NetworkX 2.5#

Release date: 22 August 2020

Supports Python 3.6, 3.7, and 3.8.

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 10 months of work with over 200 commits by 92 contributors. Highlights include:

  • Dropped support for Python 3.5.

  • add Pathlib support to work with files.

  • improve performance.

  • Updated docs and tests.

  • Removed code designed to work with Python 2.

New Functions:

  • lukes_partitioning

  • triadic analysis functions

  • functions for trophic levels analysis

  • d_separated

  • is_regular and other regular graph measures

  • graph_hash using Weisfeiler Lehman methods

  • common_neighbor_centrality (CCPA link prediction)

  • max_weight_clique

  • path_weight and is_path

  • rescale_layout_dict

  • junction_tree

New generators:

  • paley_graph

  • interval_graph

New layouts:

  • multipartite_layout

Improvements#

  • Add governance documents, developer guide and community structures

  • Implement explicit deprecation policy.

  • Initiate an NX Enhancement Proposal (NXEP) system

  • optimize single_source_shortest_path

  • improved consistent “weight” specification in shortest_path routines

  • Reduce numpy.matrix usage which is discouraged by numpy.

  • improved line color

  • better search engine treatment of docs

  • lattice and grid_graph and grid_2d_graph can use dim=tuple

  • fix initializer of kamada_kawai_layout algorithm

  • moral and threshold functions now included in namespace and docs

  • scale arrows better when drawing

  • more uniform creation of random lobster graphs

  • allow editing graph during iteration over connected_components

  • better column handling in conversion of pandas DataFrame

  • allow simrank_similarity with directed graph input

  • ensure VoteRank ability is nonnegative

  • speedup kernighan_lin_bisection

  • speedup negative weight cycle detection

  • tree_isomorphism

  • rooted_tree_isomorphism

  • Gexf edge attribute “label” is available

API Changes#

  • enabled “copy” flag parameter in contracted_nodes

  • allow partially periodic lattices

  • return value for minimum_st_node_cut now always a set

  • removed unused “has_numpy” argument from create_py_random_state

  • fixed return values when drawing empty nodes and edges

  • allow sets and frozensets of edges as input to nx.Graph()

  • “weight” can be function for astar, directional_dijksta, all_shortest_path

  • allow named key ids for GraphML edge writing

  • all keywords are now checked for validity in nx.draw and friends

  • EdgeDataView “in” operator checks if nodes are “in nbunch”

  • remove completeness condition from minimum weight full matching

  • option to sort neighbors in bfs traversal

  • draw_networkx accepts numpy array for edgelist

  • relabel_nodes with 2 nodes mapped to same node can now create multiedge

  • steiner_tree works with MultiGraph

  • Add show kwarg to view_pygraphviz (#4155)

  • Prepare for turning chordal_graph_cliques into a generator (#4162)

  • GraphML reader keyword force_multigraph creates MultiGraph even w/o multiedges

Deprecations#

  • [#3680] Deprecate make_str(x) for str(x). Deprecate is_string_like(obj) for isinstance(obj, str).

  • [#3725] Deprecate literal_stringizer and literal_destringizer.

  • [#3983] Deprecate reversed context manager.

  • [#4155] Deprecate display_pygraphviz.

  • [#4162] Deprecate chordal_graph_cliques returning a set.

  • [#4161] Deprecate betweenness_centrality_source.

  • [#4161] Deprecate edge_betweeness.

  • [#4161] Rename _naive_greedy_modularity_communities as naive_greedy_modularity_communities.

Merged PRs#

A total of 256 changes have been committed.

  • Bump release version

  • Update release process

  • Drop support for Python 3.5

  • fix typo docs

  • Remove old Python 2 code

  • Enable more doctests

  • Fix pydot tests

  • Unclear how to test the test helper function

  • Pathlib introduced in Py 3.4

  • Remove code using sys.version_info to detect Python 2

  • Use yield from

  • PEP8 fixes to tests

  • Remove unused imports

  • Use pytest.importorskip

  • PEP8 fixes

  • Remove unused imports

  • Add pep8_speaks conf

  • Use itertools accumulate

  • Fixes issue 3610: Bug in version attribute of gexf.py

  • Ignore W503

  • Run doctest without optional dependencies

  • Skip doctests when missing dependencies

  • Remove sed imports

  • Enable tests (#3678)

  • contracted_nodes copy flag added (#3646)

  • Deprecate make_str

  • Deprecate is_string_like

  • Fix PEP8 issues

  • Enable ThinGraph tests (#3681)

  • Optimize _single_shortest_path_length (#3647)

  • Fix issue 3431: Return error in case of bad input to make_small_graph (#3676)

  • avoid duplicate tests due to imports (#3684)

  • Fix typo: Laplacion -> Laplacian (#3689)

  • Add tests

  • Lukes algorithm implementation (#3666)

  • Remove shim that worked around using starmap

  • Add back to gallery

  • Add colormap and color limits to LineCollection (#3698)

  • Fix matplotlib deprecation (#3697)

  • Adapt SciPy CoC

  • Update docs to be more accurate about speed of G.neighbors (#3699)

  • Use canonical url to help search engines

  • Remove duplicate license parameter (#3710)

  • Fix documentation issues for exceptions in a few places

  • Fix more documentation issues with exceptions

  • Remove old Python 2 code

  • Remove boiler plate from top of modules

  • Remove superfluous encoding information

  • Update examples

  • Simplify package docstring

  • Remove shebang from non-executables

  • Add contributors

  • K-truss is defined for edges being in (k-2) triangles and not for k triangles (#3713)

  • Enable optional tests on Python 3.8

  • Fix test_numpy_type to pass under Python 3.8

  • Add links to data files

  • Deprecate Python 2/3 compatibility code

  • Update style

  • Update style

  • Separate easy and hard to install optional requirements

  • Install optional dependencies by default

  • Refactor tests

  • Sample code for subgraph copy: add parenthesis to is_multigraph (#3734)

  • Fixed typo (#3735)

  • fix citation links (#3741)

  • remove f strings from setup.py for clear error message < py3.6 (#3738)

  • 3511 gml list support (#3649)

  • added linestyle as argument (#3747)

  • Link to files needed for example (#3752)

  • fixed a typo

  • Merge pull request #3759 from yohm/patch-1

  • remove unused variable so grid_graph supports dim=tuple (#3760)

  • Sudoku generator issue 3756 (#3757)

  • Fix scaling of single node shells in shall_layout (#3764)

  • Adding triadic analysis functions (#3742)

  • Improve test coverage

  • Update contribs script

  • Convert %-format to fstring

  • Upgrade to Py36 syntax

  • Upgrade to Py36 syntax

  • Update string format

  • Fix scipy deprecation warnings

  • Update year

  • Silence known warnings (#3770)

  • Fix docstring for asyn_fluidc (#3779)

  • Fix #3703 (#3784)

  • fix initializer for kamada_kawai_layout (networkx #3658) (#3782)

  • Minor comments issue (#3787)

  • Adding moral and threshold packages to main namespace (#3788)

  • Add weight functions to bidirectional_dijkstra and astar (#3799)

  • Shrink the source side of an arrow properly when drawing a directed edge. #3805 (#3806)

  • option for partially-periodic lattices (networkx #3586) (#3807)

  • Prevent KeyError on subgraph_is_monomorphic (#3798)

  • Trophic Levels #3736 (#3804)

  • UnionFind’s union doesn’t accurately track set sizes (#3810)

  • Remove whitespace (#3816)

  • reconsider the lobster generator (#3822)

  • Fix typo (#3838)

  • fix typo slightly confusing the meaning (#3840)

  • Added fix for issue #3846 (#3848)

  • Remove unused variable has_numpy from create_py_random_state (#3852)

  • Fix return values when drawing empty nodes and edges #3833 (#3854)

  • Make connected_components safe to component set mutation (#3859)

  • Fix example in docstring (#3866)

  • Update README.rst website link to https (#3888)

  • typo (#3894)

  • Made CONTRIBUTING.rst more clearer (#3895)

  • Fixing docs for nx.info(), along with necessary tests (#3893)

  • added default arg for json dumps for jit_data func (#3891)

  • Fixed nx.Digraph to nx.DiGraph (#3909)

  • Use Sphinx 3.0.1

  • Fix Sphinx deprecation

  • Add logo to docs

  • allow set of edge nodes (#3907)

  • Add extra information when casting ‘id’ to int() fails. (Resolves #3910) (#3916)

  • add paley graph (#3900)

  • add paley graph to doc (#3927)

  • Update astar.py (#3947)

  • use keywords for positional arguments (#3952)

  • fix documentation (#3959)

  • Add option for named key ids to GraphML writing. (#3960)

  • fix documentation (#3958)

  • Correct handling of zero-weight edges in all_shortest_paths (#3783)

  • Fix documentation typo (#3965)

  • Fix: documentation of simrank_similarity_numpy (#3954)

  • Fix for #3930 (source & target columns not overwritten when converting to pd.DataFrame) (#3935)

  • Add weight function for shortest simple paths for #3948 (#3949)

  • Fix definition of communicability (#3973)

  • Fix simrank_similarity with directed graph input (#3961)

  • Fixed weakening of voting ability (#3970)

  • implemented faster sweep algorithm for kernighan_lin_bisection (#3858)

  • Fix issue #3926 (#3928)

  • Update CONTRIBUTORS.rst (#3982)

  • Deprecate context_manager reversed in favor of reversed_view (#3983)

  • Update CONTRIBUTORS.rst (#3987)

  • Enhancement for voterank (#3972)

  • add d-separation algorithm (#3974)

  • DOC: added see also section to find_cycle (#3999)

  • improve docs for subgraph_view filter_egde (#4010)

  • Fix exception causes in dag.py (#4000)

  • use raise from for exceptions in to_networkx_graph (#4009)

  • Fix exception causes and messages in 12 modules (#4012)

  • Fix typo: np.int -> np.int_ (#4013)

  • fix a typo (#4017)

  • change documentation (#3981)

  • algorithms for regular graphs (#3925)

  • Typo Hand should be Hans (#4025)

  • DOC: Add testing bullet to CONTRIBUTING. (#4035)

  • Update Sphinx

  • Update optional/test deps

  • Add governance/values/nexp/roadmap

  • Improve formatting of None in tutorial (#3986)

  • Fixes DiGraph spelling in docstring (#3892)

  • Update links to Py3 docs (#4042)

  • Add method to clear edges only (#3477)

  • Fix exception causes and messages all over the codebase (#4015)

  • Handle kwds explicitly in draw_networkx (#4033)

  • return empty generator instead of empty list (#3967)

  • Correctly infer numpy float types (#3919)

  • MAINT: Update from_graph6_bytes arg/docs. (#4034)

  • Add URLs/banner/titlebar to documentation (#4044)

  • Add negative cycle detection heuristic (#3879)

  • Remove unused imports (#3855)

  • Fixed Bug in generate_gml(G, stringizer=None) (#3841)

  • Raise NetworkXError when k < 2 (#3761)

  • MAINT: rm np.matrix from alg. conn. module

  • MAINT: rm np.matrix from attribute_ac.

  • MAINT,TST: Parametrize methods in TestAlgebraicConnectivity.

  • MAINT,TST: parametrize buckminsterfullerene test.

  • MAINT,TST: Remove unused _methods class attr

  • MAINT,TST: Parametrize TestSpectralOrdering.

  • excluded self/recursive edges (#4037)

  • WIP: Change EdgeDataView __contains__ feature (2nd attempt) (#3845)

  • Index edges for multi graph simple paths (#3358)

  • ENH: Add new graph_hashing feature

  • Fix pandas deprecation

  • Organize removal of deprecated code

  • Update sphinx

  • ENH: Add roots and timeout to GED (#4026)

  • Make gallery more prominent

  • Add an implementation for interval_graph and its unit tests (#3705)

  • Fixed typo in kamada_kawai_layout docstring (#4059)

  • Remove completeness condition from minimum weight full matching (#4057)

  • Implemented multipartite_layout (#3815)

  • added new Link Prediction algorithm (CCPA) (#4028)

  • add the option of sorting node’s neighbors during bfs traversal (#4029)

  • TST: remove int64 specification from test. (#4055)

  • Ran pyupgrade –py36plus

  • Remove trailing spaces

  • Tell psf/black to ignore specific np.arrays

  • Format w/ black

  • Add pre-commit hook to for psf/black

  • Merge pull request #4060 from jarrodmillman/black

  • Fix a few typos in matching docstrings (#4063)

  • fix bug for to_scipy_sparse_matrix function (#3985)

  • Update documentation of minimum weight full matching (#4062)

  • Add maximum weight clique algorithm (#4016)

  • Clear pygraphviz object after creating networkx object (#4070)

  • Use newer osx on travis (#4075)

  • Install Python after updating brew (#4079)

  • Add link to black (#4078)

  • Improves docs regarding aliases of erdos-reyni graph generators (#4074)

  • MAINT: Remove dependency version info from INSTALL (#4081)

  • Simplify top-level directory (#4087)

  • DOC: Fix return types in laplacianmatrix. (#4090)

  • add modularity to the docs (#4096)

  • Allow G.remove_edges_from(nx.selfloops_edges(G)) (#4080)

  • MAINT: rm private fn in favor of numpy builtin. (#4094)

  • Allow custom keys for multiedges in from_pandas_edgelist (#4076)

  • Fix planar_layout docstring (#4097)

  • DOC: Rewording re: numpy.matrix

  • MAINT: rm to/from_numpy_matrix internally

  • Merge pull request #4093 from rossbar/rm_npmatrix

  • Remove copyright boilerplate (#4105)

  • Update contributor guide (#4088)

  • Add function to calculate path cost for a specified path (#4069)

  • Update docstring for from_pandas_edgelist (#4108)

  • Add max_weight_clique to doc (#4110)

  • Update deprecation policyt (#4112)

  • Improve modularity calculation (#4103)

  • Add team gallery (#4117)

  • CI: Setup circle CI for documentation builds (#4119)

  • Build pdf (#4123)

  • DOC: Suggestions and improvements from tutorial readthrough (#4121)

  • Enable 3.9-dev on travis (#4124)

  • Fix parse_edgelist behavior with multiple attributes (#4125)

  • CI: temporary fix for CI latex installation issues (#4131)

  • Updated draw_networkx to accept numpy array for edgelist (#4132)

  • Add tree isomorphism (#4067)

  • MAINT: Switch to abc-based isinstance checks in to_networkx_graph (#4136)

  • Use dict instead of OrderedDict since dict is ordered by default from Python 3.6. (#4145)

  • MAINT: fixups to parse_edgelist. (#4128)

  • Update apt-get on circleci image (#4147)

  • add rescale_layout_dict to change scale of the layout_dicts (#4154)

  • Update dependencies

  • Remove gdal from requirements

  • relabel_nodes now preserves edges in multigraphs (#4066)

  • MAINT,TST: Improve coverage of nx_agraph module (#4156)

  • Get steiner_tree to work with MultiGraphs by postprocessing (#4160)

  • junction_tree for #1012 (#4004)

  • API: Add show kwarg to view_pygraphviz. (#4155)

  • Prepare for turning chordal_graph_cliques into a generator (#4162)

  • Docs update (#4161)

  • Remove unnecessary nx imports from doctests (#4163)

  • MultiGraph from graphml with explicit edge ids #3470 (#3763)

  • Update sphinx dep (#4164)

  • Add edge label in GEXF writer as an optional attribute (#3347)

  • First Draft of Release Notes for v2.5 (#4159)

  • Designate 2.5rc1 release

  • Bump release version

  • Update deprecations in release notes (#4166)

  • DOC: Update docstrings for public functions in threshold module (#4167)

  • Format python in docstrings (#4168)

  • DOC,BLD: Fix doc build warning from markup error. (#4174)

It contained the following 3 merges:

  • fixed a typo (#3759)

  • Use psf/black (#4060)

  • MAINT: Replace internal usage of to_numpy_matrix and from_numpy_matrix (#4093)

Contributors#

  • Adnan Abdulmuttaleb

  • Abhi

  • Antoine-H

  • Salim BELHADDAD

  • Ross Barnowski

  • Lukas Bernwald

  • Isaac Boates

  • Kelly Boothby

  • Matthias Bruhns

  • Mahmut Bulut

  • Rüdiger Busche

  • Gaetano Carpinato

  • Nikos Chan

  • Harold Chan

  • Camden Cheek

  • Daniel

  • Daniel-Davies

  • Bastian David

  • Christoph Deil

  • Tanguy Fardet

  • 赵丰 (Zhao Feng)

  • Andy Garfield

  • Oded Green

  • Drew H

  • Alex Henrie

  • Kang Hong Jin

  • Manas Joshi

  • Søren Fuglede Jørgensen

  • Aabir Abubaker Kar

  • Folgert Karsdorp

  • Suny Kim

  • Don Kirkby

  • Katherine Klise

  • Steve Kowalik

  • Ilia Kurenkov

  • Whi Kwon

  • Paolo Lammens

  • Zachary Lawrence

  • Sanghack Lee

  • Anton Lodder

  • Lukas Lösche

  • Eric Ma

  • Mackyboy12

  • Christoph Martin

  • Alex Marvin

  • Mattwmaster58

  • James McDermott

  • Jarrod Millman

  • Ibraheem Moosa

  • Yohsuke Murase

  • Neil

  • Harri Nieminen

  • Danny Niquette

  • Carlos G. Oliver

  • Juan Orduz

  • Austin Orr

  • Pedro Ortale

  • Aditya Pal

  • PalAditya

  • Jose Pinilla

  • PranayAnchuri

  • Jorge Martín Pérez

  • Pradeep Reddy Raamana

  • Ram Rachum

  • David Radcliffe

  • Federico Rosato

  • Tom Russell

  • Craig Schmidt

  • Jonathan Schneider

  • Dan Schult

  • Mridul Seth

  • Karthikeyan Singaravelan

  • Songyu-Wang

  • Kanishk Tantia

  • Jeremias Traub

  • James Trimble

  • Shashi Tripathi

  • Stefan van der Walt

  • Jonatan Westholm

  • Kazimierz Wojciechowski

  • Jangwon Yie

  • adnanmuttaleb

  • anentropic

  • arunwise

  • beckedorf

  • ernstklrb

  • farhanbhoraniya

  • fj128

  • gseva

  • haochenucr

  • johnthagen

  • kiryph

  • muratgu

  • ryan-duve

  • sauxpa

  • tombeek111

  • willpeppo