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Graph.Hypercube()
for creating n-dimensional hypercube graphs.Graph.Chung_Lu()
for sampling from the Chung-Lu model as well as several related models.Graph.is_complete()
to test if there is a connection between all distinct pairs of vertices.Graph.is_clique()
to test if a set of vertices forms a clique.Graph.is_independent_vertex_set()
to test if some vertices form an independent set.Graph.mean_degree()
for a convenient way to compute the average degree of a graph.Graph.rewire()
now attempts to perform edge swaps 10 times the number of edges by default.Full Changelog: https://github.com/igraph/python-igraph/compare/0.11.5...0.11.6
Published by ntamas 5 months ago
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.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
get_shortest_path()
documentation was clarified by @JDPowell648 in https://github.com/igraph/python-igraph/pull/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
Full Changelog: https://github.com/igraph/python-igraph/compare/0.11.4...0.11.5
Published by ntamas 8 months ago
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.
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.
Published by ntamas 11 months ago
Graph.__invalidate_cache()
for debugging and benchmarking purposes.loops=...
argument of Graph.is_bigraphical()
.Published by ntamas about 1 year ago
python-igraph
is now tested in Python 3.12.
Added weights=...
keyword argument to Graph.layout_kamada_kawai()
.
matplotlib
plotting infrastructure underwent major surgery and is now able to show consistent vertex and edge drawings at any level of zoom, including with animations, and for any aspect ratio.vertex_size=25
is a reasonable size for igraph.plot
.edge_loop_size
argument in igraph.plot
.matplotlib
backend when plotting a graph, igraph.plot
now does not return the Axes
anymore. Instead, it returns a container artist called GraphArtist
, which contains as children the elements of the graph plot: a VertexCollection
for the vertices, and EdgeCollection
for the edges, and so on. These objects can be used to modify the plot after the initial rendering, e.g. inside a Jupyter notebook, to fine tune the appearance of the plot. While documentation on specific graphic elements is still scant, more descriptive examples will follow in the future.Fixed drawing order of vertices in the Plotly backend (#691).
Fixed plotting of null graphs with the Matplotlib backend.
Published by ntamas about 1 year ago
Yes, the version number is correct - igraph 0.10.7 has never made it to PyPI. It is tagged in the repository, but it has never been released officially. The changelog below lists the changes between igraph 0.10.6 and 0.10.8.
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()
.
Graph.distances()
, Graph.get_shortest_path()
and Graph.get_shortest_paths()
now allow the user to select the algorithm to be used explicitly.
The C core of igraph was updated to version 0.10.7.
Graph.distances()
now uses Dijkstra's algorithm when there are zero weights but no negative weights. Earlier versions switched to Bellman-Ford or Johnson in the presence of zero weights unnecessarily.
Fixed a bug in EdgeSeq.select(_incident=...)
for undirected graphs.
Fixed a memory leak in Graph.distances()
when attempting to use Johnson's algorithm with mode != "out"
Published by ntamas over 1 year ago
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 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.
Published by ntamas over 1 year ago
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.
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.
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.Published by ntamas over 1 year ago
Graph.vertex_coloring_greedy()
to calculate a greedy vertex coloring for the graph.VertexDendrogram
instances, both in the Cairo and the Matplotlib backends.cutoff
and normalized
arguments of Graph.closeness()
did not function correctly.Published by ntamas almost 2 years ago
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.
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.
Published by ntamas about 2 years ago
python-igraph
is now tested in Python 3.11.Graph.modularity_matrix()
to calculate the modularity matrix of a graph.Graph.get_k_shortest_paths()
, thanks to @sombreslames. See PR #577 for details.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
).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.Graph.is_chordal()
that decreased the reference count of Python's built-in True
and False
constants unnecessarily.Published by ntamas about 2 years ago
Graph.minimum_cycle_basis()
and Graph.fundamental_cycles()
Graph.average_path_length()
now supports edge weights.igraph.__all__
that used to be in the main igraph
package before 0.10.0.Published by ntamas about 2 years ago
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.
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.
edge_color
and edge_width
to be setDropped 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()
.
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.
Published by ntamas over 2 years ago
musllinux
wheels on PyPI.Graph union and intersection (by name) operators now verify that there are no duplicate names within the individual graphs.
Fixed a memory leak in Graph.union()
when edge maps were used; see #534 for details.
Fixed a bug in the Cairo and Matplotlib backends that prevented edges with labels from being drawn properly; see #535 for details.
Published by ntamas over 2 years ago
Fixed plotting of curved edges in the Cairo plotting backend.
setup.py
now looks for igraph.pc
recursively in vendor/install
; this fixes building igraph from source in certain Linux distributions
Graph.shortest_paths()
does not crash with zero-length weight vectors any more
Fix a memory leak in Graph.delete_vertices()
and other functions that convert a list of vertex IDs internally to an igraph_vs_t
object, see #503 for details.
Fixed potential memory leaks in Graph.maximum_cardinality_search()
, Graph.get_all_simple_paths()
, Graph.get_subisomorphisms_lad()
, Graph.community_edge_betweenness()
, as well as the union
and intersection
operators.
Fix a crash that happened when subclassing Graph
and overriding __new__()
in the subclass; see #496 for more details.
Documentation now mentions that we now support graphs of size 5 or 6 for isomorphism / motif calculations if the graph is undirected
Published by ntamas almost 3 years ago
Fixed a performance bottleneck in VertexSeq.select()
and EdgeSeq.select()
for the case when the VertexSeq
or the EdgeSeq
represents the whole graph. See #494 for more details.
Edge labels now take the curvature of the edge into account, thanks to @Sriram-Pattabiraman. (#457)
Published by ntamas almost 3 years ago
🎉 python-igraph
is now simply igraph
, at least on PyPI.
❗ If you use python-igraph
in the dependencies of any of your projects, please replace it with igraph
instead. python-igraph
is now a stub package on PyPI that depends on the matching version of the Python package named igraph
. We will keep on updating python-igraph
until Sep 1, 2022, after which python-igraph
will not receive any updates.
🙏🏼 Many thanks to @patrickfuller for allowing us to useigraph
as the package name on PyPI.
Other than that, the only change in this release compared to python-igraph
0.9.7 is that the setup script does not use distutils
any more.
Published by ntamas about 3 years ago
Added support for graph chordality which was already available in the C core: Graph.is_chordal()
, Graph.chordal_completion()
, and
Graph.maximal_cardinality_search()
. See PR #437 for more details. Thanks to @cptwunderlich for requesting this.
Graph.write()
and Graph.Read()
now accept Path
objects as well as strings. See PR #441 for more details. Thanks to @jboynyc for the implementation.
This release contains wheels for Python 3.10, and also contains experimental Python wheels for the aarch64
architecture.
Fixed the Apple Silicon wheels so they should now work out of the box on newer Macs with Apple M1 CPUs.
Fixed a bug that resulted in an unexpected error when plotting a graph with wrap_labels=True
if the size of one of the vertices was zero or negative, thanks to @jboynyc. See PR #439 for more details.
Fixed a bug that sometimes caused random crashes in Graph.Realize_Degree_Sequence()
and at other times caused weird errors in Graph.Read_Ncol()
when it received an invalid data type.
Published by ntamas over 3 years ago
Published by ntamas over 3 years ago
plot(g, ..., mark_groups=True)
now works with the Matplotlib plotting backend.
set_random_number_generator(None)
now correctly switches back to igraph's own random number generator instead of the default one that hooks into the random
module of Python.
Improved performance in cases when igraph has to call back to Python's random
module to generate random numbers. One example is Graph.Degree_Sequence(method="vl")
, whose performance suffered a more than 30x slowdown on 32-bit platforms before, compared to the native C implementation. Now the gap is smaller. Note that if you need performance and do not care about seeding the random number generator from Python, you can now use set_random_number_generator(None)
to switch back to igraph's own RNG that does not need a roundtrip to Python.