-nb", "sphinxcontrib-bibtex>=1.0.0", "sphinx-autodoc-typehints", From a9474978676ea0b95758775dfc16f2b8440593b1 Mon Sep 17 00:00:00 2001 From: taddyb Date: Thu, 4 Apr 2024 07:00:22 -0400 Subject: [PATCH 10/10] changed struct to _class, and updated docs --- pyproject.toml | 4 ++-- src/binsparse/_io/api.py | 9 ++++----- src/binsparse/_io/methods.py | 36 ++++++++++++++++++------------------ tests/test_basic.py | 13 +++++++++++-- 4 files changed, 35 insertions(+), 27 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5d2c371..7d9cad6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,6 @@ urls.Home-page = "https://github.com/ivirshup/binsparse-python" dependencies = [ "scipy", "numpy", - "python-graphblas[default]", # for debug logging (referenced from the issue template) "session-info", ] @@ -30,7 +29,8 @@ dependencies = [ dev = [ # CLI for bumping the version number "pre-commit", - "twine>=4.0.2" + "twine>=4.0.2", + "python-graphblas[default]", ] doc = [ "docutils>=0.8,!=0.18.*,!=0.19.*", diff --git a/src/binsparse/_io/api.py b/src/binsparse/_io/api.py index be5a05b..1cdb7cd 100644 --- a/src/binsparse/_io/api.py +++ b/src/binsparse/_io/api.py @@ -1,7 +1,6 @@ from collections.abc import Mapping from types import MappingProxyType -import graphblas as gb from scipy import sparse from binsparse._io.methods import ( @@ -16,7 +15,7 @@ from binsparse._types import GroupTypes -def read(group: GroupTypes, struct: str | None = "scipy") -> gb.Matrix | sparse.spmatrix: +def read(group: GroupTypes, _class: str = "scipy") -> object: """Read a sparse matrix from a store. Parameters @@ -26,11 +25,11 @@ def read(group: GroupTypes, struct: str | None = "scipy") -> gb.Matrix | sparse. """ metadata = read_attr(group, "binsparse") if metadata["format"] == "CSR": - return read_csr(group, struct=struct) + return read_csr(group, _class=_class) elif metadata["format"] == "CSC": - return read_csc(group, struct=struct) + return read_csc(group, _class=_class) elif metadata["format"] == "COO": - return read_coo(group, struct=struct) + return read_coo(group, _class=_class) else: raise NotImplementedError(f"no implementation for format {metadata['format']}") diff --git a/src/binsparse/_io/methods.py b/src/binsparse/_io/methods.py index ef2c8fc..489e9e1 100644 --- a/src/binsparse/_io/methods.py +++ b/src/binsparse/_io/methods.py @@ -60,7 +60,7 @@ def write_csr(store: GroupTypes, key: str, x: sparse.csr_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: +def read_csr(group: GroupTypes, _class: str) -> gb.Matrix | sparse.csr_matrix: """Read a CSR matrix from a store. Parameters @@ -68,8 +68,8 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: group A Zarr or h5py group. - struct - The structure to return the data in. Either "scipy" or "graphblas" + _class + The class we will use to create the sparse matrix. Either "scipy" or "graphblas" Returns ------- @@ -80,7 +80,7 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: assert metadata["format"] == "CSR" shape = tuple(metadata["shape"]) - if struct.lower() == "scipy": + if _class.lower() == "scipy": return sparse.csr_matrix( ( group["values"][()], @@ -89,14 +89,14 @@ def read_csr(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csr_matrix: ), shape=shape, ) - elif struct.lower() == "graphblas": + elif _class.lower() == "graphblas": return gb.Matrix.from_csr( group["pointers_to_1"][()], group["indices_1"][()], group["values"][()], ) else: - raise NotImplementedError(f"no implementation for returning data using {struct}") + raise NotImplementedError(f"no implementation for returning data using {_class}") def write_csc(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwargs: Mapping = MappingProxyType({})): @@ -129,7 +129,7 @@ def write_csc(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: +def read_csc(group: GroupTypes, _class: str) -> gb.Matrix | sparse.csc_matrix: """Read a CSC matrix from a store. Parameters @@ -137,8 +137,8 @@ def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: group A Zarr or h5py group. - struct - The structure to return the data in. Either "scipy" or "graphblas" + _class + The class we will use to create the sparse matrix. Either "scipy" or "graphblas" Returns ------- @@ -149,7 +149,7 @@ def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: assert metadata["format"] == "CSC" shape = tuple(metadata["shape"]) - if struct.lower() == "scipy": + if _class.lower() == "scipy": return sparse.csc_matrix( ( group["values"][()], @@ -158,14 +158,14 @@ def read_csc(group: GroupTypes, struct: str) -> gb.Matrix | sparse.csc_matrix: ), shape=shape, ) - elif struct.lower() == "graphblas": + elif _class.lower() == "graphblas": return gb.Matrix.from_csc( group["pointers_to_1"][()], group["indices_1"][()], group["values"][()], ) else: - raise NotImplementedError(f"no implementation for returning data using {struct}") + raise NotImplementedError(f"no implementation for returning data using {_class}") def write_coo(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwargs: Mapping = MappingProxyType({})): @@ -198,7 +198,7 @@ def write_coo(store: GroupTypes, key: str, x: sparse.csc_matrix, *, dataset_kwar store.create_dataset(f"{key}/values", data=x.data, **dataset_kwargs) -def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: +def read_coo(group: GroupTypes, _class: str) -> gb.Matrix | sparse.coo_matrix: """Read a COO matrix from a store. Parameters @@ -206,8 +206,8 @@ def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: group A Zarr or h5py group. - struct - The structure to return the data in. Either "scipy" or "graphblas" + _class + The class we will use to create the sparse matrix. Either "scipy" or "graphblas" Returns ------- @@ -218,7 +218,7 @@ def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: assert metadata["format"] == "COO" shape = tuple(metadata["shape"]) - if struct.lower() == "scipy": + if _class.lower() == "scipy": return sparse.coo_matrix( ( group["values"][()], @@ -229,11 +229,11 @@ def read_coo(group: GroupTypes, struct: str) -> gb.Matrix | sparse.coo_matrix: ), shape=shape, ) - elif struct.lower() == "graphblas": + elif _class.lower() == "graphblas": return gb.Matrix.from_coo( group["indices_0"][()], group["indices_1"][()], group["values"][()], ) else: - raise NotImplementedError(f"no implementation for returning data using {struct}") + raise NotImplementedError(f"no implementation for returning data using {_class}") diff --git a/tests/test_basic.py b/tests/test_basic.py index 9869491..d2c26e5 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -50,9 +50,18 @@ def test_metadata(store, fmt): @pytest.mark.parametrize("fmt", ["csr", "csc", "coo"]) def test_graphblas_structure(store, fmt): - struct = "graphblas" orig = sparse.random(100, 100, density=0.1, format=fmt) binsparse.write(store, "X", orig) orig = gb.io.from_scipy_sparse(orig) - from_disk = binsparse.read(store["X"], struct=struct) + from_disk = binsparse.read(store["X"], _class="graphblas") assert_equal(orig, from_disk) + + +@pytest.mark.parametrize("fmt", ["csr", "csc", "coo"]) +def test_non_implemented_structure(store, fmt): + orig = sparse.random(100, 100, density=0.1, format=fmt) + binsparse.write(store, "X", orig) + orig = gb.io.from_scipy_sparse(orig) + with pytest.raises(NotImplementedError): + from_disk = binsparse.read(store["X"], _class="torch") + assert_equal(orig, from_disk)