python-graphblas · eriknw · May 14, 2023 · May 14, 2023 · May 14, 2023
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
@@ -171,22 +171,22 @@ jobs:
             npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", "=1.24", ""]))')
             spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", ""]))')
             pdver=$(python -c 'import random ; print(random.choice(["=1.2", "=1.3", "=1.4", "=1.5", "=2.0", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", "=2.2", ""]))')
           elif [[ ${{ startsWith(steps.pyver.outputs.selected, '3.9') }} == true ]]; then
             npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", "=1.24", ""]))')
             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", "=2.0", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", "=2.2", ""]))')
           elif [[ ${{ startsWith(steps.pyver.outputs.selected, '3.10') }} == true ]]; then
             npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", "=1.24", ""]))')
             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", "=2.0", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", "=2.2", ""]))')
           else  # Python 3.11
             npver=$(python -c 'import random ; print(random.choice(["=1.23", "=1.24", ""]))')
             spver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", ""]))')
             pdver=$(python -c 'import random ; print(random.choice(["=1.5", "=2.0", ""]))')
-            akver=$(python -c 'import random ; print(random.choice(["=1.10", "=2.0", "=2.1", ""]))')
+            akver=$(python -c 'import random ; print(random.choice(["=1.10", "=2.0", "=2.1", "=2.2", ""]))')
           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
@@ -43,7 +43,7 @@ repos:
       - id: isort
   # Let's keep `pyupgrade` even though `ruff --fix` probably does most of it
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.2
+    rev: v3.4.0
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -58,7 +58,7 @@ repos:
       - id: black
       - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.265
+    rev: v0.0.267
     hooks:
       - id: ruff
         args: [--fix-only, --show-fixes]
@@ -71,7 +71,7 @@ repos:
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
         - flake8==6.0.0
-        - flake8-bugbear==23.3.23
+        - flake8-bugbear==23.5.9
         - flake8-simplify==0.20.0
   - repo: https://github.com/asottile/yesqa
     rev: v1.4.0
@@ -86,7 +86,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.265
+    rev: v0.0.267
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint

diff --git a/environment.yml b/environment.yml
@@ -94,8 +94,10 @@ dependencies:
     # - python-igraph
     # - python-louvain
     # - pyupgrade
+    # - rich
     # - ruff
     # - scalene
+    # - scikit-network
     # - setuptools-git-versioning
     # - snakeviz
     # - sphinx-lint

diff --git a/graphblas/agg/__init__.py b/graphblas/agg/__init__.py
@@ -1,4 +1,4 @@
-"""`graphblas.agg` is an experimental module for exploring Aggregators.
+"""``graphblas.agg`` is an experimental module for exploring Aggregators.
 
 Aggregators may be used in reduce methods:
     - Matrix.reduce_rowwise
@@ -59,9 +59,9 @@
     - ss.argmax
 
 .. deprecated:: 2023.1.0
-    Aggregators `first`, `last`, `first_index`, `last_index`, `argmin`, and `argmax` are
-    deprecated in the `agg` namespace such as `agg.first`. Use them from `agg.ss` namespace
-    instead such as `agg.ss.first`. Will be removed in version 2023.9.0 or later.
+    Aggregators ``first``, ``last``, ``first_index``, ``last_index``, ``argmin``, and ``argmax``
+    are deprecated in the ``agg`` namespace such as ``agg.first``. Use them from ``agg.ss``
+    namespace instead such as ``agg.ss.first``. Will be removed in version 2023.9.0 or later.
 
 # Possible aggregators:
 #   - absolute_deviation, sum(abs(x - mean(x))),  sum_absminus(x, mean(x))

diff --git a/graphblas/core/agg.py b/graphblas/core/agg.py
@@ -1,8 +1,8 @@
 """graphblas.core.agg namespace is deprecated; please use graphblas.core.operator.agg instead.
 
 .. deprecated:: 2023.3.0
-`graphblas.core.agg` will be removed in a future release.
-Use `graphblas.core.operator.agg` instead.
+``graphblas.core.agg`` will be removed in a future release.
+Use ``graphblas.core.operator.agg`` instead.
 Will be removed in version 2023.11.0 or later.
 
 """

diff --git a/graphblas/core/automethods.py b/graphblas/core/automethods.py
@@ -1,6 +1,6 @@
 """Define functions to use as property methods on expressions.
 
-These will automatically compute the value and avoid the need for `.new()`.
+These will automatically compute the value and avoid the need for ``.new()``.
 
 To automatically create the functions, run:
 

diff --git a/graphblas/core/mask.py b/graphblas/core/mask.py
@@ -35,7 +35,7 @@ def new(self, dtype=None, *, complement=False, mask=None, name=None, **opts):
         """Return a new object with True values determined by the mask(s).
 
         By default, the result is True wherever the mask(s) would have been applied,
-        and empty otherwise.  If `complement` is True, then these are switched:
+        and empty otherwise.  If ``complement`` is True, then these are switched:
         the result is empty where the mask(s) would have been applied, and True otherwise.
 
         In other words, these are equivalent if complement is False (and mask keyword is None):
@@ -48,14 +48,14 @@ def new(self, dtype=None, *, complement=False, mask=None, name=None, **opts):
         >>> C(self) << expr
         >>> C(~result.S) << expr  # equivalent when complement is True
 
-        This can also efficiently merge two masks by using the `mask=` argument.
+        This can also efficiently merge two masks by using the ``mask=`` argument.
         This is equivalent to the following (but uses more efficient recipes):
 
         >>> val = Matrix(...)
         >>> val(self) << True
         >>> val(mask, replace=True) << val
 
-        If `complement=` argument is True, then the *complement* will be returned.
+        If ``complement=`` argument is True, then the *complement* will be returned.
         This is equivalent to the following (but uses more efficient recipes):
 
         >>> val = Matrix(...)
@@ -83,7 +83,7 @@ def new(self, dtype=None, *, complement=False, mask=None, name=None, **opts):
     def __and__(self, other, **opts):
         """Return the intersection of two masks as a new mask.
 
-        `new_mask = mask1 & mask2` is equivalent to the following:
+        ``new_mask = mask1 & mask2`` is equivalent to the following:
 
         >>> val = Matrix(bool, nrows, ncols)
         >>> val(mask1) << True
@@ -109,7 +109,7 @@ def __and__(self, other, **opts):
     def __or__(self, other, **opts):
         """Return the union of two masks as a new mask.
 
-        `new_mask = mask1 | mask2` is equivalent to the following:
+        ``new_mask = mask1 | mask2`` is equivalent to the following:
 
         >>> val = Matrix(bool, nrows, ncols)
         >>> val(mask1) << True

diff --git a/graphblas/core/matrix.py b/graphblas/core/matrix.py
@@ -355,7 +355,7 @@ def isclose(self, other, *, rel_tol=1e-7, abs_tol=0.0, check_dtype=False, **opts
         Returns
         -------
         bool
-            Whether all values of the Matrix are close to the values in `other`.
+            Whether all values of the Matrix are close to the values in ``other``.
         """
         other = self._expect_type(
             other, (Matrix, TransposedMatrix), within="isclose", argname="other"
@@ -448,19 +448,19 @@ def to_values(self, dtype=None, *, rows=True, columns=True, values=True, sort=Tr
         corresponding to the COO format of the Matrix.
 
         .. deprecated:: 2022.11.0
-            `Matrix.to_values` will be removed in a future release.
-            Use `Matrix.to_coo` instead. Will be removed in version 2023.9.0 or later
+            ``Matrix.to_values`` will be removed in a future release.
+            Use ``Matrix.to_coo`` instead. Will be removed in version 2023.9.0 or later
 
         Parameters
         ----------
         dtype :
             Requested dtype for the output values array.
         rows : bool, default=True
-            Whether to return rows; will return `None` for rows if `False`
+            Whether to return rows; will return ``None`` for rows if ``False``
         columns  :bool, default=True
-            Whether to return columns; will return `None` for columns if `False`
+            Whether to return columns; will return ``None`` for columns if ``False``
         values : bool, default=True
-            Whether to return values; will return `None` for values if `False`
+            Whether to return values; will return ``None`` for values if ``False``
         sort : bool, default=True
             Whether to require sorted indices.
             If internally stored rowwise, the sorting will be first by rows, then by column.
@@ -488,11 +488,11 @@ def to_coo(self, dtype=None, *, rows=True, columns=True, values=True, sort=True)
         dtype :
             Requested dtype for the output values array.
         rows : bool, default=True
-            Whether to return rows; will return `None` for rows if `False`
+            Whether to return rows; will return ``None`` for rows if ``False``
         columns  :bool, default=True
-            Whether to return columns; will return `None` for columns if `False`
+            Whether to return columns; will return ``None`` for columns if ``False``
         values : bool, default=True
-            Whether to return values; will return `None` for values if `False`
+            Whether to return values; will return ``None`` for values if ``False``
         sort : bool, default=True
             Whether to require sorted indices.
             If internally stored rowwise, the sorting will be first by rows, then by column.
@@ -559,7 +559,7 @@ def to_edgelist(self, dtype=None, *, values=True, sort=True):
         dtype :
             Requested dtype for the output values array.
         values : bool, default=True
-            Whether to return values; will return `None` for values if `False`
+            Whether to return values; will return ``None`` for values if ``False``
         sort : bool, default=True
             Whether to require sorted indices.
             If internally stored rowwise, the sorting will be first by rows, then by column.
@@ -585,7 +585,7 @@ def build(self, rows, columns, values, *, dup_op=None, clear=False, nrows=None,
         The typical use case is to create a new Matrix and insert values
         at the same time using :meth:`from_coo`.
 
-        All the arguments are used identically in :meth:`from_coo`, except for `clear`, which
+        All the arguments are used identically in :meth:`from_coo`, except for ``clear``, which
         indicates whether to clear the Matrix prior to adding the new values.
         """
         # TODO: accept `dtype` keyword to match the dtype of `values`?
@@ -781,8 +781,8 @@ def from_values(
         """Create a new Matrix from row and column indices and values.
 
         .. deprecated:: 2022.11.0
-            `Matrix.from_values` will be removed in a future release.
-            Use `Matrix.from_coo` instead. Will be removed in version 2023.9.0 or later
+            ``Matrix.from_values`` will be removed in a future release.
+            Use ``Matrix.from_coo`` instead. Will be removed in version 2023.9.0 or later
 
         Parameters
         ----------
@@ -1086,7 +1086,7 @@ def from_csr(
         Parameters
         ----------
         indptr : list or np.ndarray
-            Pointers for each row into col_indices and values; `indptr.size == nrows + 1`.
+            Pointers for each row into col_indices and values; ``indptr.size == nrows + 1``.
         col_indices : list or np.ndarray
             Column indices.
         values : list or np.ndarray or scalar, default 1.0
@@ -1133,7 +1133,7 @@ def from_csc(
         Parameters
         ----------
         indptr : list or np.ndarray
-            Pointers for each column into row_indices and values; `indptr.size == ncols + 1`.
+            Pointers for each column into row_indices and values; ``indptr.size == ncols + 1``.
         col_indices : list or np.ndarray
             Column indices.
         values : list or np.ndarray or scalar, default 1.0

diff --git a/graphblas/core/operator/base.py b/graphblas/core/operator/base.py
@@ -398,7 +398,7 @@ def _find(cls, funcname):
     def _initialize(cls, include_in_ops=True):
         """
         include_in_ops determines whether the operators are included in the
-        `gb.ops` namespace in addition to the defined module.
+        ``gb.ops`` namespace in addition to the defined module.
         """
         if cls._initialized:  # pragma: no cover (safety)
             return

diff --git a/graphblas/core/recorder.py b/graphblas/core/recorder.py
@@ -34,7 +34,7 @@ def gbstr(arg):
 class Recorder:
     """Record GraphBLAS C calls.
 
-    The recorder can use `.start()` and `.stop()` to enable/disable recording,
+    The recorder can use ``.start()`` and ``.stop()`` to enable/disable recording,
     or it can be used as a context manager.
 
     For example,

diff --git a/graphblas/core/scalar.py b/graphblas/core/scalar.py
@@ -1056,7 +1056,7 @@ def _as_scalar(scalar, dtype=None, *, is_cscalar):
 
 
 def _dict_to_record(np_type, d):
-    """Converts e.g. `{"x": 1, "y": 2.3}` to `(1, 2.3)`."""
+    """Converts e.g. ``{"x": 1, "y": 2.3}`` to ``(1, 2.3)``."""
     rv = []
     for name, (dtype, _) in np_type.fields.items():
         val = d[name]

diff --git a/graphblas/core/ss/descriptor.py b/graphblas/core/ss/descriptor.py
@@ -132,7 +132,7 @@ def get_descriptor(**opts):
     sort : bool, default False
         A hint for whether methods may return a "jumbled" matrix
     secure_import : bool, default False
-        Whether to trust the data for `import` and `pack` functions.
+        Whether to trust the data for ``import`` and ``pack`` functions.
         When True, checks are performed to ensure input data is valid.
     compression : str, {"none", "default", "lz4", "lz4hc", "zstd"}
         Whether and how to compress the data for serialization.