Add floyd_warshall (#42)

* Add `floyd_warshall`

* Optimization: better handle sparsity such as skip empty nodes

* Simplify (so this PR can be a reference)

* Better name ("Outer", not "temp")

Author: eriknw

README.md

@@ -147,6 +147,7 @@ dispatch pattern shown above.
   - is_k_regular
   - is_regular
 - Shortest Paths
+  - floyd_warshall
   - has_path
 - Simple Paths
   - is_simple_path

graphblas_algorithms/algorithms/shortest_paths/__init__.py

@@ -1 +1,2 @@
+from .dense import *
 from .generic import *

graphblas_algorithms/algorithms/shortest_paths/dense.py

@@ -0,0 +1,47 @@
+from graphblas import Matrix, Vector, binary
+from graphblas.select import offdiag
+from graphblas.semiring import any_plus
+
+__all__ = ["floyd_warshall"]
+
+
+def floyd_warshall(G, is_weighted=False):
+    # By using `offdiag` instead of `G._A`, we ensure that D will not become dense.
+    # Dense D may be better at times, but not including the diagonal will result in less work.
+    # Typically, Floyd-Warshall algorithms sets the diagonal of D to 0 at the beginning.
+    # This is unnecessary with sparse matrices, and we set the diagonal to 0 at the end.
+    # We also don't iterate over index `i` if either row i or column i are empty.
+    if G.is_directed():
+        A, row_degrees, column_degrees = G.get_properties("offdiag row_degrees- column_degrees-")
+        nonempty_nodes = binary.pair(row_degrees & column_degrees).new(name="nonempty_nodes")
+    else:
+        A, nonempty_nodes = G.get_properties("offdiag degrees-")
+
+    if A.dtype == bool or not is_weighted:
+        dtype = int
+    else:
+        dtype = A.dtype
+    n = A.nrows
+    D = Matrix(dtype, nrows=n, ncols=n, name="floyd_warshall")
+    if is_weighted:
+        D << A
+    else:
+        D(A.S) << 1  # Like `D << unary.one[int](A)`
+    del A
+
+    Row = Matrix(dtype, nrows=1, ncols=n, name="Row")
+    Col = Matrix(dtype, nrows=n, ncols=1, name="Col")
+    Outer = Matrix(dtype, nrows=n, ncols=n, name="Outer")
+    for i in nonempty_nodes:
+        Col << D[:, [i]]
+        Row << D[[i], :]
+        Outer << any_plus(Col @ Row)  # Like `col.outer(row, binary.plus)`
+        D(binary.min) << offdiag(Outer)
+
+    # Set diagonal values to 0 (this way seems fast).
+    # The missing values are implied to be infinity, so we set diagonals explicitly to 0.
+    mask = Vector(bool, size=n, name="mask")
+    mask << True
+    Mask = mask.diag(name="Mask")
+    D(Mask.S) << 0
+    return D

graphblas_algorithms/interface.py

@@ -55,6 +55,7 @@ class Dispatcher:
     is_k_regular = nxapi.regular.is_k_regular
     is_regular = nxapi.regular.is_regular
     # Shortest Paths
+    floyd_warshall = nxapi.shortest_paths.dense.floyd_warshall
     has_path = nxapi.shortest_paths.generic.has_path
     # Simple Paths
     is_simple_path = nxapi.simple_paths.is_simple_path
@@ -99,14 +100,16 @@ def on_start_tests(items):
             import pytest
         except ImportError:  # pragma: no cover (import)
             return
-        skip = [
-            ("test_attributes", {"TestBoruvka", "test_mst.py"}),
-            ("test_weight_attribute", {"TestBoruvka", "test_mst.py"}),
-        ]
+        multi_attributed = "unable to handle multi-attributed graphs"
+        multidigraph = "unable to handle MultiDiGraph"
+        freeze = frozenset
+        skip = {
+            ("test_attributes", freeze({"TestBoruvka", "test_mst.py"})): multi_attributed,
+            ("test_weight_attribute", freeze({"TestBoruvka", "test_mst.py"})): multi_attributed,
+            ("test_zero_weight", freeze({"TestFloyd", "test_dense.py"})): multidigraph,
+        }
         for item in items:
             kset = set(item.keywords)
-            for test_name, keywords in skip:
+            for (test_name, keywords), reason in skip.items():
                 if item.name == test_name and keywords.issubset(kset):
-                    item.add_marker(
-                        pytest.mark.xfail(reason="unable to handle multi-attributed graphs")
-                    )
+                    item.add_marker(pytest.mark.xfail(reason=reason))

graphblas_algorithms/nxapi/shortest_paths/__init__.py

@@ -1 +1,2 @@
+from .dense import *
 from .generic import *

graphblas_algorithms/nxapi/shortest_paths/dense.py

@@ -0,0 +1,10 @@
+from graphblas_algorithms import algorithms
+from graphblas_algorithms.classes.digraph import to_graph
+
+__all__ = ["floyd_warshall"]
+
+
+def floyd_warshall(G, weight="weight"):
+    G = to_graph(G, weight=weight)
+    D = algorithms.floyd_warshall(G, is_weighted=weight is not None)
+    return G.matrix_to_dicts(D)