Move files around to match NetworkX file and directory structure (#7)

Author: eriknw

graphblas_algorithms/__init__.py

@@ -1,6 +1,4 @@
 from . import _version
-from .cluster import average_clustering, clustering, transitivity, triangles  # noqa
-from .link_analysis import pagerank  # noqa
-from .reciprocity import overall_reciprocity, reciprocity  # noqa
+from .algorithms import *
 
 __version__ = _version.get_versions()["version"]

graphblas_algorithms/algorithms/__init__.py

@@ -0,0 +1,3 @@
+from .cluster import average_clustering, clustering, transitivity, triangles
+from .link_analysis import pagerank
+from .reciprocity import overall_reciprocity, reciprocity

graphblas_algorithms/cluster.py renamed to graphblas_algorithms/algorithms/cluster.py

@@ -6,7 +6,7 @@
 from networkx import clustering as _nx_clustering
 from networkx.utils import not_implemented_for
 
-from ._utils import graph_to_adjacency, list_to_mask, vector_to_dict
+from graphblas_algorithms._utils import graph_to_adjacency, list_to_mask, vector_to_dict
 
 
 def get_properties(G, names, *, L=None, U=None, degrees=None, has_self_edges=True):

graphblas_algorithms/algorithms/link_analysis/__init__.py

@@ -0,0 +1 @@
+from .pagerank_alg import pagerank

graphblas_algorithms/link_analysis.py renamed to graphblas_algorithms/algorithms/link_analysis/pagerank_alg.py

@@ -4,7 +4,7 @@
 from graphblas import Vector, binary, unary
 from graphblas.semiring import plus_first, plus_times
 
-from ._utils import dict_to_vector, graph_to_adjacency, vector_to_dict
+from graphblas_algorithms._utils import dict_to_vector, graph_to_adjacency, vector_to_dict
 
 
 def pagerank_core(

graphblas_algorithms/tests/__init__.py renamed to graphblas_algorithms/algorithms/link_analysis/tests/__init__.py

@@ -0,0 +1,3 @@
+from graphblas_algorithms import pagerank
+
+from networkx.algorithms.link_analysis.tests.test_pagerank import *  # isort:skip

graphblas_algorithms/algorithms/link_analysis/tests/test_pagerank.py

@@ -2,7 +2,7 @@
 from networkx import NetworkXError
 from networkx.utils import not_implemented_for
 
-from ._utils import graph_to_adjacency, list_to_mask, vector_to_dict
+from graphblas_algorithms._utils import graph_to_adjacency, list_to_mask, vector_to_dict
 
 
 def reciprocity_core(G, mask=None):

graphblas_algorithms/reciprocity.py renamed to graphblas_algorithms/algorithms/reciprocity.py

@@ -1,8 +1,8 @@
 import graphblas as gb
 import networkx as nx
 
-import graphblas_algorithms as ga
-from graphblas_algorithms import average_clustering, clustering, transitivity, triangles  # noqa
+from graphblas_algorithms import average_clustering, clustering, transitivity, triangles
+from graphblas_algorithms.algorithms import cluster
 
 
 def test_triangles_full():
@@ -12,47 +12,47 @@ def test_triangles_full():
     G2 = gb.select.offdiag(G).new()
     L = gb.select.tril(G, -1).new(name="L")
     U = gb.select.triu(G, 1).new(name="U")
-    result = ga.cluster.triangles_core(G, L=L, U=U)
+    result = cluster.triangles_core(G, L=L, U=U)
     expected = gb.Vector(int, 5)
     expected[:] = 6
     assert result.isequal(expected)
-    result = ga.cluster.triangles_core(G2, L=L, U=U)
+    result = cluster.triangles_core(G2, L=L, U=U)
     assert result.isequal(expected)
     mask = gb.Vector(bool, 5)
     mask[0] = True
     mask[3] = True
-    result = ga.cluster.triangles_core(G, mask=mask.S)
+    result = cluster.triangles_core(G, mask=mask.S)
     expected = gb.Vector(int, 5)
     expected[0] = 6
     expected[3] = 6
     assert result.isequal(expected)
-    result = ga.cluster.triangles_core(G2, mask=mask.S)
+    result = cluster.triangles_core(G2, mask=mask.S)
     assert result.isequal(expected)
-    assert ga.cluster.single_triangle_core(G, 1) == 6
-    assert ga.cluster.single_triangle_core(G, 0, L=L) == 6
-    assert ga.cluster.single_triangle_core(G2, 0, has_self_edges=False) == 6
-    assert ga.cluster.total_triangles_core(G2) == 10
-    assert ga.cluster.total_triangles_core(G) == 10
-    assert ga.cluster.total_triangles_core(G, L=L, U=U) == 10
-    assert ga.cluster.transitivity_core(G) == 1.0
-    assert ga.cluster.transitivity_core(G2) == 1.0
-    result = ga.cluster.clustering_core(G)
+    assert cluster.single_triangle_core(G, 1) == 6
+    assert cluster.single_triangle_core(G, 0, L=L) == 6
+    assert cluster.single_triangle_core(G2, 0, has_self_edges=False) == 6
+    assert cluster.total_triangles_core(G2) == 10
+    assert cluster.total_triangles_core(G) == 10
+    assert cluster.total_triangles_core(G, L=L, U=U) == 10
+    assert cluster.transitivity_core(G) == 1.0
+    assert cluster.transitivity_core(G2) == 1.0
+    result = cluster.clustering_core(G)
     expected = gb.Vector(float, 5)
     expected[:] = 1
     assert result.isequal(expected)
-    result = ga.cluster.clustering_core(G2)
+    result = cluster.clustering_core(G2)
     assert result.isequal(expected)
-    assert ga.cluster.single_clustering_core(G, 0) == 1
-    assert ga.cluster.single_clustering_core(G2, 0) == 1
+    assert cluster.single_clustering_core(G, 0) == 1
+    assert cluster.single_clustering_core(G2, 0) == 1
     expected(mask.S, replace=True) << 1
-    result = ga.cluster.clustering_core(G, mask=mask.S)
+    result = cluster.clustering_core(G, mask=mask.S)
     assert result.isequal(expected)
-    result = ga.cluster.clustering_core(G2, mask=mask.S)
+    result = cluster.clustering_core(G2, mask=mask.S)
     assert result.isequal(expected)
-    assert ga.cluster.average_clustering_core(G) == 1
-    assert ga.cluster.average_clustering_core(G2) == 1
-    assert ga.cluster.average_clustering_core(G, mask=mask.S) == 1
-    assert ga.cluster.average_clustering_core(G2, mask=mask.S) == 1
+    assert cluster.average_clustering_core(G) == 1
+    assert cluster.average_clustering_core(G2) == 1
+    assert cluster.average_clustering_core(G, mask=mask.S) == 1
+    assert cluster.average_clustering_core(G2, mask=mask.S) == 1
 
 
 def test_directed(orig):

graphblas_algorithms/algorithms/tests/__init__.py

@@ -0,0 +1,3 @@
+from graphblas_algorithms import overall_reciprocity, reciprocity
+
+from networkx.algorithms.tests.test_reciprocity import *  # isort:skip

graphblas_algorithms/tests/test_cluster.py renamed to graphblas_algorithms/algorithms/tests/test_cluster.py

@@ -1,20 +1,21 @@
 [aliases]
 test=pytest
 
-[tool:pytest]
-testpaths = graphblas_algorithms/tests
-
 [flake8]
 max-line-length = 100
 inline-quotes = "
 exclude =
     versioneer.py,
-    graphblas_algorithms/tests/,
+    graphblas_algorithms/*/tests/,
+    graphblas_algorithms/*/*/tests/,
     build/
 ignore =
     E203,   # whitespace before ':'
     E231,   # Multiple spaces around ","
     W503,   # line break before binary operator
+per-file-ignores =
+    __init__.py:F401,F403,  # allow unused and star imports
+    test_*.py:F401,F403,
 
 [isort]
 sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER