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NetworkX 2.5

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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 <https://networkx.org/>_ and our gallery of examples <https://networkx.org/documentation/latest/auto_examples/index.html>. Please send comments and questions to the networkx-discuss mailing list <http://groups.google.com/group/networkx-discuss>.

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_dijkstra, 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 <https://github.com/networkx/networkx/pull/3680>_] Deprecate make_str(x) for str(x). Deprecate is_string_like(obj) for isinstance(obj, str).

  • [#3725 <https://github.com/networkx/networkx/pull/3725>_] Deprecate literal_stringizer and literal_destringizer.

  • [#3983 <https://github.com/networkx/networkx/pull/3983>_] Deprecate reversed context manager.

  • [#4155 <https://github.com/networkx/networkx/pull/4155>_] Deprecate display_pygraphviz.

  • [#4162 <https://github.com/networkx/networkx/pull/4162>_] Deprecate chordal_graph_cliques returning a set.

  • [#4161 <https://github.com/networkx/networkx/pull/4161>_] Deprecate betweenness_centrality_source.

  • [#4161 <https://github.com/networkx/networkx/pull/4161>_] Deprecate edge_betweenness.

  • [#4161 <https://github.com/networkx/networkx/pull/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: Laplacian -> 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_edge (#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 policy (#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