Use scipy.sparse array datastructure (#5139)

* 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>

2 files changed, 2 insertions, 1 deletions

diff --git a/doc/reference/convert.rst b/doc/reference/convert.rst
index bc21a8cc..64812d92 100644
--- a/doc/reference/convert.rst
+++ b/doc/reference/convert.rst
@@ -48,6 +48,7 @@ Scipy
 .. autosummary::
    :toctree: generated/
 
+   to_scipy_sparse_array
    to_scipy_sparse_matrix
    from_scipy_sparse_matrix
 
diff --git a/doc/reference/readwrite/matrix_market.rst b/doc/reference/readwrite/matrix_market.rst
index d3450699..37173830 100644
--- a/doc/reference/readwrite/matrix_market.rst
+++ b/doc/reference/readwrite/matrix_market.rst
@@ -72,7 +72,7 @@ sparse matrices::
     >>> fh = io.BytesIO()
 
     >>> G = nx.path_graph(5)
-    >>> m = nx.to_scipy_sparse_matrix(G)
+    >>> m = nx.to_scipy_sparse_array(G)
     >>> print(m)
       (0, 1)        1
       (1, 0)        1