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Commit 09776b6

Browse files
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Add a few more BFS-based algorithms (#51)
* Add a few more BFS-based algorithms - Components - `is_connected` - `is_weakly_connected` - `node_connected_component` - Shortest Paths - `all_pairs_shortest_path_length` - `negative_edge_cycle` - `single_source_shortest_path_length` - `single_target_shortest_path_length` - Traversal - `bfs_layers` - `descendants_at_distance` * Fix `partition(evenly=True)` * Remove flake8-comprehensions (use ruff instead)
1 parent 888e092 commit 09776b6

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-56
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‎.pre-commit-config.yaml

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@@ -4,6 +4,11 @@
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# To run: `pre-commit run --all-files`
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# To update: `pre-commit autoupdate`
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# - &flake8_dependencies below needs updated manually
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ci:
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# See: https://pre-commit.ci/#configuration
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autofix_prs: false
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autoupdate_schedule: monthly
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skip: [no-commit-to-branch]
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fail_fast: true
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default_language_version:
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python: python3
@@ -20,12 +25,13 @@ repos:
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- id: mixed-line-ending
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- id: trailing-whitespace
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- repo: https://github.com/abravalheri/validate-pyproject
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rev: v0.12.1
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rev: v0.12.2
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hooks:
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- id: validate-pyproject
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name: Validate pyproject.toml
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# I don't yet trust ruff to do what autoflake does
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- repo: https://github.com/myint/autoflake
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rev: v2.0.1
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rev: v2.0.2
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hooks:
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- id: autoflake
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args: [--in-place]
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- id: auto-walrus
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args: [--line-length, "100"]
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- repo: https://github.com/psf/black
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rev: 23.1.0
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rev: 23.3.0
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hooks:
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- id: black
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# - id: black-jupyter
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: v0.0.261
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hooks:
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- id: ruff
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args: [--fix-only, --show-fixes]
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- repo: https://github.com/PyCQA/flake8
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rev: 6.0.0
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hooks:
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- id: flake8
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additional_dependencies: &flake8_dependencies
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# These versions need updated manually
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- flake8==6.0.0
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- flake8-comprehensions==3.10.1
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- flake8-bugbear==23.2.13
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- flake8-simplify==0.19.3
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- flake8-bugbear==23.3.23
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- flake8-simplify==0.20.0
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- repo: https://github.com/asottile/yesqa
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rev: v1.4.0
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hooks:
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- id: yesqa
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additional_dependencies: *flake8_dependencies
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.2
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rev: v2.2.4
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hooks:
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- id: codespell
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types_or: [python, rst, markdown]
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additional_dependencies: [tomli]
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files: ^(graphblas_algorithms|docs)/
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: v0.0.253
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rev: v0.0.261
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hooks:
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- id: ruff
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# `pyroma` may help keep our package standards up to date if best practices change.
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# This is probably a "low value" check though and safe to remove if we want faster pre-commit.
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- repo: https://github.com/regebro/pyroma
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rev: "4.2"
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hooks:
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- id: pyroma
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args: [-n, "10", .]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:

‎README.md

Lines changed: 13 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -117,6 +117,10 @@ dispatch pattern shown above.
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- Community
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- inter_community_edges
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- intra_community_edges
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- Components
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- is_connected
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- is_weakly_connected
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- node_connected_component
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- Core
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- k_truss
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- Cuts
@@ -147,11 +151,15 @@ dispatch pattern shown above.
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- is_k_regular
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- is_regular
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- Shortest Paths
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- all_pairs_bellman_ford_path_length
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- all_pairs_shortest_path_length
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- floyd_warshall
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- floyd_warshall_predecessor_and_distance
152-
- single_source_bellman_ford_path_length
153-
- all_pairs_bellman_ford_path_length
154158
- has_path
159+
- negative_edge_cycle
160+
- single_source_bellman_ford_path_length
161+
- single_source_shortest_path_length
162+
- single_target_shortest_path_length
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- Simple Paths
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- is_simple_path
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- S Metric
@@ -162,5 +170,8 @@ dispatch pattern shown above.
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- is_tournament
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- score_sequence
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- tournament_matrix
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- Traversal
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- bfs_layers
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- descendants_at_distance
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- Triads
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- is_triad

‎graphblas_algorithms/algorithms/__init__.py

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@@ -3,6 +3,7 @@
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from .centrality import *
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from .cluster import *
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from .community import *
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from .components import *
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from .core import *
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from .cuts import *
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from .dag import *
@@ -16,4 +17,5 @@
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from .smetric import *
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from .structuralholes import *
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from .tournament import *
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from .traversal import *
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from .triads import *

‎graphblas_algorithms/algorithms/centrality/eigenvector.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ def eigenvector_centrality(G, max_iter=100, tol=1.0e-6, nstart=None, name="eigen
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# Power iteration: make up to max_iter iterations
2828
A = G._A
2929
xprev = Vector(float, N, name="x_prev")
30-
for _ in range(max_iter):
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for _i in range(max_iter):
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xprev << x
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x += x @ A
3333
normalize(x, "L2")

‎graphblas_algorithms/algorithms/centrality/katz.py

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Original file line numberDiff line numberDiff line change
@@ -44,7 +44,7 @@ def katz_centrality(
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4545
# Power iteration: make up to max_iter iterations
4646
xprev = Vector(float, N, name="x_prev")
47-
for _ in range(max_iter):
47+
for _i in range(max_iter):
4848
xprev, x = x, xprev
4949
# x << alpha * semiring(xprev @ A) + beta
5050
x << semiring(xprev @ A)
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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
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from .connected import *
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from .weakly_connected import *
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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
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from graphblas import Vector, replace
2+
from graphblas.semiring import any_pair
3+
4+
from graphblas_algorithms.algorithms.exceptions import PointlessConcept
5+
6+
7+
def is_connected(G):
8+
if len(G) == 0:
9+
raise PointlessConcept("Connectivity is undefined for the null graph.")
10+
return _plain_bfs(G, next(iter(G))).nvals == len(G)
11+
12+
13+
def node_connected_component(G, n):
14+
return _plain_bfs(G, n)
15+
16+
17+
def _plain_bfs(G, source):
18+
index = G._key_to_id[source]
19+
A = G.get_property("offdiag")
20+
n = A.nrows
21+
v = Vector(bool, n, name="bfs_plain")
22+
q = Vector(bool, n, name="q")
23+
v[index] = True
24+
q[index] = True
25+
any_pair_bool = any_pair[bool]
26+
for _i in range(1, n):
27+
q(~v.S, replace) << any_pair_bool(q @ A)
28+
if q.nvals == 0:
29+
break
30+
v(q.S) << True
31+
return v
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@@ -0,0 +1,77 @@
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from graphblas import Vector, binary, replace
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from graphblas.semiring import any_pair
3+
4+
from graphblas_algorithms.algorithms.exceptions import PointlessConcept
5+
6+
7+
def is_weakly_connected(G):
8+
if len(G) == 0:
9+
raise PointlessConcept("Connectivity is undefined for the null graph.")
10+
return _plain_bfs(G, next(iter(G))).nvals == len(G)
11+
12+
13+
# TODO: benchmark this and the version commented out below
14+
def _plain_bfs(G, source):
15+
# Bi-directional BFS w/o symmetrizing the adjacency matrix
16+
index = G._key_to_id[source]
17+
A = G.get_property("offdiag")
18+
# XXX: should we use `AT` if available?
19+
n = A.nrows
20+
v = Vector(bool, n, name="bfs_plain")
21+
q_out = Vector(bool, n, name="q_out")
22+
q_in = Vector(bool, n, name="q_in")
23+
v[index] = True
24+
q_in[index] = True
25+
any_pair_bool = any_pair[bool]
26+
is_out_empty = True
27+
is_in_empty = False
28+
for _i in range(1, n):
29+
# Traverse out-edges from the most recent `q_in` and `q_out`
30+
if is_out_empty:
31+
q_out(~v.S) << any_pair_bool(q_in @ A)
32+
else:
33+
q_out << binary.any(q_out | q_in)
34+
q_out(~v.S, replace) << any_pair_bool(q_out @ A)
35+
is_out_empty = q_out.nvals == 0
36+
if not is_out_empty:
37+
v(q_out.S) << True
38+
elif is_in_empty:
39+
break
40+
# Traverse in-edges from the most recent `q_in` and `q_out`
41+
if is_in_empty:
42+
q_in(~v.S) << any_pair_bool(A @ q_out)
43+
else:
44+
q_in << binary.any(q_out | q_in)
45+
q_in(~v.S, replace) << any_pair_bool(A @ q_in)
46+
is_in_empty = q_in.nvals == 0
47+
if not is_in_empty:
48+
v(q_in.S) << True
49+
elif is_out_empty:
50+
break
51+
return v
52+
53+
54+
"""
55+
def _plain_bfs(G, source):
56+
# Bi-directional BFS w/o symmetrizing the adjacency matrix
57+
index = G._key_to_id[source]
58+
A = G.get_property("offdiag")
59+
n = A.nrows
60+
v = Vector(bool, n, name="bfs_plain")
61+
q = Vector(bool, n, name="q")
62+
q2 = Vector(bool, n, name="q_2")
63+
v[index] = True
64+
q[index] = True
65+
any_pair_bool = any_pair[bool]
66+
for _i in range(1, n):
67+
q2(~v.S, replace) << any_pair_bool(q @ A)
68+
v(q2.S) << True
69+
q(~v.S, replace) << any_pair_bool(A @ q)
70+
if q.nvals == 0:
71+
if q2.nvals == 0:
72+
break
73+
q, q2 = q2, q
74+
elif q2.nvals != 0:
75+
q << binary.any(q | q2)
76+
return v
77+
"""

‎graphblas_algorithms/algorithms/dag.py

Lines changed: 11 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
from graphblas import Vector, replace
2-
from graphblas.semiring import lor_pair
2+
from graphblas.semiring import any_pair
33

44
__all__ = ["descendants", "ancestors"]
55

@@ -10,10 +10,12 @@ def descendants(G, source):
1010
raise KeyError(f"The node {source} is not in the graph")
1111
index = G._key_to_id[source]
1212
A = G.get_property("offdiag")
13-
q = Vector.from_coo(index, True, size=A.nrows, name="q")
13+
q = Vector(bool, size=A.nrows, name="q")
14+
q[index] = True
1415
rv = q.dup(name="descendants")
15-
for _ in range(A.nrows):
16-
q(~rv.S, replace) << lor_pair(q @ A)
16+
any_pair_bool = any_pair[bool]
17+
for _i in range(A.nrows):
18+
q(~rv.S, replace) << any_pair_bool(q @ A)
1719
if q.nvals == 0:
1820
break
1921
rv(q.S) << True
@@ -26,10 +28,12 @@ def ancestors(G, source):
2628
raise KeyError(f"The node {source} is not in the graph")
2729
index = G._key_to_id[source]
2830
A = G.get_property("offdiag")
29-
q = Vector.from_coo(index, True, size=A.nrows, name="q")
31+
q = Vector(bool, size=A.nrows, name="q")
32+
q[index] = True
3033
rv = q.dup(name="descendants")
31-
for _ in range(A.nrows):
32-
q(~rv.S, replace) << lor_pair(A @ q)
34+
any_pair_bool = any_pair[bool]
35+
for _i in range(A.nrows):
36+
q(~rv.S, replace) << any_pair_bool(A @ q)
3337
if q.nvals == 0:
3438
break
3539
rv(q.S) << True
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Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
1-
from graphblas.semiring import lor_pair
1+
from graphblas.semiring import any_pair
22

33
__all__ = ["is_dominating_set"]
44

55

66
def is_dominating_set(G, nbunch):
7-
nbrs = lor_pair(nbunch @ G._A).new(mask=~nbunch.S) # A or A.T?
7+
nbrs = any_pair[bool](nbunch @ G._A).new(mask=~nbunch.S) # A or A.T?
88
return nbrs.size - nbunch.nvals - nbrs.nvals == 0

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