From e458cadb01fb1c57cdf01161472c1cf832edce18 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Sat, 18 Feb 2023 23:21:44 +0100
Subject: [PATCH 01/15] Read Matrix Market with `fast_matrix_market`

---
 .github/workflows/test_and_build.yml |  3 +-
 environment.yml                      |  2 +-
 graphblas/io.py                      | 75 +++++++++++++++++++++++++---
 graphblas/tests/test_io.py           | 54 +++++++++++++++-----
 pyproject.toml                       |  2 +
 scripts/check_versions.sh            |  1 +
 6 files changed, 115 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index ea82052f8..c85641061 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -143,6 +143,7 @@ jobs:
           nxver=$(python -c 'import random ; print(random.choice(["=2.7", "=2.8", "=3.0", ""]))')
           yamlver=$(python -c 'import random ; print(random.choice(["=5.4", "=6.0", ""]))')
           sparsever=$(python -c 'import random ; print(random.choice(["=0.12", "=0.13", ""]))')
+          fmmver=$(python -c 'import random ; print(random.choice(["=1.4", ""]))')
           if [[ ${{ steps.pyver.outputs.selected }} == "3.8" ]]; then
             npver=$(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", ""]))')
@@ -188,7 +189,7 @@ jobs:
 
           # Once we have wheels for all OSes, we can delete the last two lines.
           mamba install pytest coverage coveralls=3.3.1 pytest-randomly cffi donfig pyyaml${yamlver} sparse${sparsever} \
-            pandas${pdver} scipy${spver} numpy${npver} awkward${akver} networkx${nxver} numba${numbaver} \
+            pandas${pdver} scipy${spver} numpy${npver} awkward${akver} networkx${nxver} numba${numbaver} fast_matrix_market${fmmver} \
             ${{ matrix.slowtask == 'pytest_bizarro' && 'black' || '' }} \
             ${{ matrix.slowtask == 'notebooks' && 'matplotlib nbconvert jupyter "ipython>=7"' || '' }} \
             ${{ steps.sourcetype.outputs.selected == 'upstream' && 'cython' || '' }} \
diff --git a/environment.yml b/environment.yml
index 90675527c..5153b7aae 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,7 +23,7 @@ dependencies:
     - pandas
     # For I/O
     - awkward
-    # - fast_matrix_market  # Coming soon...
+    - fast_matrix_market
     - networkx
     - scipy
     - sparse
diff --git a/graphblas/io.py b/graphblas/io.py
index 32a5f3f0d..2c7cec80a 100644
--- a/graphblas/io.py
+++ b/graphblas/io.py
@@ -603,16 +603,27 @@ def to_pydata_sparse(A, format="coo"):
     return s.asformat(format)
 
 
-def mmread(source, *, dup_op=None, name=None):
+def mmread(source, engine="auto", *, dup_op=None, name=None, **kwargs):
     """Create a GraphBLAS Matrix from the contents of a Matrix Market file.
 
     This uses `scipy.io.mmread
-    <https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.mmread.html>`_.
+    <https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.mmread.html>`_
+    or `fast_matrix_market.mmread
+    <https://github.com/alugowski/fast_matrix_market/tree/main/python>`_.
+
+    By default, ``fast_matrix_market`` will be used if available, because it
+    is faster. Additional keyword arguments in ``**kwargs`` will be passed
+    to the engine's ``mmread``. For example, ``parallelism=8`` will set the
+    number of threads to use to 8 when using ``fast_matrix_market``.
 
     Parameters
     ----------
-    filename : str or file
+    source : str or file
         Filename (.mtx or .mtz.gz) or file-like object
+    engine : {"auto", "scipy", "fmm", "fast_matrix_market"}, default "auto"
+        How to read the matrix market file. "scipy" uses ``scipy.io.mmread``,
+        "fmm" and "fast_matrix_market" uses ``fast_matrix_market.mmread``,
+        and "auto" will use "fast_matrix_market" if available.
     dup_op : BinaryOp, optional
         Aggregation function for duplicate coordinates (if found)
     name : str, optional
@@ -627,7 +638,21 @@ def mmread(source, *, dup_op=None, name=None):
         from scipy.sparse import isspmatrix_coo
     except ImportError:  # pragma: no cover (import)
         raise ImportError("scipy is required to read Matrix Market files") from None
-    array = mmread(source)
+    engine = engine.lower()
+    if engine in {"auto", "fmm", "fast_matrix_market"}:
+        try:
+            from fast_matrix_market import mmread  # noqa: F811
+        except ImportError:  # pragma: no cover (import)
+            if engine != "auto":
+                raise ImportError(
+                    "fast_matrix_market is required to read Matrix Market files "
+                    f'using the "{engine}" engine'
+                ) from None
+    elif engine != "scipy":
+        raise ValueError(
+            f'Bad engine value: {engine!r}. Must be "auto", "scipy", "fmm", or "fast_matrix_market"'
+        )
+    array = mmread(source, **kwargs)
     if isspmatrix_coo(array):
         nrows, ncols = array.shape
         return _Matrix.from_coo(
@@ -636,7 +661,17 @@ def mmread(source, *, dup_op=None, name=None):
     return _Matrix.from_dense(array, name=name)
 
 
-def mmwrite(target, matrix, *, comment="", field=None, precision=None, symmetry=None):
+def mmwrite(
+    target,
+    matrix,
+    engine="auto",
+    *,
+    comment="",
+    field=None,
+    precision=None,
+    symmetry=None,
+    **kwargs,
+):
     """Write a Matrix Market file from the contents of a GraphBLAS Matrix.
 
     This uses `scipy.io.mmwrite
@@ -644,10 +679,14 @@ def mmwrite(target, matrix, *, comment="", field=None, precision=None, symmetry=
 
     Parameters
     ----------
-    filename : str or file target
+    target : str or file target
         Filename (.mtx) or file-like object opened for writing
     matrix : Matrix
         Matrix to be written
+    engine : {"auto", "scipy", "fmm", "fast_matrix_market"}, default "auto"
+        How to read the matrix market file. "scipy" uses ``scipy.io.mmwrite``,
+        "fmm" and "fast_matrix_market" uses ``fast_matrix_market.mmwrite``,
+        and "auto" will use "fast_matrix_market" if available.
     comment : str, optional
         Comments to be prepended to the Matrix Market file
     field : str
@@ -661,8 +700,30 @@ def mmwrite(target, matrix, *, comment="", field=None, precision=None, symmetry=
         from scipy.io import mmwrite
     except ImportError:  # pragma: no cover (import)
         raise ImportError("scipy is required to write Matrix Market files") from None
+    engine = engine.lower()
+    if engine in {"auto", "fmm", "fast_matrix_market"}:
+        try:
+            from fast_matrix_market import mmwrite  # noqa: F811
+        except ImportError:  # pragma: no cover (import)
+            if engine != "auto":
+                raise ImportError(
+                    "fast_matrix_market is required to write Matrix Market files "
+                    f'using the "{engine}" engine'
+                ) from None
+    elif engine != "scipy":
+        raise ValueError(
+            f'Bad engine value: {engine!r}. Must be "auto", "scipy", "fmm", or "fast_matrix_market"'
+        )
     if _backend == "suitesparse" and matrix.ss.format in {"fullr", "fullc"}:
         array = matrix.ss.export()["values"]
     else:
         array = to_scipy_sparse(matrix, format="coo")
-    mmwrite(target, array, comment=comment, field=field, precision=precision, symmetry=symmetry)
+    mmwrite(
+        target,
+        array,
+        comment=comment,
+        field=field,
+        precision=precision,
+        symmetry=symmetry,
+        **kwargs,
+    )
diff --git a/graphblas/tests/test_io.py b/graphblas/tests/test_io.py
index 0f78430c1..c8b1cfc28 100644
--- a/graphblas/tests/test_io.py
+++ b/graphblas/tests/test_io.py
@@ -30,6 +30,10 @@
     except ImportError:  # pragma: no cover (import)
         ak = None
 
+try:
+    import fast_matrix_market as fmm
+except ImportError:  # pragma: no cover (import)
+    fmm = None
 
 suitesparse = gb.backend == "suitesparse"
 
@@ -161,7 +165,10 @@ def test_matrix_to_from_networkx():
 
 
 @pytest.mark.skipif("not ss")
-def test_mmread_mmwrite():
+@pytest.mark.parametrize("engine", ["auto", "scipy", "fmm"])
+def test_mmread_mmwrite(engine):
+    if engine == "fmm" and fmm is None:  # pragma: no cover (import)
+        pytest.skip("needs fast_matrix_market")
     from scipy.io.tests import test_mmio
 
     p31 = 2**31
@@ -258,10 +265,16 @@ def test_mmread_mmwrite():
             continue
         mm_in = StringIO(getattr(test_mmio, example))
         if over64:
-            with pytest.raises(OverflowError):
-                M = gb.io.mmread(mm_in)
+            with pytest.raises((OverflowError, ValueError)):
+                # fast_matrix_market v1.4.5 raises ValueError instead of OverflowError
+                M = gb.io.mmread(mm_in, engine)
         else:
-            M = gb.io.mmread(mm_in)
+            if example == "_empty_lines_example" and engine in {"fmm", "auto"} and fmm is not None:
+                # TODO MAINT: is this a bug in fast_matrix_market, or does scipy.io.mmread
+                # read an invalid file? `fast_matrix_market` v1.4.5 does not handle this.
+                continue
+            print(example)
+            M = gb.io.mmread(mm_in, engine)
             if not M.isequal(expected):  # pragma: no cover (debug)
                 print(example)
                 print("Expected:")
@@ -270,12 +283,12 @@ def test_mmread_mmwrite():
                 print(M)
                 raise AssertionError("Matrix M not as expected.  See print output above")
             mm_out = BytesIO()
-            gb.io.mmwrite(mm_out, M)
+            gb.io.mmwrite(mm_out, M, engine)
             mm_out.flush()
             mm_out.seek(0)
             mm_out_str = b"".join(mm_out.readlines()).decode()
             mm_out.seek(0)
-            M2 = gb.io.mmread(mm_out)
+            M2 = gb.io.mmread(mm_out, engine)
             if not M2.isequal(expected):  # pragma: no cover (debug)
                 print(example)
                 print("Expected:")
@@ -304,23 +317,38 @@ def test_from_scipy_sparse_duplicates():
 
 
 @pytest.mark.skipif("not ss")
-def test_matrix_market_sparse_duplicates():
-    mm = StringIO(
-        """%%MatrixMarket matrix coordinate real general
+@pytest.mark.parametrize("engine", ["auto", "scipy", "fast_matrix_market"])
+def test_matrix_market_sparse_duplicates(engine):
+    if engine == "fast_matrix_market" and fmm is None:  # pragma: no cover (import)
+        pytest.skip("needs fast_matrix_market")
+    string = """%%MatrixMarket matrix coordinate real general
         3 3 4
         1 3 1
         2 2 2
         3 1 3
         3 1 4"""
-    )
+    mm = StringIO(string)
     with pytest.raises(ValueError, match="Duplicate indices found"):
-        gb.io.mmread(mm)
-    mm.seek(0)
-    a = gb.io.mmread(mm, dup_op=gb.binary.plus)
+        gb.io.mmread(mm, engine)
+    # mm.seek(0)  # Doesn't work with `fast_matrix_market` 1.4.5
+    mm = StringIO(string)
+    a = gb.io.mmread(mm, engine, dup_op=gb.binary.plus)
     expected = gb.Matrix.from_coo([0, 1, 2], [2, 1, 0], [1, 2, 7])
     assert a.isequal(expected)
 
 
+@pytest.mark.skipif("not ss")
+def test_matrix_market_bad_engine():
+    A = gb.Matrix.from_coo([0, 0, 3, 5], [1, 4, 0, 2], [1, 0, 2, -1], nrows=7, ncols=6)
+    with pytest.raises(ValueError, match="Bad engine value"):
+        gb.io.mmwrite(BytesIO(), A, engine="bad_engine")
+    mm_out = BytesIO()
+    gb.io.mmwrite(mm_out, A)
+    mm_out.seek(0)
+    with pytest.raises(ValueError, match="Bad engine value"):
+        gb.io.mmread(mm_out, engine="bad_engine")
+
+
 @pytest.mark.skipif("not ss")
 def test_scipy_sparse():
     a = np.arange(12).reshape(3, 4)
diff --git a/pyproject.toml b/pyproject.toml
index 7dea49e98..16d8b5cc2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -70,6 +70,7 @@ io = [
     "scipy >=1.8",
     "awkward >=1.9",
     "sparse >=0.12",
+    "fast-matrix-market >=1.4.5",
 ]
 viz = [
     "matplotlib >=3.5",
@@ -85,6 +86,7 @@ complete = [
     "scipy >=1.8",
     "awkward >=1.9",
     "sparse >=0.12",
+    "fast-matrix-market >=1.4.5",
     "matplotlib >=3.5",
     "pytest",
 ]
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index ff7c88b32..8b356d834 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -8,6 +8,7 @@ conda search 'pandas[channel=conda-forge]>=1.5.3'
 conda search 'scipy[channel=conda-forge]>=1.10.0'
 conda search 'networkx[channel=conda-forge]>=3.0'
 conda search 'awkward[channel=conda-forge]>=2.0.8'
+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-comprehensions[channel=conda-forge]>=3.10.1'

From 8795df1eb171aa689729ef92c77dec4f88a7a722 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Sun, 19 Feb 2023 05:06:36 +0100
Subject: [PATCH 02/15] oops print statement

---
 graphblas/tests/test_io.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/graphblas/tests/test_io.py b/graphblas/tests/test_io.py
index c8b1cfc28..b546c5457 100644
--- a/graphblas/tests/test_io.py
+++ b/graphblas/tests/test_io.py
@@ -273,7 +273,6 @@ def test_mmread_mmwrite(engine):
                 # TODO MAINT: is this a bug in fast_matrix_market, or does scipy.io.mmread
                 # read an invalid file? `fast_matrix_market` v1.4.5 does not handle this.
                 continue
-            print(example)
             M = gb.io.mmread(mm_in, engine)
             if not M.isequal(expected):  # pragma: no cover (debug)
                 print(example)

From faaf1c7b42f87f1a37783ee703ca772407dcd5a5 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Fri, 24 Feb 2023 17:43:18 +0100
Subject: [PATCH 03/15] Update usage of `from_dense` and `to_dense` in docs and
 notebooks

---
 .pre-commit-config.yaml    |  2 +-
 README.md                  | 12 +++++++-----
 docs/user_guide/io.rst     | 14 +++++++-------
 graphblas/core/operator.py |  9 ++++-----
 graphblas/dtypes.py        |  3 +--
 graphblas/viz.py           |  2 +-
 notebooks/Louvain.ipynb    |  6 +++---
 pyproject.toml             |  1 +
 8 files changed, 25 insertions(+), 24 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index df37d4461..0c9c94988 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -71,7 +71,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.249
+    rev: v0.0.252
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/README.md b/README.md
index 0b8318b3f..34c1c1994 100644
--- a/README.md
+++ b/README.md
@@ -186,11 +186,6 @@ Similar methods exist for BinaryOp, Monoid, and Semiring.
 ```python
 import graphblas as gb
 
-# numpy arrays
-# 1-D array becomes Vector, 2-D array becomes Matrix
-A = gb.io.from_numpy(m)
-m = gb.io.to_numpy(A)
-
 # scipy.sparse matrices
 A = gb.io.from_scipy_sparse(m)
 m = gb.io.to_scipy_sparse(m, format='csr')
@@ -198,4 +193,11 @@ m = gb.io.to_scipy_sparse(m, format='csr')
 # networkx graphs
 A = gb.io.from_networkx(g)
 g = gb.io.to_networkx(A)
+
+# numpy arrays can use `from_dense` and `to_dense` on Vector and Matrix
+v = gb.Vector.from_dense(m)
+m = v.to_dense()
+
+A = gb.Matrix.from_dense(m, missing_value=0)
+m = A.to_dense(fill_value=0)
 ```
diff --git a/docs/user_guide/io.rst b/docs/user_guide/io.rst
index 52211c465..9431ff413 100644
--- a/docs/user_guide/io.rst
+++ b/docs/user_guide/io.rst
@@ -14,7 +14,7 @@ Matrix and Vector, instead, have a ``.from_coo()`` and a ``.to_coo()`` method.
 ``.from_coo()`` takes index(es) and values as either:
 
   - Python lists
-  - Numpy arrays
+  - NumPy arrays
 
 If no dtype is provided, the data type is inferred from the values.
 
@@ -77,17 +77,17 @@ A python-graphblas Matrix can be created from a 2-D (PyData) sparse array or mat
 ``gb.io.to_pydata_sparse()`` will output a 2-D (PyData) sparse array given a python-graphblas Matrix.
 The sparse format can be specified. It defaults to "coo".
 
-Numpy (Dense)
+NumPy (Dense)
 -------------
 
 While not useful for very large graphs, converting to and from small dense numpy arrays can be useful.
 
-``gb.io.from_numpy()`` will convert a 1-D array into a Vector and a 2-D array into a Matrix. When converting
-from numpy, zeros are treated as missing values.
-
-``gb.io.to_numpy()`` will convert a Vector or Matrix into the dense equivalent in numpy, filling missing
-values with zero.
+``Vector.from_dense()`` converts a 1-D array into a Vector and
+``Matrix.from_dense()`` a 2-D array into a Matrix. When converting from numpy, a value may be
+chosen to become a missing value, such as ``Matrix.from_dense(a, missing_value=0)``.
 
+``.to_dense()`` converts a Vector or Matrix into a numpy array. If there are missing values, a fill
+value should be given such as ``.to_dense(fill_value=0)``.
 
 SuiteSparse Export/Import
 -------------------------
diff --git a/graphblas/core/operator.py b/graphblas/core/operator.py
index eca7c9d75..bfd03d9df 100644
--- a/graphblas/core/operator.py
+++ b/graphblas/core/operator.py
@@ -941,8 +941,7 @@ def __contains__(self, type_):
             self[type_]
         except (TypeError, KeyError, numba.NumbaError):
             return False
-        else:
-            return True
+        return True
 
     @classmethod
     def _remove_nesting(cls, funcname, *, module=None, modname=None, strict=True):
@@ -2740,9 +2739,9 @@ def _initialize(cls):
                 cur_op._typed_ops[dtype] = bool_op
 
         # Builtin monoids that are idempotent; i.e., `op(x, x) == x` for any x
-        for name in {"any", "band", "bor", "land", "lor", "max", "min"}:
+        for name in ["any", "band", "bor", "land", "lor", "max", "min"]:
             getattr(monoid, name)._is_idempotent = True
-        for name in {
+        for name in [
             "bitwise_and",
             "bitwise_or",
             "fmax",
@@ -2752,7 +2751,7 @@ def _initialize(cls):
             "logical_or",
             "maximum",
             "minimum",
-        }:
+        ]:
             getattr(monoid.numpy, name)._is_idempotent = True
 
         # Allow some functions to work on UDTs
diff --git a/graphblas/dtypes.py b/graphblas/dtypes.py
index 2f8b40e43..22d98b8f1 100644
--- a/graphblas/dtypes.py
+++ b/graphblas/dtypes.py
@@ -44,8 +44,7 @@ def __lt__(self, other):
             t2 = lookup_dtype(other).np_type
         except ValueError:
             raise TypeError(f"Invalid or unknown datatype: {other}") from None
-        else:
-            return (t1.kind, t1.itemsize, t1.name) < (t2.kind, t2.itemsize, t2.name)
+        return (t1.kind, t1.itemsize, t1.name) < (t2.kind, t2.itemsize, t2.name)
 
     def __reduce__(self):
         if self._is_udt:
diff --git a/graphblas/viz.py b/graphblas/viz.py
index 72e18361a..89010bc3d 100644
--- a/graphblas/viz.py
+++ b/graphblas/viz.py
@@ -182,7 +182,7 @@ def datashade(M, agg="count", *, width=None, height=None, opts_kwargs=None, **kw
             images.extend(image_row)
         return hv.Layout(images).cols(ncols)
 
-    kwds = dict(  # noqa: C408
+    kwds = dict(  # noqa: C408 pylint: disable=use-dict-literal
         x="col",
         y="row",
         c="val",
diff --git a/notebooks/Louvain.ipynb b/notebooks/Louvain.ipynb
index f1b042a49..eb523ef9e 100644
--- a/notebooks/Louvain.ipynb
+++ b/notebooks/Louvain.ipynb
@@ -270,7 +270,7 @@
     "        [0, 0, 1, 0, 0, 1, 0],\n",
     "    ]\n",
     ")\n",
-    "g = gb.io.from_numpy(m)"
+    "g = Matrix.from_dense(m, missing_value=0)"
    ]
   },
   {
@@ -370,7 +370,7 @@
     "        [0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n",
     "    ]\n",
     ")\n",
-    "g = gb.io.from_numpy(m)"
+    "g = Matrix.from_dense(m, missing_value=0)"
    ]
   },
   {
@@ -469,7 +469,7 @@
     "        [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0],\n",
     "    ]\n",
     ")\n",
-    "g = gb.io.from_numpy(m)"
+    "g = Matrix.from_dense(m, missing_value=0)"
    ]
   },
   {
diff --git a/pyproject.toml b/pyproject.toml
index 8e673eb81..7c2d7dba0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -273,6 +273,7 @@ ignore = [
     "PLR0913",  # Too many arguments to function call
     "PLR0915",  # Too many statements
     "PLR2004",  # Magic number used in comparison, consider replacing magic with a constant variable
+    "PLW2901",  # Outer for loop variable ... overwritten by inner assignment target (Note: good advice, but too strict)
     "RET502",  # Do not implicitly `return None` in function able to return non-`None` value
     "RET503",  # Missing explicit `return` at the end of function able to return non-`None` value
     "RET504",  # Unnecessary variable assignment before `return` statement

From 00c653969013636824ce34c96ea79b38f7297d37 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Fri, 24 Feb 2023 22:46:14 +0100
Subject: [PATCH 04/15] Ignore warning from new version of pydata/sparse (we
 should investigate later)

---
 .github/workflows/test_and_build.yml | 2 +-
 pyproject.toml                       | 3 +++
 scripts/check_versions.sh            | 3 ++-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index c85641061..c4474dd8a 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -142,7 +142,7 @@ jobs:
           # Consider removing old versions when they become problematic or very old (>=2 years).
           nxver=$(python -c 'import random ; print(random.choice(["=2.7", "=2.8", "=3.0", ""]))')
           yamlver=$(python -c 'import random ; print(random.choice(["=5.4", "=6.0", ""]))')
-          sparsever=$(python -c 'import random ; print(random.choice(["=0.12", "=0.13", ""]))')
+          sparsever=$(python -c 'import random ; print(random.choice(["=0.12", "=0.13", "=0.14", ""]))')
           fmmver=$(python -c 'import random ; print(random.choice(["=1.4", ""]))')
           if [[ ${{ steps.pyver.outputs.selected }} == "3.8" ]]; then
             npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", ""]))')
diff --git a/pyproject.toml b/pyproject.toml
index 7c2d7dba0..c7d7b30b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -149,6 +149,9 @@ filterwarnings = [
     "error",
     # MAINT: we can drop support for sparse <0.13 at any time
     "ignore:`np.bool` is a deprecated alias:DeprecationWarning:sparse._umath",  # sparse <0.13
+    # sparse 0.14.0 (2022-02-24) began raising this warning; we should investigate to understand why.
+    "ignore:coords should be an ndarray. This will raise a ValueError:DeprecationWarning:sparse._coo.core",
+
     # setuptools v67.3.0 deprecated `pkg_resources.declare_namespace` on 13 Feb 2023. See:
     # https://setuptools.pypa.io/en/latest/history.html#v67-3-0
     # MAINT: check if this is still necessary in 2025
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index 8b356d834..714109951 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -5,9 +5,10 @@
 # Tip: add `--json` for more information.
 conda search 'numpy[channel=conda-forge]>=1.24.2'
 conda search 'pandas[channel=conda-forge]>=1.5.3'
-conda search 'scipy[channel=conda-forge]>=1.10.0'
+conda search 'scipy[channel=conda-forge]>=1.10.1'
 conda search 'networkx[channel=conda-forge]>=3.0'
 conda search 'awkward[channel=conda-forge]>=2.0.8'
+conda search 'sparse[channel=conda-forge]>=0.14.0'
 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'

From 632ebefebcdf32837d7de30577a057039e1ac43d Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Sat, 25 Feb 2023 14:19:21 +0100
Subject: [PATCH 05/15] `to_pydata_sparse(v)` on Vector should create 1-d array

---
 graphblas/io.py            | 17 ++++++++++-------
 graphblas/tests/test_io.py |  9 ++++++---
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/graphblas/io.py b/graphblas/io.py
index 107d1d09b..fa9a0e5e7 100644
--- a/graphblas/io.py
+++ b/graphblas/io.py
@@ -550,14 +550,17 @@ def to_pydata_sparse(A, format="coo"):
     if format not in {"coo", "dok", "gcxs"}:
         raise ValueError(f"Invalid format: {format}")
 
-    if format == "gcxs":
-        B = to_scipy_sparse(A, format="csr")
+    if _output_type(A) is _Vector:
+        indices, values = A.to_coo(sort=False)
+        s = COO(indices, values, shape=A.shape)
     else:
-        # obtain an intermediate conversion via hardcoded 'coo' intermediate object
-        B = to_scipy_sparse(A, format="coo")
-
-    # convert to pydata.sparse
-    s = COO.from_scipy_sparse(B)
+        if format == "gcxs":
+            B = to_scipy_sparse(A, format="csr")
+        else:
+            # obtain an intermediate conversion via hardcoded 'coo' intermediate object
+            B = to_scipy_sparse(A, format="coo")
+        # convert to pydata.sparse
+        s = COO.from_scipy_sparse(B)
 
     # express in the desired format
     return s.asformat(format)
diff --git a/graphblas/tests/test_io.py b/graphblas/tests/test_io.py
index 404acac44..ada092025 100644
--- a/graphblas/tests/test_io.py
+++ b/graphblas/tests/test_io.py
@@ -433,7 +433,8 @@ def test_vector_to_from_pydata_sparse():
     assert v.isequal(gb.Vector.from_coo(coords, data, dtype=dtypes.INT64), check_dtype=True)
 
     t = gb.io.to_pydata_sparse(v)
-    assert t == s
+    assert t.shape == s.shape
+    assert (t == s).all()
 
 
 @pytest.mark.skipif("not sparse")
@@ -445,7 +446,8 @@ def test_matrix_to_from_pydata_sparse():
     assert v.isequal(gb.Matrix.from_coo(*coords, data, dtype=dtypes.INT64), check_dtype=False)
 
     t = gb.io.to_pydata_sparse(v)
-    assert t == s
+    assert t.shape == s.shape
+    assert (t == s).all()
 
     # test ndim
     e = sparse.random(shape=(5, 5, 5), density=0)
@@ -464,7 +466,8 @@ def test_matrix_to_from_pydata_sparse():
     assert w.isequal(gb.Matrix.from_coo(*coords, data, dtype=dtypes.INT64), check_dtype=False)
 
     r = gb.io.to_pydata_sparse(w, format="gcxs")
-    assert r == g
+    assert r.shape == g.shape
+    assert (r == g).all()
     with pytest.raises(ValueError, match="format"):
         gb.io.to_pydata_sparse(w, format="badformat")
     with pytest.raises(TypeError, match="sparse.pydata"):

From 64d32a03d7ba77c381b86eea88e2452d73a89f4b Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 27 Feb 2023 22:20:16 +0100
Subject: [PATCH 06/15] ruff 253

---
 .pre-commit-config.yaml        |  2 +-
 graphblas/core/expr.py         |  5 ++---
 graphblas/core/matrix.py       | 11 ++++-------
 graphblas/core/ss/matrix.py    | 31 +++++++++++--------------------
 graphblas/core/ss/vector.py    | 15 ++++++---------
 graphblas/core/vector.py       |  9 ++++-----
 graphblas/tests/test_matrix.py | 15 +++++++--------
 pyproject.toml                 |  1 +
 8 files changed, 36 insertions(+), 53 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0c9c94988..2ea865ad9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -71,7 +71,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.252
+    rev: v0.0.253
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/graphblas/core/expr.py b/graphblas/core/expr.py
index 9046795db..affe06112 100644
--- a/graphblas/core/expr.py
+++ b/graphblas/core/expr.py
@@ -160,9 +160,8 @@ def parse_indices(self, indices, shape):
                 raise TypeError(f"Index for {type(self.obj).__name__} cannot be a tuple")
             # Convert to tuple for consistent processing
             indices = (indices,)
-        else:  # len(shape) == 2
-            if type(indices) is not tuple or len(indices) != 2:
-                raise TypeError(f"Index for {type(self.obj).__name__} must be a 2-tuple")
+        elif type(indices) is not tuple or len(indices) != 2:
+            raise TypeError(f"Index for {type(self.obj).__name__} must be a 2-tuple")
 
         out = []
         for i, idx in enumerate(indices):
diff --git a/graphblas/core/matrix.py b/graphblas/core/matrix.py
index 8b9b4b678..1935fcee7 100644
--- a/graphblas/core/matrix.py
+++ b/graphblas/core/matrix.py
@@ -3154,14 +3154,11 @@ def _prep_for_assign(self, resolved_indexes, value, mask, is_submask, replace, o
                             mask = _vanilla_subassign_mask(
                                 self, mask, rowidx, colidx, replace, opts
                             )
+                    elif backend == "suitesparse":
+                        cfunc_name = "GxB_Matrix_subassign_Scalar"
                     else:
-                        if backend == "suitesparse":
-                            cfunc_name = "GxB_Matrix_subassign_Scalar"
-                        else:
-                            cfunc_name = "GrB_Matrix_assign_Scalar"
-                            mask = _vanilla_subassign_mask(
-                                self, mask, rowidx, colidx, replace, opts
-                            )
+                        cfunc_name = "GrB_Matrix_assign_Scalar"
+                        mask = _vanilla_subassign_mask(self, mask, rowidx, colidx, replace, opts)
                     expr_repr = (
                         "[[{2._expr_name} rows], [{4._expr_name} cols]]"
                         f"({mask.name})"
diff --git a/graphblas/core/ss/matrix.py b/graphblas/core/ss/matrix.py
index b455d760e..b1869f198 100644
--- a/graphblas/core/ss/matrix.py
+++ b/graphblas/core/ss/matrix.py
@@ -895,9 +895,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no branch (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > nvals:  # pragma: no branch (suitesparse)
-                        values = values[:nvals]
+                elif values.size > nvals:  # pragma: no branch (suitesparse)
+                    values = values[:nvals]
             # Note: nvals is also at `indptr[nrows]`
             rv = {
                 "indptr": indptr,
@@ -937,9 +936,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no cover (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > nvals:
-                        values = values[:nvals]
+                elif values.size > nvals:
+                    values = values[:nvals]
             # Note: nvals is also at `indptr[ncols]`
             rv = {
                 "indptr": indptr,
@@ -989,9 +987,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no cover (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > nvals:
-                        values = values[:nvals]
+                elif values.size > nvals:
+                    values = values[:nvals]
             # Note: nvals is also at `indptr[nvec]`
             rv = {
                 "indptr": indptr,
@@ -1044,9 +1041,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no cover (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > nvals:
-                        values = values[:nvals]
+                elif values.size > nvals:
+                    values = values[:nvals]
             # Note: nvals is also at `indptr[nvec]`
             rv = {
                 "indptr": indptr,
@@ -3480,15 +3476,10 @@ def _import_any(
                     format = "cooc"
                 else:
                     format = "coo"
+            elif isinstance(values, np.ndarray) and values.ndim == 2 and values.flags.f_contiguous:
+                format = "fullc"
             else:
-                if (
-                    isinstance(values, np.ndarray)
-                    and values.ndim == 2
-                    and values.flags.f_contiguous
-                ):
-                    format = "fullc"
-                else:
-                    format = "fullr"
+                format = "fullr"
         else:
             format = format.lower()
         if method == "pack":
diff --git a/graphblas/core/ss/vector.py b/graphblas/core/ss/vector.py
index d13d78ac3..343335773 100644
--- a/graphblas/core/ss/vector.py
+++ b/graphblas/core/ss/vector.py
@@ -551,9 +551,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no cover (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > nvals:
-                        values = values[:nvals]
+                elif values.size > nvals:
+                    values = values[:nvals]
             rv = {
                 "size": size,
                 "indices": indices,
@@ -589,9 +588,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:  # pragma: no cover (suitesparse)
                         values = values[:1]
-                else:
-                    if values.size > size:  # pragma: no branch (suitesparse)
-                        values = values[:size]
+                elif values.size > size:  # pragma: no branch (suitesparse)
+                    values = values[:size]
             rv = {
                 "bitmap": bitmap,
                 "nvals": nvals[0],
@@ -616,9 +614,8 @@ def _export(self, format=None, *, sort=False, give_ownership=False, raw=False, m
                 if is_iso:
                     if values.size > 1:
                         values = values[:1]
-                else:
-                    if values.size > size:  # pragma: no branch (suitesparse)
-                        values = values[:size]
+                elif values.size > size:  # pragma: no branch (suitesparse)
+                    values = values[:size]
             rv = {}
             if raw or is_iso:
                 rv["size"] = size
diff --git a/graphblas/core/vector.py b/graphblas/core/vector.py
index dd183d856..8231691c6 100644
--- a/graphblas/core/vector.py
+++ b/graphblas/core/vector.py
@@ -1868,12 +1868,11 @@ def _prep_for_assign(self, resolved_indexes, value, mask, is_submask, replace, o
                     else:
                         cfunc_name = f"GrB_Vector_assign_{dtype_name}"
                         mask = _vanilla_subassign_mask(self, mask, idx, replace, opts)
+                elif backend == "suitesparse":
+                    cfunc_name = "GxB_Vector_subassign_Scalar"
                 else:
-                    if backend == "suitesparse":
-                        cfunc_name = "GxB_Vector_subassign_Scalar"
-                    else:
-                        cfunc_name = "GrB_Vector_assign_Scalar"
-                        mask = _vanilla_subassign_mask(self, mask, idx, replace, opts)
+                    cfunc_name = "GrB_Vector_assign_Scalar"
+                    mask = _vanilla_subassign_mask(self, mask, idx, replace, opts)
                 expr_repr = (
                     "[[{2._expr_name} elements]]"
                     f"({mask.name})"  # fmt: skip
diff --git a/graphblas/tests/test_matrix.py b/graphblas/tests/test_matrix.py
index 40676f71a..1d42035a3 100644
--- a/graphblas/tests/test_matrix.py
+++ b/graphblas/tests/test_matrix.py
@@ -2173,15 +2173,14 @@ def test_ss_import_export(A, do_iso, methods):
             C1.ss.pack_any(**d)
             assert C1.isequal(C)
             assert C1.ss.is_iso is do_iso
+    elif in_method == "import":
+        D1 = Matrix.ss.import_any(**d)
+        assert D1.isequal(C)
+        assert D1.ss.is_iso is do_iso
     else:
-        if in_method == "import":
-            D1 = Matrix.ss.import_any(**d)
-            assert D1.isequal(C)
-            assert D1.ss.is_iso is do_iso
-        else:
-            C1.ss.pack_any(**d)
-            assert C1.isequal(C)
-            assert C1.ss.is_iso is do_iso
+        C1.ss.pack_any(**d)
+        assert C1.isequal(C)
+        assert C1.ss.is_iso is do_iso
 
     C2 = C.dup()
     d = getattr(C2.ss, out_method)("fullc")
diff --git a/pyproject.toml b/pyproject.toml
index 9be600f04..73871c718 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -278,6 +278,7 @@ ignore = [
     "PLR0913",  # Too many arguments to function call
     "PLR0915",  # Too many statements
     "PLR2004",  # Magic number used in comparison, consider replacing magic with a constant variable
+    "PLW0603",  # Using the global statement to update ... is discouraged (Note: yeah, discouraged, but too strict)
     "PLW2901",  # Outer for loop variable ... overwritten by inner assignment target (Note: good advice, but too strict)
     "RET502",  # Do not implicitly `return None` in function able to return non-`None` value
     "RET503",  # Missing explicit `return` at the end of function able to return non-`None` value

From 46e0c623a58271814a195c954525d7341658503b Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Fri, 10 Mar 2023 11:21:32 -0600
Subject: [PATCH 07/15] bump awkward to 2.1.0

---
 .github/workflows/test_and_build.yml | 8 ++++----
 .pre-commit-config.yaml              | 4 ++--
 scripts/check_versions.sh            | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
index 31008e156..0dfa08859 100644
--- a/.github/workflows/test_and_build.yml
+++ b/.github/workflows/test_and_build.yml
@@ -148,22 +148,22 @@ jobs:
             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", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
           elif [[ ${{ steps.pyver.outputs.selected }} == "3.9" ]]; then
             npver=$(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=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
           elif [[ ${{ steps.pyver.outputs.selected }} == "3.10" ]]; then
             npver=$(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", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
           else  # Python 3.11
             npver=$(python -c 'import random ; print(random.choice(["=1.23", ""]))')
             spver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", ""]))')
             pdver=$(python -c 'import random ; print(random.choice(["=1.5", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.10", "=2.0.5", "=2.0.6", "=2.0.7", "=2.0.8", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.10", "=2.0", "=2.1", ""]))')
           fi
           if [[ ${{ steps.sourcetype.outputs.selected }} == "source" || ${{ steps.sourcetype.outputs.selected }} == "upstream" ]]; then
             # TODO: there are currently issues with some numpy versions when
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2ea865ad9..dfa1c5ee0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -64,14 +64,14 @@ repos:
       - id: yesqa
         additional_dependencies: *flake8_dependencies
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.4
     hooks:
       - id: codespell
         types_or: [python, rst, markdown]
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.253
+    rev: v0.0.254
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index 714109951..bc813b28c 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -7,7 +7,7 @@ conda search 'numpy[channel=conda-forge]>=1.24.2'
 conda search 'pandas[channel=conda-forge]>=1.5.3'
 conda search 'scipy[channel=conda-forge]>=1.10.1'
 conda search 'networkx[channel=conda-forge]>=3.0'
-conda search 'awkward[channel=conda-forge]>=2.0.8'
+conda search 'awkward[channel=conda-forge]>=2.1.0'
 conda search 'sparse[channel=conda-forge]>=0.14.0'
 conda search 'fast_matrix_market[channel=conda-forge]>=1.4.5'
 conda search 'numba[channel=conda-forge]>=0.56.4'

From 2faf4996f2713fd7f58d04ad5fb8f8950eff5d5e Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 13 Mar 2023 08:23:40 -0500
Subject: [PATCH 08/15] Maybe trust `ruff` to fix some things

But run `autoflake`, `isort`, `pyupgrade`, and `black` first (for now).
---
 .pre-commit-config.yaml | 7 ++++++-
 pyproject.toml          | 1 +
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dfa1c5ee0..9d61cdede 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -25,7 +25,7 @@ repos:
       - id: validate-pyproject
         name: Validate pyproject.toml
   - repo: https://github.com/myint/autoflake
-    rev: v2.0.1
+    rev: v2.0.2
     hooks:
       - id: autoflake
         args: [--in-place]
@@ -48,6 +48,11 @@ repos:
     hooks:
       - id: black
       - id: black-jupyter
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.254
+    hooks:
+      - id: ruff
+        args: [--fix-only]
   - repo: https://github.com/PyCQA/flake8
     rev: 6.0.0
     hooks:
diff --git a/pyproject.toml b/pyproject.toml
index b80938267..3dda43430 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,6 +15,7 @@ license = {file = "LICENSE"}
 authors = [
     {name = "Erik Welch"},
     {name = "Jim Kitchen"},
+    {name = "Python-graphblas contributors"},
 ]
 maintainers = [
     {name = "Erik Welch", email = "erik.n.welch@gmail.com"},

From b0544d8e75c5705d634f35a62b4c1487adf9ad38 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 13 Mar 2023 08:57:26 -0500
Subject: [PATCH 09/15] Add a few notes to pre-commit hooks

---
 .pre-commit-config.yaml | 15 ++++++++++++++-
 pyproject.toml          |  2 +-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9d61cdede..db152d265 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,15 +24,19 @@ repos:
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
+  # We can probably remove `autoflake` if we come to trust `ruff --fix`
   - repo: https://github.com/myint/autoflake
     rev: v2.0.2
     hooks:
       - id: autoflake
         args: [--in-place]
+  # We can probably remove `isort` if we come to trust `ruff --fix`,
+  # but we'll need to figure out the configuration to do this in `ruff`
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
+  # Let's keep `pyupgrade` even though `ruff --fix` probably does most of it
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.3.1
     hooks:
@@ -53,6 +57,8 @@ repos:
     hooks:
       - id: ruff
         args: [--fix-only]
+  # Let's keep `flake8` even though `ruff` does much of the same.
+  # `flake8-bugbear` and `flake8-simplify` have caught things missed by `ruff`.
   - repo: https://github.com/PyCQA/flake8
     rev: 6.0.0
     hooks:
@@ -60,7 +66,7 @@ repos:
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
         - flake8==6.0.0
-        - flake8-comprehensions==3.10.1
+        - flake8-comprehensions==3.10.1  # Consider removing and rely on `ruff` instead
         - flake8-bugbear==23.2.13
         - flake8-simplify==0.19.3
   - repo: https://github.com/asottile/yesqa
@@ -84,6 +90,13 @@ repos:
     hooks:
       - id: sphinx-lint
         args: [--enable, all, "--disable=line-too-long,leaked-markup"]
+  # `pyroma` may help keep our package standards up to date if best practices change.
+  # This is probably a "low value" check though and safe to remove if we want faster pre-commit.
+  - repo: https://github.com/regebro/pyroma
+    rev: "4.2"
+    hooks:
+      - id: pyroma
+        args: [-n, "10", .]
   - repo: local
     hooks:
       # Add `--hook-stage manual` to pre-commit command to run (very slow)
diff --git a/pyproject.toml b/pyproject.toml
index 3dda43430..0b3f38577 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ readme = "README.md"
 requires-python = ">=3.8"
 license = {file = "LICENSE"}
 authors = [
-    {name = "Erik Welch"},
+    {name = "Erik Welch", email = "erik.n.welch@gmail.com"},
     {name = "Jim Kitchen"},
     {name = "Python-graphblas contributors"},
 ]

From 5969089c9c77987b2a98bfbd4c32e90183f135f9 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 13 Mar 2023 09:06:34 -0500
Subject: [PATCH 10/15] Add `fast-matrix-market` to optional dependencies
 documentation

---
 README.md                      | 3 ++-
 docs/getting_started/index.rst | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 2c4b2d1b7..dab91782a 100644
--- a/README.md
+++ b/README.md
@@ -40,7 +40,8 @@ The following are not required by python-graphblas, but may be needed for certai
 - `pandas` – required for nicer `__repr__`;
 - `matplotlib` – required for basic plotting of graphs;
 - `scipy` – used in io module to read/write `scipy.sparse` format;
-- `networkx` – used in `io` module to interface with `networkx` graphs.
+- `networkx` – used in `io` module to interface with `networkx` graphs;
+- `fast-matrix-market` - for faster read/write of Matrix Market files with `gb.io.mmread` and `gb.io.mmwrite`.
 
 ## Description
 Currently works with [SuiteSparse:GraphBLAS](https://github.com/DrTimothyAldenDavis/GraphBLAS), but the goal is to make it work with all implementations of the GraphBLAS spec.
diff --git a/docs/getting_started/index.rst b/docs/getting_started/index.rst
index 661550803..d603df30b 100644
--- a/docs/getting_started/index.rst
+++ b/docs/getting_started/index.rst
@@ -34,6 +34,7 @@ to work.
   - `matplotlib <https://matplotlib.org>`__ -- required for basic plotting of graphs
   - `scipy <https://scipy.org/>`__ -- used in ``io`` module to read/write ``scipy.sparse`` format
   - `networkx <https://networkx.org>`__ -- used in ``io`` module to interface with networkx graphs
+  - `fast-matrix-market <https://github.com/alugowski/fast_matrix_market>`__ -- for faster read/write of Matrix Market files with ``gb.io.mmread`` and ``gb.io.mmwrite``
 
 GraphBLAS Fundamentals
 ----------------------

From d9ceebcf1214e0e96663b91c6a89ec42bdf1fd55 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 13 Mar 2023 18:44:32 -0500
Subject: [PATCH 11/15] Drop autoflake in pre-commit (use ruff instead)

---
 .pre-commit-config.yaml   | 11 ++-------
 graphblas/viz.py          | 48 +++++++++++++++++++--------------------
 pyproject.toml            |  2 +-
 scripts/check_versions.sh |  1 -
 4 files changed, 27 insertions(+), 35 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db152d265..75d1d0b89 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,12 +24,6 @@ repos:
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
-  # We can probably remove `autoflake` if we come to trust `ruff --fix`
-  - repo: https://github.com/myint/autoflake
-    rev: v2.0.2
-    hooks:
-      - id: autoflake
-        args: [--in-place]
   # We can probably remove `isort` if we come to trust `ruff --fix`,
   # but we'll need to figure out the configuration to do this in `ruff`
   - repo: https://github.com/pycqa/isort
@@ -53,7 +47,7 @@ repos:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.254
+    rev: v0.0.255
     hooks:
       - id: ruff
         args: [--fix-only]
@@ -66,7 +60,6 @@ repos:
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
         - flake8==6.0.0
-        - flake8-comprehensions==3.10.1  # Consider removing and rely on `ruff` instead
         - flake8-bugbear==23.2.13
         - flake8-simplify==0.19.3
   - repo: https://github.com/asottile/yesqa
@@ -82,7 +75,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.254
+    rev: v0.0.255
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/graphblas/viz.py b/graphblas/viz.py
index 89010bc3d..d8a96d343 100644
--- a/graphblas/viz.py
+++ b/graphblas/viz.py
@@ -182,30 +182,30 @@ def datashade(M, agg="count", *, width=None, height=None, opts_kwargs=None, **kw
             images.extend(image_row)
         return hv.Layout(images).cols(ncols)
 
-    kwds = dict(  # noqa: C408 pylint: disable=use-dict-literal
-        x="col",
-        y="row",
-        c="val",
-        aggregator=agg,
-        frame_width=width,
-        frame_height=height,
-        cmap="fire",
-        cnorm="eq_hist",
-        xlim=(0, M.ncols),
-        ylim=(0, M.nrows),
-        rasterize=True,
-        flip_yaxis=True,
-        hover=True,
-        xlabel="",
-        ylabel="",
-        data_aspect=1,
-        x_sampling=1,
-        y_sampling=1,
-        xaxis="top",
-        xformatter="%d",
-        yformatter="%d",
-        rot=60,
-    )
+    kwds = {
+        "x": "col",
+        "y": "row",
+        "c": "val",
+        "aggregator": agg,
+        "frame_width": width,
+        "frame_height": height,
+        "cmap": "fire",
+        "cnorm": "eq_hist",
+        "xlim": (0, M.ncols),
+        "ylim": (0, M.nrows),
+        "rasterize": True,
+        "flip_yaxis": True,
+        "hover": True,
+        "xlabel": "",
+        "ylabel": "",
+        "data_aspect": 1,
+        "x_sampling": 1,
+        "y_sampling": 1,
+        "xaxis": "top",
+        "xformatter": "%d",
+        "yformatter": "%d",
+        "rot": 60,
+    }
     # Only show axes on outer-most plots
     if kwargs.pop("_col", 0) != 0:
         kwds["yaxis"] = None
diff --git a/pyproject.toml b/pyproject.toml
index 0b3f38577..2603e72b3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -209,7 +209,7 @@ select = [
     "B",  # flake8-bugbear
     "A",  # flake8-builtins
     "COM",  # flake8-commas
-    "C4",  # flake8-comprehensions
+    "C40",  # flake8-comprehensions
     "DTZ",  # flake8-datetimez
     "T10",  # flake8-debugger
     # "DJ",  # flake8-django (We don't use django)
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index bc813b28c..ade1c3313 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -12,6 +12,5 @@ conda search 'sparse[channel=conda-forge]>=0.14.0'
 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-comprehensions[channel=conda-forge]>=3.10.1'
 conda search 'flake8-bugbear[channel=conda-forge]>=23.2.13'
 conda search 'flake8-simplify[channel=conda-forge]>=0.19.3'

From 47c9bdfda0b0e191f0187a284ef6450d8ae6d3c4 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Wed, 15 Mar 2023 08:41:27 -0500
Subject: [PATCH 12/15] bump

---
 .pre-commit-config.yaml   | 6 +++---
 pyproject.toml            | 2 +-
 scripts/check_versions.sh | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 75d1d0b89..b8e74e3e3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -47,7 +47,7 @@ repos:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.255
+    rev: v0.0.256
     hooks:
       - id: ruff
         args: [--fix-only]
@@ -60,7 +60,7 @@ repos:
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
         - flake8==6.0.0
-        - flake8-bugbear==23.2.13
+        - flake8-bugbear==23.3.12
         - flake8-simplify==0.19.3
   - repo: https://github.com/asottile/yesqa
     rev: v1.4.0
@@ -75,7 +75,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.255
+    rev: v0.0.256
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/pyproject.toml b/pyproject.toml
index 2603e72b3..0b3f38577 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -209,7 +209,7 @@ select = [
     "B",  # flake8-bugbear
     "A",  # flake8-builtins
     "COM",  # flake8-commas
-    "C40",  # flake8-comprehensions
+    "C4",  # flake8-comprehensions
     "DTZ",  # flake8-datetimez
     "T10",  # flake8-debugger
     # "DJ",  # flake8-django (We don't use django)
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index ade1c3313..63eb8dba5 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -12,5 +12,5 @@ conda search 'sparse[channel=conda-forge]>=0.14.0'
 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]>=23.2.13'
+conda search 'flake8-bugbear[channel=conda-forge]>=23.3.12'
 conda search 'flake8-simplify[channel=conda-forge]>=0.19.3'

From 7bf394d240940d3403cc66b52a108044031b78e9 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Sat, 18 Mar 2023 13:58:27 -0500
Subject: [PATCH 13/15] bump ruff

---
 .pre-commit-config.yaml | 4 ++--
 graphblas/io.py         | 3 +++
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b8e74e3e3..ab097216e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -47,7 +47,7 @@ repos:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.256
+    rev: v0.0.257
     hooks:
       - id: ruff
         args: [--fix-only]
@@ -75,7 +75,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.256
+    rev: v0.0.257
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint
diff --git a/graphblas/io.py b/graphblas/io.py
index fa9a0e5e7..3286eb98c 100644
--- a/graphblas/io.py
+++ b/graphblas/io.py
@@ -26,6 +26,7 @@ def draw(m):  # pragma: no cover
     _warn(
         "`graphblas.io.draw` is deprecated; it has been moved to `graphblas.viz.draw`",
         DeprecationWarning,
+        stacklevel=2,
     )
     viz.draw(m)
 
@@ -93,6 +94,7 @@ def from_numpy(m):  # pragma: no cover (deprecated)
         "`graphblas.io.from_numpy` is deprecated; "
         "use `Matrix.from_dense` and `Vector.from_dense` instead.",
         DeprecationWarning,
+        stacklevel=2,
     )
     if m.ndim > 2:
         raise _GraphblasException("m.ndim must be <= 2")
@@ -336,6 +338,7 @@ def to_numpy(m):  # pragma: no cover (deprecated)
         "`graphblas.io.to_numpy` is deprecated; "
         "use `Matrix.to_dense` and `Vector.to_dense` instead.",
         DeprecationWarning,
+        stacklevel=2,
     )
     try:
         import scipy  # noqa: F401

From eb60ec56dd03cc272a8b86b60c998926b6799964 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Mon, 20 Mar 2023 11:10:17 -0500
Subject: [PATCH 14/15] Note that `scipy` is needed for all backends for mmread
 and mmwrite

---
 graphblas/io.py           | 2 ++
 scripts/check_versions.sh | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/graphblas/io.py b/graphblas/io.py
index 3286eb98c..bc57c2084 100644
--- a/graphblas/io.py
+++ b/graphblas/io.py
@@ -600,6 +600,7 @@ def mmread(source, engine="auto", *, dup_op=None, name=None, **kwargs):
     :class:`~graphblas.Matrix`
     """
     try:
+        # scipy is currently needed for *all* engines
         from scipy.io import mmread
         from scipy.sparse import isspmatrix_coo
     except ImportError:  # pragma: no cover (import)
@@ -663,6 +664,7 @@ def mmwrite(
         {"general", "symmetric", "skew-symmetric", "hermetian"}
     """
     try:
+        # scipy is currently needed for *all* engines
         from scipy.io import mmwrite
     except ImportError:  # pragma: no cover (import)
         raise ImportError("scipy is required to write Matrix Market files") from None
diff --git a/scripts/check_versions.sh b/scripts/check_versions.sh
index 63eb8dba5..d08ad6476 100755
--- a/scripts/check_versions.sh
+++ b/scripts/check_versions.sh
@@ -7,7 +7,7 @@ conda search 'numpy[channel=conda-forge]>=1.24.2'
 conda search 'pandas[channel=conda-forge]>=1.5.3'
 conda search 'scipy[channel=conda-forge]>=1.10.1'
 conda search 'networkx[channel=conda-forge]>=3.0'
-conda search 'awkward[channel=conda-forge]>=2.1.0'
+conda search 'awkward[channel=conda-forge]>=2.1.1'
 conda search 'sparse[channel=conda-forge]>=0.14.0'
 conda search 'fast_matrix_market[channel=conda-forge]>=1.4.5'
 conda search 'numba[channel=conda-forge]>=0.56.4'

From 00045205c6d9c0611263fd3ecd0bc1670c6e7de1 Mon Sep 17 00:00:00 2001
From: Erik Welch <erik.n.welch@gmail.com>
Date: Tue, 21 Mar 2023 16:37:31 -0500
Subject: [PATCH 15/15] Add Matrix Market to `io` docs

---
 dev-requirements.txt   |  2 ++
 docs/user_guide/io.rst | 16 ++++++++++++++++
 2 files changed, 18 insertions(+)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index b84c0e849..273980db9 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -6,6 +6,7 @@ pyyaml
 pandas
 # For I/O
 awkward
+fast_matrix_market
 networkx
 scipy
 sparse
@@ -16,6 +17,7 @@ matplotlib
 # For linting
 pre-commit
 # For testing
+packaging
 pytest-cov
 # For debugging
 icecream
diff --git a/docs/user_guide/io.rst b/docs/user_guide/io.rst
index 9431ff413..c13fda5d6 100644
--- a/docs/user_guide/io.rst
+++ b/docs/user_guide/io.rst
@@ -129,3 +129,19 @@ Note that A is unchanged in the above example.
 The SuiteSparse export has a ``give_ownership`` option. This performs a zero-copy
 move operation and invalidates the original python-graphblas object. When extreme speed is needed or memory is
 too limited to make a copy, this option may be needed.
+
+Matrix Market files
+-------------------
+
+The `Matrix Market file format <https://math.nist.gov/MatrixMarket/formats.html>`_ is a common
+file format for storing sparse arrays in human-readable ASCII.
+Matrix Market files--also called MM files--often use ".mtx" file extension.
+For example, many datasets in MM format can be found in `the SuiteSparse Matrix Collection <https://sparse.tamu.edu/>`_.
+
+Use ``gb.io.mmread()`` to read a Matrix Market file to a python-graphblas Matrix,
+and ``gb.io.mmwrite()`` to write a Matrix to a Matrix Market file.
+These names match the equivalent functions in `scipy.sparse <https://docs.scipy.org/doc/scipy/reference/generated/scipy.io.mmread.html>`_.
+
+``scipy`` is required to be installed to read Matrix Market files.
+If ``fast_matrix_market`` is installed, it will be used by default for
+`much better performance <https://github.com/alugowski/fast_matrix_market>`_.