python-graphblas · eriknw · Dec 17, 2023 · Dec 16, 2023 · Dec 17, 2023 · Dec 17, 2023
diff --git a/.github/workflows/test_and_build.yml b/.github/workflows/test_and_build.yml
@@ -173,12 +173,12 @@ jobs:
           # Randomly choosing versions of dependencies based on Python version works surprisingly well...
           if [[ ${{ startsWith(steps.pyver.outputs.selected, '3.9') }} == true ]]; then
             npver=$(python -c 'import random ; print(random.choice(["=1.21", "=1.22", "=1.23", "=1.24", "=1.25", "=1.26", ""]))')
-            spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", "=1.11", ""]))')
+            spver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=1.11", ""]))')
             pdver=$(python -c 'import random ; print(random.choice(["=1.2", "=1.3", "=1.4", "=1.5", "=2.0", "=2.1", ""]))')
             akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", "=2.2", "=2.3", "=2.4", "=2.5", ""]))')
           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", "=1.25", "=1.26", ""]))')
-            spver=$(python -c 'import random ; print(random.choice(["=1.8", "=1.9", "=1.10", "=1.11", ""]))')
+            spver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=1.11", ""]))')
             pdver=$(python -c 'import random ; print(random.choice(["=1.3", "=1.4", "=1.5", "=2.0", "=2.1", ""]))')
             akver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=2.0", "=2.1", "=2.2", "=2.3", "=2.4", "=2.5", ""]))')
           elif [[ ${{ startsWith(steps.pyver.outputs.selected, '3.11') }} == true ]]; then
@@ -196,9 +196,6 @@ jobs:
           if [[ ${pdver} == "=2.1" && ${npver} == "=1.21" ]]; then
             pdver="=2.0"
           fi
-          if [[ ${nxver} == "=3.2" && ${spver} == "=1.8" ]]; then
-            spver="=1.9"
-          fi
           if [[ ${{ steps.sourcetype.outputs.selected }} == "source" || ${{ steps.sourcetype.outputs.selected }} == "upstream" ]]; then
             # TODO: there are currently issues with some numpy versions when
             # installing python-suitesparse-grphblas from source or upstream.
@@ -230,14 +227,11 @@ jobs:
           fi
           if [[ ${npver} == "=1.26" ]] ; then
             numbaver=""
-            if [[ ${spver} == "=1.8" || ${spver} == "=1.9" ]] ; then
+            if [[ ${spver} == "=1.9" ]] ; then
               spver=$(python -c 'import random ; print(random.choice(["=1.10", "=1.11", ""]))')
             fi
           elif [[ ${npver} == "=1.25" ]] ; then
             numbaver=""
-            if [[ ${spver} == "=1.8" ]] ; then
-              spver=$(python -c 'import random ; print(random.choice(["=1.9", "=1.10", "=1.11", ""]))')
-            fi
           elif [[ ${npver} == "=1.24" || ${{ startsWith(steps.pyver.outputs.selected, '3.11') }} == true ]] ; then
             numbaver=$(python -c 'import random ; print(random.choice(["=0.57", "=0.58", ""]))')
           elif [[ ${npver} == "=1.21" ]] ; then

diff --git a/docs/api_reference/io.rst b/docs/api_reference/io.rst
@@ -10,15 +10,18 @@ These methods require `networkx <https://networkx.org/>`_ to be installed.
 
 .. autofunction:: graphblas.io.to_networkx
 
-Numpy
+NumPy
 ~~~~~
 
-These methods require `scipy <https://scipy.org/>`_ to be installed, as some
-of the scipy.sparse machinery is used during the conversion process.
+These methods convert to and from dense arrays. For more, see :ref:`IO in the user guide <from-to-values>`.
 
-.. autofunction:: graphblas.io.from_numpy
+.. automethod:: graphblas.core.matrix.Matrix.from_dense
 
-.. autofunction:: graphblas.io.to_numpy
+.. automethod:: graphblas.core.matrix.Matrix.to_dense
+
+.. automethod:: graphblas.core.vector.Vector.from_dense
+
+.. automethod:: graphblas.core.vector.Vector.to_dense
 
 Scipy Sparse
 ~~~~~~~~~~~~

diff --git a/docs/user_guide/collections.rst b/docs/user_guide/collections.rst
@@ -145,7 +145,7 @@ The shape and dtype remain unchanged, but the collection will be fully sparse (i
 to_coo
 ~~~~~~
 
-To go from a collection back to the index and values, ``.to_coo()`` can be called. Numpy arrays
+To go from a collection back to the index and values, ``.to_coo()`` can be called. NumPy arrays
 will be returned in a tuple.
 
 .. code-block:: python

diff --git a/docs/user_guide/io.rst b/docs/user_guide/io.rst
@@ -4,6 +4,8 @@ Input/Output
 
 There are several ways to get data into and out of python-graphblas.
 
+.. _from-to-values:
+
 From/To Values
 --------------
 

diff --git a/graphblas/io/__init__.py b/graphblas/io/__init__.py
@@ -1,6 +1,5 @@
 from ._awkward import from_awkward, to_awkward
 from ._matrixmarket import mmread, mmwrite
 from ._networkx import from_networkx, to_networkx
-from ._numpy import from_numpy, to_numpy  # deprecated
 from ._scipy import from_scipy_sparse, to_scipy_sparse
 from ._sparse import from_pydata_sparse, to_pydata_sparse
diff --git a/graphblas/io/_numpy.py b/graphblas/io/_numpy.py
diff --git a/graphblas/tests/test_io.py b/graphblas/tests/test_io.py
@@ -38,17 +38,6 @@
 suitesparse = gb.backend == "suitesparse"
 
 
-@pytest.mark.skipif("not ss")
-def test_deprecated():
-    a = np.array([0.0, 2.0, 4.1])
-    with pytest.warns(DeprecationWarning):
-        v = gb.io.from_numpy(a)
-    assert v.isequal(gb.Vector.from_coo([1, 2], [2.0, 4.1]), check_dtype=True)
-    with pytest.warns(DeprecationWarning):
-        a2 = gb.io.to_numpy(v)
-    np.testing.assert_array_equal(a, a2)
-
-
 @pytest.mark.skipif("not ss")
 def test_vector_to_from_numpy():
     a = np.array([0.0, 2.0, 4.1])
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,8 @@ Input/Output @@
     There are several ways to get data into and out of python-graphblas.
+    .. _from-to-values:
     From/To Values
     --------------
@@ Expand Down @@