[PATCH NNGT] Maintenance: fix doc + deprecated igraph functions
Export this patch
From: Tanguy Fardet <tanguyfardet@protonmail.com>
---
doc/conf.py | 8 +++-----
nngt/analysis/graph_analysis.py | 18 +++++++++---------
nngt/analysis/ig_functions.py | 20 ++++++++++----------
3 files changed, 22 insertions(+), 24 deletions(-)
diff --git a/doc/conf.py b/doc/conf.py
index a2e1edf..c8a98a2 100755
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -57,13 +57,11 @@ try:
# NEST is not available
raise ImportError
except:
- import mock
- mock_object = mock.Mock(__name__ = "Mock", __bases__ = (object,))
-
class Mock(object):
def __init__(self, *args, **kwargs):
- super(Mock, self).__init__()
+ super().__init__()
+ self.__file__ = None
def __call__(self, *args, **kwargs):
return self
@@ -175,7 +173,7 @@ gen_autosum(source, target, 'nngt', 'summary', dtype="class",
"GroupProperty"))
gen_autosum(target, target, 'nngt.Group', 'summary', dtype="classmembers")
-gen_autosum(target, target, 'nngt.NeuralGroup', 'summary',
+gen_autosum(target, target, 'nngt.NeuralGroup', 'summary',
dtype="classmembers")
gen_autosum(target, target, 'nngt.Structure', 'summary', dtype="classmembers")
gen_autosum(target, target, 'nngt.NeuralPop', 'summary', dtype="classmembers")
diff --git a/nngt/analysis/graph_analysis.py b/nngt/analysis/graph_analysis.py
index e73fa50..f415bef 100755
--- a/nngt/analysis/graph_analysis.py
+++ b/nngt/analysis/graph_analysis.py
@@ -52,17 +52,17 @@ __all__ = [
"betweenness",
"betweenness_distrib",
"binning",
- "closeness",
- "connected_components",
+ "closeness",
+ "connected_components",
"degree_distrib",
- "diameter",
+ "diameter",
"node_attributes",
- "num_iedges",
- "reciprocity",
+ "num_iedges",
+ "reciprocity",
"shortest_distance",
"shortest_path",
"small_world_propensity",
- "spectral_radius",
+ "spectral_radius",
"subgraph_centrality",
"transitivity",
]
@@ -477,7 +477,7 @@ def shortest_path(g, source, target, directed=True, weights=None):
References
----------
.. [gt-sd] :gtdoc:`topology.shortest_distance`
- .. [ig-sp] :igdoc:`shortest_paths`
+ .. [ig-dist] :igdoc:`distances`
.. [nx-sp] :nxdoc:`algorithms.shortest_paths.generic.shortest_path`
'''
raise NotImplementedError(_backend_required)
@@ -554,7 +554,7 @@ def shortest_distance(g, sources=None, targets=None, directed=True,
References
----------
.. [gt-sd] :gtdoc:`topology.shortest_distance`
- .. [ig-sp] :igdoc:`shortest_paths`
+ .. [ig-dist] :igdoc:`distances`
.. [nx-sp] :nxdoc:`algorithms.shortest_paths.weighted.multi_source_dijkstra`
'''
raise NotImplementedError(_backend_required)
@@ -602,7 +602,7 @@ def average_path_length(g, sources=None, targets=None, directed=None,
References
----------
.. [gt-sd] :gtdoc:`topology.shortest_distance`
- .. [ig-sp] :igdoc:`shortest_paths`
+ .. [ig-dist] :igdoc:`distances`
.. [nx-sp] :nxdoc:`algorithms.shortest_paths.generic.average_shortest_path_length`
See also
diff --git a/nngt/analysis/ig_functions.py b/nngt/analysis/ig_functions.py
index 85d19c3..ed1091c 100644
--- a/nngt/analysis/ig_functions.py
+++ b/nngt/analysis/ig_functions.py
@@ -295,7 +295,7 @@ def connected_components(g, ctype=None):
References
----------
- .. [ig-connected-components] :igdoc:`clusters`
+ .. [ig-connected-components] :igdoc:`connected_components`
'''
if ctype is None:
ctype = "scc" if g.is_directed() else "wcc"
@@ -307,14 +307,14 @@ def connected_components(g, ctype=None):
elif ctype != "scc":
raise ValueError("`ctype` must be either 'scc' or 'wcc'.")
- clusters = g.graph.clusters(ig_type)
+ igcc = g.graph.connected_components(ig_type)
cc = np.zeros(g.node_nb(), dtype=int)
- for i, nodes in enumerate(clusters):
+ for i, nodes in enumerate(igcc):
cc[nodes] = i
- hist = np.array([len(c) for c in clusters], dtype=int)
+ hist = np.array([len(c) for c in igcc], dtype=int)
return cc, hist
@@ -469,7 +469,7 @@ def shortest_distance(g, sources=None, targets=None, directed=None,
References
----------
- .. [ig-sp] :igdoc:`shortest_paths`
+ .. [ig-dist] :igdoc:`distances`
'''
# weighted or selective algorithm
g, graph, w = _get_ig_graph(g, directed, weights, combine_weights,
@@ -479,12 +479,12 @@ def shortest_distance(g, sources=None, targets=None, directed=None,
# special case for one source/one target
if is_integer(sources) and is_integer(targets):
- return graph.shortest_paths(source=sources, target=targets,
- weights=w)[0][0]
+ return graph.distances(source=sources, target=targets,
+ weights=w)[0][0]
# multiple sources/targets
- mat_dist = graph.shortest_paths(source=sources, target=targets,
- weights=w)
+ mat_dist = graph.distances(source=sources, target=targets,
+ weights=w)
mat_dist = np.array(mat_dist, dtype=float)
@@ -549,7 +549,7 @@ def average_path_length(g, sources=None, targets=None, directed=None,
References
----------
- .. [ig-sp] :igdoc:`shortest_paths`
+ .. [ig-dist] :igdoc:`distances`
'''
directed = g.is_directed() if directed is None else directed
--
2.34.4
NNGT/patches/.build.yml: SUCCESS in 29m9s
[Maintenance: fix doc + deprecated igraph functions][0] from [~tfardet][1]
[0]: https://lists.sr.ht/~tfardet/nngt-developers/patches/35633
[1]: mailto:tanguyfardet@protonmail.com
✓ #851531 SUCCESS NNGT/patches/.build.yml https://builds.sr.ht/~tfardet/job/851531