Announcement: NetworkX 2.4¶
We’re happy to announce the release of NetworkX 2.4! NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
For more information, please visit our website and our gallery of examples. Please send comments and questions to the networkx-discuss mailing list.
Highlights¶
This release is the result of 6 months of work with over 200 commits by 67 contributors. Highlights include:
Remove deprecated code from 1.x
Support for Python 3.8
Switched to pytest for testing
Last release to support Python 3.5
New Functions:
barycenter functions
Bethe Hessian matrix function
Eulerian Path methods
group centrality measures
subgraph monomorphisms
k-truss algorithms
onion decomposition
resistance distance
asteroidal triples
non-randomness measures
linear prufing
minimum weight bipartite matching
Incremental closeness centrality
ISMAGS subgraph isomorphism algorithm
create chordal graph of a graph
New generators
Binomial tree generator
Directed joint degree generator
Random internet AS graph generator
New for Layouts
spiral node layout routine
support for 3d layouts
Improvements¶
allow average shortest path to use Floyd-Warshall method
improve read/write of GML, GEXF, GraphML
allow string or json object as input to jit_graph
attempt to allow numpy.array input in place of lists in more places
faster strongly connected components
faster Floyd-Warshall Optimization
faster global efficiency
faster transitive closure
fix unionfind; betweenness_subset; lexico-topo-sort; A*; inverse_line_graph; async label propagation; edgelist reading; Gomory-Hu flow method; label_propagation; partial_duplication; shell_layout with 1 node in shell; from_pandas_edgelist
Documentation improvement and fixes
API Changes¶
A utility function is_list_of_ints became is_bunch_of_ints and now tests int(item)==item instead of isinstance(_, int) This allows e.g. floats whose values are integer.
Added utility make_list_of_ints to convert containers of integer values to lists of integers
Deprecations¶
Removed functions (marked as deprecated in NetworkX 2.1):
attracting_component_subgraphs
connected_component_subgraphs
weakly_connected_component_subgraphs
strongly_connected_component_subgraphs
biconnected_component_subgraphs
See docs for component functions for how to get subgraphs.
Graph Object methods removed (marked as deprecated 2.1)
G.add_path
G.add_cycle
G.add_star
G.nodes_with_selfloops
G.number_of_selfloops
G.selfloop_edges
These are now NetworkX functions, e.g. nx.add_star(G, 5)
G.node –> use G.nodes
G.fresh_copy –> use G.__class__
Remove old names for graphview functions.
ReverseView
SubGraph
SubMultiGraph
SubMultiDiGraph
SubDiGraph
GraphView
DiGraphView
MultiGraphView
MultiDiGraphView
MultiReverseView
Use reverse_view, subgraph_view and generic_graph_view.
Pull requests and commits merged in this release¶
A total of 205 changes have been committed.
Bump release version
algorithms/traversal/edgebfs name fix (#3397)
Add see also links (#3403)
Add the reference for the Harary graph generators (#3407)
typo: swap source and target (#3413)
Fix spring_layout bug with fixed nodes (#3415)
Move LFR_benchmark to generators (#3411)
Add barycenter algorithm (#2939)
Add bethe hessian matrix (#3401)
Binomial trees generator (#3409)
Fix edge_color inconsistency with node_color and description. (#3395)
Adding module for group centrality measures (#3421)
Improve edgelist See Also (#3423)
Typo fix (#3424)
Add doc warning about self-loops for adamic_adar_index (#3427)
Fix UnionFind set extraction (#3224)
add required argument to
write_graphml
example (#3429)Fix centrality betweeness subset (#3425)
Add two versions of Simrank similarity (#3222)
Fixed typo
Merge pull request #3436 from nandahkrishna/fix-typo-betweenness-centrality-subset-test
Reorder and complete doc (#3438)
added topo_order parameter to functions that rely on topological_sort (#3447)
Implemented subgraph monomorphism (#3435)
Set seed in random_degree_sequence_graph docstring test (#3451)
Replace cb.iterable with np.iterable (#3458)
don’t remove ticks of other pyplot axes (#3476)
Fix typo in “G>raph Modelling Language” (#3468)
Naive k-truss algorithm implementation. (#3462)
Adding onion decomposition (#3461)
New Feature - Resistance Distance (#3385)
No multigraphs for betweenness (#3454)
Wheels are python 3 only
Fix deprecation warning with Python 3.7 (#3487)
Fix dfs_preorder_nodes docstring saying “edges” instead of “nodes” (#3484)
Added group closeness and group degree centralities (#3437)
Fixed incorrect docs (#3495)
Fixes Issue #3493 - Bug in lexicographical_topological_sort() (#3494)
AT-free graph recognition (#3377)
Update introduction.rst (#3504)
Full join operation and cograph generator (#3503)
Optimize the strongly connected components algorithm. (#3516)
Adding non-randomness measures for graphs (#3515)
Added safeguards (input graph G) for non-randomness measures (#3526)
Optimize the strongly connected components algorithm - Take 2 (#3519)
Small fix for bug found @ issue #3524 (#3529)
Restore checking PyPy3 (#3514)
Linear prufer coding (#3535)
Fix inverse_line_graph. (#3507)
Fix A* returning wrong solution (#3508)
Implement minimum weight full matching of bipartite graphs (#3527)
Get chordal graph for #1054 (#3353)
Faster transitive closure computation for DAGs (#3445)
Write mixed-type attributes correctly in write_graphml_lxml (#3536)
Fixes some edge cases for inverse_line_graph(). (#3538)
explicitly stated i.j convention in to_numpy_array
Incremental Closeness Centrality (undirected, unweighted graphs) (#3444)
Implement ISMAGS subgraph isomorphism algorithm (#3312)
Fixes bug in networkx.algorithms.community.label_propagation.asyn_lpa_communities (#3545)
When exporting to GML, write non 32-bit numbers as strings. (#3540)
Try to bug Fix #3552 (#3554)
add Directed Joint Degree Graph generator (#3551)
typo (#3557)
Fix a few documentation issues for the bipartite algorithm reference (#3555)
i,j convention in adj mat i/o in relevant funcs
Merge pull request #3542 from malch2/doc/update
Add 3.8-dev to travis
Fix dict iteration for Py3.8
Ignore other failures for now
Fix a typo in docstring for get_edge_data (#3564)
Fix wrong title (#3566)
Fix typo in doctring (#3568)
Fix and Improve docstrings in graph.py (#3569)
Improved graph class selection table (#3570)
Add spiral layout for graph drawing (#3534)
#3575 return coordinates of 3d layouts (#3576)
Handle k==n within the Watts-Strogatz graph generator (#3579)
Floyd-Warshall Optimization (#3400)
Use Sphinx 2.2
Add missing link to asteroidal docs
Fix Sphinx warnings
Fix Sphinx latexpdf build
Updated Contributor list (#3592)
Prim from list to set (#3512)
Fix issue 3491 (#3588)
Make Travis fail on Python 3.8 failures
Fix test_gexf to handle default serialisation order of the XML attributes
Remove future imports needed by Py2
add internet_as_graph generator (#3574)
remove cyclical references from OutEdgeDataView (#3598)
Add minimum source and target margin to draw_networkx_edges. (#3390)
fix to_directed function (#3599)
Fixes #3573:GEXF output problem (#3606)
Global efficiency attempt to speed up (#3604)
Bugfix: Added flexibility in reading values for label and id (#3603)
Add method floyd-warshall to average_shortest_path_length (#3267)
Replaced is with == and minor pycodestyle fixes (#3608)
Fix many documentation based Issues (#3609)
Resolve many documentation issues (#3611)
Fixes #3187 transitive_closure now returns self-loops when cycles present (#3613)
Add support for initializing pagerank_scipy (#3183)
Add last 7 lines of Gomory-hu algorithm Fixes #3293 (#3614)
Implemented Euler Path functions (#3399)
Fix the direction of edges in label_propagation.py (#3619)
Removed unused import of random module (#3620)
Fix operation order in partial_duplication_graph (#3626)
Keep shells with 1 node away from origin in shell_layout (#3629)
Allow jit_graph to read json string or json object (#3628)
Fix typo within incode documentation (#3621)
pycodestyle and update docs for greedy_coloring.py+tests (#3631)
Add version badges
Load long description from README
Add missing code block (#3630)
Change is_list_of_ints to make_list_of_ints (#3617)
Handle edgeattr in from_pandas_edgelist when no columns match request (#3634)
Make draft of release notes for v2.4
Shift notes from dev to v2.4 filename.
Use recent pypy
Test Py 3.8 on macos
add check of attr type before converting inf/nan in GEXF (#3636)
Fix sphinx errors And add links to single_source_dijkstra in docs for dijkstra_path/length (#3638)
Document subgraph_view (#3627)
First round of pytest fixes
Use class methods for class setup/teardown
Have CIs use pytest
Use class methods for class setup/teardown, cont.
Do less testing (until we get it working)
replace idiom from networkx import * in test files
Fix assert funcs override
Fix static methods in link_prediction
Partially fix v2userfunc tests
Fix graph/digraph tests
Fix multigraph checks
Fix multidigraph checks
Fix test_function checks
Fix distance_measures tests
Fix decorators tests
Fix some raises in test_mst
Fix clique tests
Fix yaml tests
Fix tests in reportviews
Fix vf2 tests
Fix mst tests
Fix gdal tests
Convert nose.tools.assert_* functions into asserts
Remove unused imports
Fix some warnings
Update testing instructions
Reenable all test platforms
Fix some __init__ warnings
replace nose yield tests in test_coloring.py
Add testing, coverage, and dev environment info
Try pytestimportorskip
Another pair of variations on pytest.importorskip
fix typo and try again
Remove deprecated weakly_connected_component_subgraphs
replace assert_almost_equal and raises in algorithms/tests
set places=0 on tests that use old almost_equal
Update nx.test()
Have pytest run doctests / not sphinx
Revert “Remove deprecated weakly_connected_component_subgraphs”
remove warnings for using deprecated function
Remove deprecated functions and methods. add to release notes.
Fix subgraph_view testing
remove tests of deprecated views and fix use of deprecated G.node
tracking down use of deprecated functions
Fix deprecated use of add_path/star/cycle
reduce warnings for deprecated functions
skirt issues wih raises in test_harmonic
reduce the number of warnings by removing deprecated functions
convert_matrix demo of one way to get doctests to work
Remove deprecated from examples
Changes to convert_matrix and others that depend on np.matrix
clean up doctest deprecated code
More doctest corrections
Fix examples
Remove nose from generators
Remove nose from utils
Remove nose from classes
Replace nose.assert_raises with pytest.raises
Replace nose.raises with pytest.raises context manager
Replace
eq_
,ok_
with assertUse pytest for doctest
Highlight switch to pytest in release notes
Remove
from nose.tools import *
Remove nose.tools.SkipTest
Finalize transition to pytest
Merge pull request #3639 from stefanv/pytest-port
Test Python 3.8 with AppVeyor
Merge pull request #3648 from jarrodmillman/windows-py3.8
Remove deprecated weakly_connected_component_subgraphs
Update release notes
Update README
Announce Python 3.8 support
Designate 2.4rc1 release
Bump release version
Remove remaining SkipTests
fix documentation notes (#3644) (#3645)
Test Py 3.8.0 on AppVeyor
Speed up AppVeyor
Cleanup travis config
Improve CI caching
Update Py 3.8 on travis
Merge pull request #3652 from jarrodmillman/speedup-appveyor
Finalize release notes
It contained the following 5 merges:
Fixed typo in betweenness centrality subset test (#3436)
explicitly stated i.j convention in to_numpy_array (#3542)
pytest port (#3639)
Test Python 3.8 with AppVeyor (#3648)
Cleanup and speedup CI (#3652)
Contributors to this release¶
Rajendra Adhikari
Antoine Allard
Antoine
Salim BELHADDAD
Luca Baldesi
Tamás Bitai
Tobias Blass
Malayaja Chutani
Peter Cock
Almog Cohen
Diogo Cruz
Martin Darmüntzel
Elan Ernest
Jacob Jona Fahlenkamp
Michael Fedell
Andy Garfield
Ramiro Gómez
Haakon
Alex Henrie
Steffen Hirschmann
Martin James McHugh III
Jacob
Søren Fuglede Jørgensen
Omer Katz
Julien Klaus
Matej Klemen
Nanda H Krishna
Peter C Kroon
Anthony Labarre
Anton Lodder
MCer4294967296
Eric Ma
Fil Menczer
Erwan Le Merrer
Alexander Metz
Jarrod Millman
Subhendu Ranajn Mishra
Jamie Morton
James Myatt
Kevin Newman
Aaron Opfer
Aditya Pal
Pascal-Ortiz
Peter
Jose Pinilla
Alexios Polyzos
Michael Recachinas
Efraim Rodrigues
Adam Rosenthal
Dan Schult
William Schwartz
Weisheng Si
Kanishk Tantia
Ivan Tham
George Valkanas
Stefan van der Walt
Hsi-Hsuan Wu
Haochen Wu
Xiangyu Xu
Jean-Gabriel Young
bkief
daniel-karl
michelb7398
mikedeltalima
nandahkrishna
skhiuk
tbalint