chore(deps): update dependency python_igraph to v0.11.8

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
python_igraph (source, changelog)	==0.9.11 -> ==0.11.8

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Release Notes

igraph/python-igraph (python_igraph)

v0.11.8

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Fixed

• Fixed documentation build on Read The Docs. No other changes compared to
  0.11.7.

v0.11.6

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Added

• Added Graph.Hypercube() for creating n-dimensional hypercube graphs.

• Added Graph.Chung_Lu() for sampling from the Chung-Lu model as well as
  several related models.

• Added Graph.is_complete() to test if there is a connection between all
  distinct pairs of vertices.

• Added Graph.is_clique() to test if a set of vertices forms a clique.

• Added Graph.is_independent_vertex_set() to test if some vertices form an
  independent set.

• Added Graph.mean_degree() for a convenient way to compute the average
  degree of a graph.

Changed

• The C core of igraph was updated to version 0.10.13.

• Graph.rewire() now attempts to perform edge swaps 10 times the number of
  edges by default.

• Error messages issued when an attribute is not found now mention the name
  and type of that attribute.

v0.11.5

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Added

• Added a prefixattr=... keyword argument to Graph.write_graphml() that
  allows the user to strip the g_, v_ and e_ prefixes from GraphML files
  written by igraph.

Changed

• Graph.are_connected() has now been renamed to Graph.are_adjacent(),
  following up a similar change in the C core. The old name of the function
  is deprecated but will be kept around until at least 0.12.0.

• The C core of igraph was updated to version 0.10.12.

• Deprecated PyCObject API calls in the C code were replaced by calls to
  PyCapsule, thanks to @​DavidRConnell in
  https://github.com/igraph/python-igraph/pull/763/763

• get_shortest_path() documentation was clarified by @​JDPowell648 in
  https://github.com/igraph/python-igraph/pull/764/764

• It is now possible to link to an existing igraph C core on MSYS2, thanks to
  @​Kreijstal in https://github.com/igraph/python-igraph/pull/770

Fixed

• Bugfix in the NetworkX graph conversion code by @​rmmaf in
  https://github.com/igraph/python-igraph/pull/767/767

v0.11.4

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Added

• Added Graph.Prufer() to construct a graph from a Prüfer sequence.

• Added Graph.Bipartite_Degree_Sequence() to construct a bipartite graph from
  a bidegree sequence.

• Added Graph.is_biconnected() to check if a graph is biconnected.

Fixed

• Fixed import of graph-tool graphs for vertex properties where each property
  has a vector value.

• Graph.Adjacency() now accepts Matrix instances and other sequences as an
  input, it is not limited to lists-of-lists-of-ints any more.

v0.11.3

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Added

• Added Graph.__invalidate_cache() for debugging and benchmarking purposes.

Changed

• The C core of igraph was updated to version 0.10.8.

Fixed

• Removed incorrectly added loops=... argument of Graph.is_bigraphical().

• Fixed a bug in the Matplotlib graph drawing backend that filled the interior of undirected curved edges.

v0.11.2

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Fixed

• Fixed plotting of null graphs with the Matplotlib backend.

v0.10.8

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Added

• Added is_bigraphical() to test whether a pair of integer sequences can be the degree sequence of some bipartite graph.

• Added weights=... keyword argument to Graph.radius() and Graph.eccentricity().

v0.10.6

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Changed

• The C core of igraph was updated to version 0.10.6.

• Graph.Incidence() is now deprecated in favour of Graph.Biadjacency() as it constructs a bipartite graph from a bipartite adjacency matrix. (The previous name was a mistake). Future versions might re-introduce Graph.Incidence() to construct a graph from its incidence matrix.

• Graph.get_incidence() is now deprecated in favour of Graph.get_biadjacency() as it returns the bipartite adjacency matrix of a graph and not its incidence matrix. (The previous name was a mistake). Future versions might re-introduce Graph.get_incidence() to return the incidence matrix of a graph.

• Reverted the change in 0.10.5 that prevented adding vertices with integers as vertex names. Now we show a deprecation warning instead, and the addition of vertices with integer names will be prevented from version 0.11.0 only.

Fixed

• Fixed a minor memory leak in Graph.decompose().

• The default vertex size of the Plotly backend was fixed so the vertices are
  now visible by default without specifying an explicit size for them.

v0.10.5

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Added

• The plot() function now takes a backend keyword argument that can be used
  to specify the plotting backend explicitly.

• The VertexClustering object returned from Graph.community_leiden() now
  contains an extra property named quality that stores the value of the
  internal quality function optimized by the algorithm.

• Graph.Adjacency() and Graph.Weighted_Adjacency() now supports
  loops="once", loops="twice" and loops="ignore" to control how loop
  edges are handled in a more granular way. loops=True and loops=False
  keep on working as in earlier versions.

• Added Graph.get_shortest_path() as a convenience function for cases when
  only one shortest path is needed between a given source and target vertices.

• Added Graph.get_shortest_path_astar() to calculate the shortest path
  between two vertices using the A-star algorithm and an appropriate
  heuristic function.

• Added Graph.count_automorphisms() to count the number of automorphisms
  of a graph and Graph.automorphism_group() to calculate the generators of
  the automorphism group of a graph.

• The VertexCover constructor now allows referring to vertices by names
  instead of IDs.

Fixed

• resolution parameter is now correctly taken into account when calling
  Graph.modularity()

• VertexClustering.giant() now accepts the null graph. The giant component of
  a null graph is the null graph according to our conventions.

• Graph.layout_reingold_tilford() now accepts vertex names in the roots=...
  keyword argument.

• The plotting of curved directed edges with the Cairo backend is now fixed;
  arrowheads were placed at the wrong position before this fix.

Changed

• The C core of igraph was updated to version 0.10.5.

Removed

• Removed defunct Graph.community_leading_eigenvector_naive() method. Not a
  breaking change because it was already removed from the C core a long time
  ago so the function in the Python interface did not do anything useful
  either.

v0.10.4

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Added

• Added Graph.vertex_coloring_greedy() to calculate a greedy vertex coloring
  for the graph.

• Betweenness and edge betweenness scores can now be calculated for a subset of
  the shortest paths originating from or terminating in a certain set of
  vertices only.

Fixed

• Fixed the drawing of VertexDendrogram instances, both in the Cairo and the
  Matplotlib backends.
• The cutoff and normalized arguments of Graph.closeness() did not function correctly.

v0.10.3

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Changed

• The C core of igraph was updated to version 0.10.3.

• UMAP layout now exposes the computation of the symmetrized edge weights via
  umap_compute_weights(). The layout function, Graph.layout_umap(), can
  now be called either on a directed graph with edge distances, or on an
  undirected graph with edge weights, typically computed via
  umap_compute_weights() or precomputed by the user. Moreover, the
  sampling_prob argument was faulty and has been removed. See PR
  #​613 for details.

• The resolution_parameter argument of Graph.community_leiden() was renamed
  to resolution for sake of consistency. The old variant still works with a
  deprecation warning, but will be removed in a future version.

Fixed

• Graph.Data_Frame() now handles the Int64 data type from pandas, thanks
  to @​Adriankhl. See PR
  #​609 for details.

• Graph.layout_lgl() root argument is now optional (as it should have been).

• The VertexClustering class now handles partial dendrograms correctly.

v0.10.2

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Added

• python-igraph is now tested in Python 3.11.

• Added Graph.modularity_matrix() to calculate the modularity matrix of
  a graph.

• Added Graph.get_k_shortest_paths(), thanks to
  @​sombreslames. See PR
  #​577 for details.

• The setup.py script now also accepts environment variables instead of
  command line arguments to configure several aspects of the build process
  (i.e. whether a fully static extension is being built, or whether it is
  allowed to use pkg-config to retrieve the compiler and linker flags for
  an external igraph library instead of the vendored one). The environment
  variables are named similarly to the command line arguments but in
  uppercase, dashes replaced with underscores, and they are prefixed with
  IGRAPH_ (i.e. --use-pkg-config becomes IGRAPH_USE_PKG_CONFIG).

Changed

• The C core of igraph was updated to version 0.10.2, fixing a range of bugs
  originating from the C core.

Fixed

• Fixed a crash in Graph.decompose() that was accidentally introduced in
  0.10.0 during the transition to igraph_graph_list_t in the C core.

• Clustering.sizes() now works correctly even if the membership vector
  contains None items.

• Graph.modularity() and Graph.community_multilevel() now correctly expose
  the resolution parameter.

• Fixed a reference leak in Graph.is_chordal() that decreased the reference
  count of Python's built-in True and False constants unnecessarily.

• Unit tests updated to get rid of deprecation warnings in Python 3.11.

v0.10.1

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Added

• Added Graph.minimum_cycle_basis() and Graph.fundamental_cycles()

• Graph.average_path_length() now supports edge weights.

Fixed

• Restored missing exports from igraph.__all__ that used to be in the main
  igraph package before 0.10.0.

v0.10.0

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Added

• More robust support for Matplotlib and initial support for plotly as graph
  plotting backends, controlled by a configuration option. See PR
  #​425 for more details.

• Added support for additional ways to construct a graph, such as from a
  dictionary of dictionaries, and to export a graph object back to those
  data structures. See PR #​434
  for more details.

• Graph.list_triangles() lists all triangles in a graph.

• Graph.reverse_edges() reverses some or all edges of a graph.

• Graph.Degree_Sequence() now supports the "no_multiple_uniform" generation
  method, which generates simple graphs, sampled uniformly, using rejection
  sampling.

• Graph.Lattice() now supports per-dimension periodicity control.

• Graph.get_adjacency() now allows the user to specify whether loop edges
  should be counted once or twice, or not at all.

• Graph.get_laplacian() now supports left-, right- and symmetric normalization.

• Graph.modularity() now supports setting the resolution with the
  resolution=... parameter.

Changed

• The C core of igraph was updated to version 0.10.0.

• We now publish abi3 wheels on PyPI from CPython 3.9 onwards, making it
  possible to use an already-built Python wheel with newer minor Python
  releases (and also reducing the number of wheels we actually need to
  publish). Releases for CPython 3.7 and 3.8 still use version-specific wheels
  because the code of the C part of the extension contains conditional macros
  for CPython 3.7 and 3.8.

• Changed default value of the use_vids=... argument of Graph.DataFrame()
  to True, thanks to @​fwitter.

• Graph.Degree_Sequence() now accepts all sorts of sequences as inputs, not
  only lists.

Fixed

• The Matplotlib backend now allows edge_color and edge_width to be set
  on an edge-by-edge basis.

Removed

• Dropped support for Python 3.6.

• Removed deprecated UbiGraphDrawer.

• Removed deprecated show() method of Plot instances as well as the feature
  that automatically shows the plot when plot() is called with no target.

• Removed the eids keyword argument of get_adjacency().

Deprecated

• Graph.clusters() is now deprecated; use Graph.connected_components() or
  its already existing shorter alias, Graph.components().

• Graph.shortest_paths() is now deprecated; use Graph.distances() instead.

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[szhorvat]

Please depend on igraph instead of python-igraph. python_igraph (with an underscore instead of a dash) was never used as a name, but PyPI replaces underscores by dashed anyway ...

See igraph/python-igraph#699 for details.