Repository: networkx/networkx

Issue:
readwrite.cytoscape_graph(data) removes "source" and "target" fields from edges
Hi,

I realized the function to get a graph from cytoscape data modifies the data that is received as argument. Is there any reason for that? I couldn't find that in the documentation, and I found it when browsing the code.

Thank you in advance!


Discussion:
pep8speaks: Hello @cgrtrifork! Thanks for opening this PR. 



* In the file [`networkx/readwrite/json_graph/tests/test_cytoscape.py`](https://github.com/networkx/networkx/blob/c567b52ab8b16155cd51138abe2ac6fed29aa892/networkx/readwrite/json_graph/tests/test_cytoscape.py):

> [Line 19:9](https://github.com/networkx/networkx/blob/c567b52ab8b16155cd51138abe2ac6fed29aa892/networkx/readwrite/json_graph/tests/test_cytoscape.py#L19): [F841](https://duckduckgo.com/?q=pep8%20F841) local variable 'H' is assigned to but never used

Please install and run [psf/black](https://github.com/psf/black).

Patch:
diff --git a/doc/developer/release.rst b/doc/developer/release.rst
index 182586274..41379ea51 100644
--- a/doc/developer/release.rst
+++ b/doc/developer/release.rst
@@ -22,7 +22,12 @@ Release Process
 
   7. Update ``doc/news.rst``.
 
-- Comment out ``dev_banner.html`` in ``doc/_templates/layout.html``.
+- Delete the following from ``doc/_templates/layout.html``::
+
+    {% block document %}
+      {% include "dev_banner.html" %}
+      {{ super() }}
+    {% endblock %}
 
 - Toggle ``dev = True`` to ``dev = False`` in ``networkx/release.py``.
 
@@ -77,13 +82,18 @@ Release Process
 
  - Increase the version number
 
-  - Uncomment ``dev_banner.html`` in ``doc/_templates/layout.html``.
   - Toggle ``dev = False`` to ``dev = True`` in ``networkx/release.py``.
   - Update ``major`` and ``minor`` in ``networkx/release.py``.
+  - Append the following to ``doc/_templates/layout.html``::
+
+    {% block document %}
+      {% include "dev_banner.html" %}
+      {{ super() }}
+    {% endblock %}
 
  - Commit and push changes::
 
-    git add networkx/release.py
+    git add networkx/release.py doc/_templates/layout.html
     git commit -m "Bump release version"
     git push upstream master
 
@@ -93,8 +103,8 @@ Release Process
   - Sync your branch with the remote repo: ``git pull``.
     If you try to ``make github`` when your branch is out of sync, it
     creates headaches.
-  - Update ``_templates/sidebar_versions.html``.
-  - Edit ``_static/docversions.js`` and commit
+  - Update ``build/index.html``.
+  - Edit ``build/_static/docversions.js`` and commit
   - Push your changes to the repo.
   - Deploy using ``make github``.
 
diff --git a/doc/news.rst b/doc/news.rst
index 1539912ed..0abbc8a50 100644
--- a/doc/news.rst
+++ b/doc/news.rst
@@ -3,6 +3,18 @@
 Release Log
 ===========
 
+NetworkX 2.5
+------------
+Release date: 22 August 2020
+
+Supports Python 3.6, 3.7, and 3.8.
+
+Release notes
+~~~~~~~~~~~~~
+
+See :doc:`release/release_2.5`.
+
+
 NetworkX 2.4
 ------------
 Release date: 16 October 2019
diff --git a/doc/release/release_2.5.rst b/doc/release/release_2.5.rst
new file mode 100644
index 000000000..e89ab49a6
--- /dev/null
+++ b/doc/release/release_2.5.rst
@@ -0,0 +1,493 @@
+Announcement: NetworkX 2.5
+==========================
+
+We're happy to announce the release of NetworkX 2.5!
+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 <http://networkx.github.io/>`_
+and our `gallery of examples
+<https://networkx.github.io/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 coversion 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 <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_betweeness`.
+
+- [`#4161 <https://github.com/networkx/networkx/pull/4161>`_]
+  Rename `_naive_greedy_modularity_communities` as `naive_greedy_modularity_communities`.
+
+Pull requests merged in this release
+------------------------------------
+
+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 defination 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 improvments 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 to this release
+----------------------------
+- 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
diff --git a/doc/release/release_dev.rst b/doc/release/release_dev.rst
index ed08abaa4..2dae5e5fc 100644
--- a/doc/release/release_dev.rst
+++ b/doc/release/release_dev.rst
@@ -1,7 +1,7 @@
-Announcement: NetworkX 2.5
+Announcement: NetworkX 2.6
 ==========================
 
-We're happy to announce the release of NetworkX 2.5!
+We're happy to announce the release of NetworkX 2.6!
 NetworkX is a Python package for the creation, manipulation, and study of the
 structure, dynamics, and functions of complex networks.
 
@@ -14,460 +14,29 @@ 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
+This release is the result of X of work with over X pull requests by
+X contributors. Highlights include:
 
 
 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 coversion 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 <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`.
+Contributors to this release
+----------------------------
 
-- [`#4161 <https://github.com/networkx/networkx/pull/4161>`_]
-  Deprecate `edge_betweeness`.
+<output of contribs.py>
 
-- [`#4161 <https://github.com/networkx/networkx/pull/4161>`_]
-  Rename `_naive_greedy_modularity_communities` as `naive_greedy_modularity_communities`.
 
 Pull requests merged in this release
 ------------------------------------
 
-A total of 233 changes have been committed.
-
-- Designate 2.4 release
-- 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 defination 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)
--  orithms 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 improvments 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)
-
-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 to this release
-----------------------------
-- 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
+<output of contribs.py>
diff --git a/networkx/readwrite/json_graph/cytoscape.py b/networkx/readwrite/json_graph/cytoscape.py
index 1a6f0c06c..5e0e3b3de 100644
--- a/networkx/readwrite/json_graph/cytoscape.py
+++ b/networkx/readwrite/json_graph/cytoscape.py
@@ -98,8 +98,8 @@ def cytoscape_graph(data, attrs=None):
 
     for d in data["elements"]["edges"]:
         edge_data = d["data"].copy()
-        sour = d["data"].pop("source")
-        targ = d["data"].pop("target")
+        sour = d["data"]["source"]
+        targ = d["data"]["target"]
         if multigraph:
             key = d["data"].get("key", 0)
             graph.add_edge(sour, targ, key=key)
diff --git a/networkx/release.py b/networkx/release.py
index 49ac4bcf9..8a591e3e1 100644
--- a/networkx/release.py
+++ b/networkx/release.py
@@ -171,7 +171,7 @@ def get_info(dynamic=True):
 # Version information
 name = "networkx"
 major = "2"
-minor = "5rc2"
+minor = "6rc1"
 
 
 # Declare current release as a development release.


Test patch:
diff --git a/networkx/readwrite/json_graph/tests/test_cytoscape.py b/networkx/readwrite/json_graph/tests/test_cytoscape.py
index ee4799fb6..ba5e0c413 100644
--- a/networkx/readwrite/json_graph/tests/test_cytoscape.py
+++ b/networkx/readwrite/json_graph/tests/test_cytoscape.py
@@ -1,6 +1,7 @@
 import json
 import pytest
 import networkx as nx
+import copy
 from networkx.readwrite.json_graph import cytoscape_data, cytoscape_graph
 
 
@@ -10,6 +11,14 @@ class TestCytoscape:
         H = cytoscape_graph(cytoscape_data(G))
         nx.is_isomorphic(G, H)
 
+    def test_input_data_is_not_modified_when_building_graph(self):
+        G = nx.path_graph(4)
+        input_data = cytoscape_data(G)
+        orig_data = copy.deepcopy(input_data)
+        # Ensure input is unmodified by cytoscape_graph (gh-4173)
+        cytoscape_graph(input_data)
+        assert input_data == orig_data
+
     def test_graph_attributes(self):
         G = nx.path_graph(4)
         G.add_node(1, color="red")