Add from_dense and to_dense methods (python-graphblas#382)

* Add `from_dense` and `to_dense` methods

* Add warning that `to_dense` can create very large arrays

* Add `from_iso_value`, `missing_value=` to `from_dense`, and deprecate `io.from_numpy`

* Rename `from_iso_value` to `from_scalar`

* Update `flake8-bugbear` and make improvements

* Add comment for how to create iso-valued objects with structure and scalar

.pre-commit-config.yaml

@@ -56,7 +56,7 @@ repos:
         # These versions need updated manually
         - flake8==6.0.0
         - flake8-comprehensions==3.10.1
-        - flake8-bugbear==23.1.20
+        - flake8-bugbear==23.2.13
         - flake8-simplify==0.19.3
   - repo: https://github.com/asottile/yesqa
     rev: v1.4.0
@@ -71,7 +71,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.241
+    rev: v0.0.247
     hooks:
       - id: ruff
   - repo: https://github.com/sphinx-contrib/sphinx-lint

graphblas/agg/__init__.py

@@ -91,6 +91,7 @@ def __getattr__(key):
             f"`{key}` is specific to SuiteSparse:GraphBLAS. "
             f"`gb.agg.{key}` will be removed in version 2023.9.0 or later.",
             DeprecationWarning,
+            stacklevel=2,
         )
         rv = _deprecated[key]
         globals()[key] = rv

graphblas/binary/__init__.py

@@ -24,6 +24,7 @@ def __getattr__(key):
             f"`{key}` is specific to SuiteSparse:GraphBLAS. "
             f"`gb.binary.{key}` will be removed in version 2023.9.0 or later.",
             DeprecationWarning,
+            stacklevel=2,
         )
         rv = _deprecated[key]
         globals()[key] = rv

graphblas/core/automethods.py

@@ -261,6 +261,10 @@ def to_dcsr(self):
     return self._get_value("to_dcsr")
 
 
+def to_dense(self):
+    return self._get_value("to_dense")
+
+
 def to_dict(self):
     return self._get_value("to_dict")
 
@@ -389,6 +393,7 @@ def _main():
         "reposition",
         "ss",
         "to_coo",
+        "to_dense",
         "to_values",
     }
     vector = {

graphblas/core/infix.py

@@ -208,6 +208,7 @@ def dup(self, dtype=None, *, clear=False, mask=None, name=None, **opts):
     else:
         ss = Vector.__dict__["ss"]  # raise if used
     to_coo = wrapdoc(Vector.to_coo)(property(automethods.to_coo))
+    to_dense = wrapdoc(Vector.to_dense)(property(automethods.to_dense))
     to_dict = wrapdoc(Vector.to_dict)(property(automethods.to_dict))
     to_values = wrapdoc(Vector.to_values)(property(automethods.to_values))
     vxm = wrapdoc(Vector.vxm)(property(automethods.vxm))
@@ -343,6 +344,7 @@ def dup(self, dtype=None, *, clear=False, mask=None, name=None, **opts):
     to_csr = wrapdoc(Matrix.to_csr)(property(automethods.to_csr))
     to_dcsc = wrapdoc(Matrix.to_dcsc)(property(automethods.to_dcsc))
     to_dcsr = wrapdoc(Matrix.to_dcsr)(property(automethods.to_dcsr))
+    to_dense = wrapdoc(Matrix.to_dense)(property(automethods.to_dense))
     to_dicts = wrapdoc(Matrix.to_dicts)(property(automethods.to_dicts))
     to_edgelist = wrapdoc(Matrix.to_edgelist)(property(automethods.to_edgelist))
     to_values = wrapdoc(Matrix.to_values)(property(automethods.to_values))