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* Add graph_str
Formatted
Fix bug in choosing the source
Fix test
* Fixed issue in choosing source verticies for directed graphs
* reasonable working state
* Fixed logic issues
Fix test, cleanup, formatting
more tests, better comments, fix parent labels
fix pypy issue
Fix format
* Fixes based on review
* Cleaned up test names
* Use open_file decor and remove graph_str
* Remove useage of forest_str from doctest
* Fix style
* style
* Update networkx/readwrite/text.py
Co-authored-by: Dan Schult <dschult@colgate.edu>
* Fixed half sentense
* Add max_depth
* moved comment position
* Describe max depth in algo description
* Allow with_labels to be specified as a str
* Update networkx/readwrite/text.py
Co-authored-by: Mridul Seth <mail@mriduls.com>
* Add network text autodoc stub
* Add removal note for forest_str
---------
Co-authored-by: Dan Schult <dschult@colgate.edu>
Co-authored-by: Mridul Seth <mail@mriduls.com>
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* Remove gdal dependency
* [skip ci] Rm mention of gdal from roadmap.
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
Co-authored-by: Mridul Seth <seth.mridul@gmail.com>
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Co-authored-by: dtuncturk <dilaramemis@sabanciuniv.edu>
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* Step 1: use sparse arrays in nx.to_scipy_sparse_matrix.
Seems like a reasonable place to start.
nx.to_scipy_sparse_matrix is one of the primary interfaces to
scipy.sparse from within NetworkX.
* 1: Use np.outer instead of mult col/row vectors
Fix two instances in modularitymatrix where a new 2D array was being
created via an outer product of two \"vectors\".
In the matrix case, this was a row vector \* a column vector. In the
array case this can be disambiguated by being explicit with np.outer.
* Update _transition_matrix in laplacianmatrix module
- A few instances of matrix multiplication operator
- Add np.newaxis + transpose to get shape right for broadcasting
- Explicitly convert e.g. sp.sparse.spdiags to a csr_array.
* Update directed_combinitorial_laplacian w/ sparse array.
- Wrap spdiags in csr_array and update matmul operators.
* Rm matrix-specific code from lgc and hmn modules
- Replace .A call with appropriate array semantics
- wrap sparse.diags in csr_array.
* Change hits to use sparse array semantics.
- Replace * with @
- Remove superfluous calls to flatten.
* Update sparse matrix usage in layout module.
- Simplify lil.getrowview call
- Wrap spdiags in csr_array.
* lil_matrix -> lil_array in graphmatrix.py.
* WIP: Start working on algebraic connectivity module.
* Incorporate auth mat varname feedback.
* Revert 1D slice and comment for 1D sparse future.
* Add TODOs: rm csr_array wrapper around spdiags etc.
* WIP: cleanup algebraicconn: tracemin_fiedler.
* Typo.
* Finish reviewing algebraicconnectivity.
* Convert bethe_hessian matrix to use sparse arrays.
* WIP: update laplacian.
Update undirected laplacian functions.
* WIP: laplacian - add comment about _transition_matrix return types.
* Finish laplacianmatrix review.
* Update attrmatrix.
* Switch to official laplacian function.
* Update pagerank to use sparse array.
* Switch bipartite matrix to sparse arrays.
* Check from_scipy_sparse_matrix works with arrays.
Modifies test suite.
* Apply changes from review.
* Fix failing docstring tests.
* Fix missing axis for in-place multiplication.
* Use scipy==1.8rc2
* Use matrix multiplication
* Fix PyPy CI
* [MRG] Create plot_subgraphs.py example (#5165)
* Create plot_subgraphs.py
https://github.com/networkx/networkx/issues/4220
* Update plot_subgraphs.py
black
* Update plot_subgraphs.py
lint plus font_size
* Update plot_subgraphs.py
added more plots
* Update plot_subgraphs.py
removed plots from the unit test and added comments
* Update plot_subgraphs.py
lint
* Update plot_subgraphs.py
typos fixed
* Update plot_subgraphs.py
added nodes to the plot of the edges removed that was commented out for whatever reason
* Update plot_subgraphs.py
revert the latest commit - the line was commented out for a reason - it's broken
* Update plot_subgraphs.py
fixed node color issue
* Update plot_subgraphs.py
format fix
* Update plot_subgraphs.py
forgot to draw the nodes... now fixed
* Fix sphinx warnings about heading length.
* Update examples/algorithms/plot_subgraphs.py
* Update examples/algorithms/plot_subgraphs.py
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
Co-authored-by: Dan Schult <dschult@colgate.edu>
* Add traveling salesman problem to example gallery (#4874)
Adds an example of the using Christofides to solve the TSP problem to the example galery.
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Fixed inconsistent documentation for nbunch parameter in DiGraph.edges() (#5037)
* Fixed inconsistent documentation for nbunch parameter in DiGraph.edges()
* Resolved Requested Changes
* Revert changes to degree docstrings.
* Update comments in example.
* Apply wording to edges method in all graph classes.
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
* Compatibility updates from testing with numpy/scipy/pytest rc's (#5226)
* Rm deprecated scipy subpkg access.
* Use recwarn fixture in place of deprecated pytest pattern.
* Rm unnecessary try/except from tests.
* Replace internal `close` fn with `math.isclose`. (#5224)
* Replace internal close fn with math.isclose.
* Fix lines in docstring examples.
* Fix Python 3.10 deprecation warning w/ int div. (#5231)
* Touchups and suggestions for subgraph gallery example (#5225)
* Simplify construction of G with edges rm'd
* Rm unused graph attribute.
* Shorten categorization by node type.
* Simplify node coloring.
* Simplify isomorphism check.
* Rm unit test.
* Rm redundant plotting of each subgraph.
* Use new package name (#5234)
* Allowing None edges in weight function of bidirectional Dijkstra (#5232)
* added following feature also to bidirectional dijkstra: The weight function can be used to hide edges by returning None.
* changed syntax for better readability and code duplicate avoidance
Co-authored-by: Hohmann, Nikolas <nikolas.hohmann@tu-darmstadt.de>
* Add an FAQ about assigning issues. (#5182)
* Add FAQ about assigning issues.
* Add note about linking issues from new PRs.
* Update dev deps (#5243)
* Update minor doc issues with tex notation (#5244)
* Add FutureWarnings to fns that return sparse matrices
- biadjacency_matrix.
- bethe_hessian_matrix.
- incidence_matrix.
- laplacian functions.
- modularity_matrix functions.
- adjacency_matrix.
* Add to_scipy_sparse_array and use it everywhere.
Add a new conversion function to preserve array semantics internally
while not altering behavior for users.
Also adds FutureWarning to to_scipy_sparse_matrix.
* Add from_scipy_sparse_array. Supercedes from_scipy_sparse_matrix.
* Handle deprecations in separate PR.
* Fix docstring examples.
Co-authored-by: Mridul Seth <mail@mriduls.com>
Co-authored-by: Jarrod Millman <jarrod.millman@gmail.com>
Co-authored-by: Andrew Knyazev <andrew.knyazev@ucdenver.edu>
Co-authored-by: Dan Schult <dschult@colgate.edu>
Co-authored-by: eskountis <56514439+eskountis@users.noreply.github.com>
Co-authored-by: Anutosh Bhat <87052487+anutosh491@users.noreply.github.com>
Co-authored-by: NikHoh <nikhoh@web.de>
Co-authored-by: Hohmann, Nikolas <nikolas.hohmann@tu-darmstadt.de>
Co-authored-by: Sultan Orazbayev <contact@econpoint.com>
Co-authored-by: Mridul Seth <mail@mriduls.com>
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* Add matrix_market reference stub.
* Add R/W examples to matrix_market stub.
* Add matrix market to toctree.
* Remove irrelevant factoid.
* Re-name according to review suggestion.
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* WIP: adding getattr to nx_yaml module.
* WIP: Tests that informative exceptions raised.
* Add tests for informative messages.
* Add getattrs to higher-up pkgs.
* Remove test_yaml.py
* Remove pyyaml from requirements.
* Update examples in warning messages.
Ensure they are correct, runnable examples.
* Add security warning and removal time to message.
* Cp __getattr__ to other mods/pkgs.
* Update deprecation notes w/ getattrs.
* Remove yaml section from docs.
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* Update docs with all functions not added to rst files
Also add script to find these functions
* put back removed periods after references
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* Finish directory reorg and make minor text edits
* Remove cruft from conf.py
* Fix broken links and comply with pep8
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