adding tree broadcast algorithm #2

Transurgeon · 2023-09-08T13:19:30Z

This PR adds the algorithm detailed on page 3 of the paper titled: "Information Dissemination In Trees".
It also adds a test-case for the example on page 4.
The next steps would be to return the broadcast centre (perhaps as another separate API function) and also improve the unit-tests suite.

* Add Kirchhoff index Add the computation of the Kirchhoff index to networkx * minor fixes * scipy not necessary * scipy not necessary * style fixes * small doc change * change digraph, add test * vectorise final computation * style fix * minor cleanup tests * Add Kirchhoff index Add the computation of the Kirchhoff index to networkx * minor fixes * scipy not necessary * scipy not necessary * style fixes * small doc change * change digraph, add test * vectorise final computation * style fix * minor cleanup tests * fix * change name * remove return var

…etworkx#6584) * Fixed return types and modified tests * Resolved check failures in centrality\reaching.py * Fixed doc_str examples * Minor edit

Co-authored-by: Mridul Seth <[email protected]> Co-authored-by: Ross Barnowski <[email protected]>

…tead) (networkx#7157) Backends should have had enough time to update by now.

* DOC: consistent spelling of neighbor and rename vars * rename more vars

* use ruff format instead of black * Rm pylint comment guards. --------- Co-authored-by: Ross Barnowski <[email protected]>

* updated See also sec of argmap class * Update decorators.py

* Modify GML test to fix invalid octal character warning. * Switch to unicode char. * Rm extra unicode string indicators.

…le to users (networkx#7161) * Update shortest_path warning. * Update single_target_shortest_path_length futurewarning. * Update warnings filters in conftest. * Update developer docs.

Improve consistency of property-checking functions (i.e. is_something) for empty graph inputs. Tend towards NetworkXPointlessConcept exceptions for consistency. Co-authored-by: Ross Barnowski <[email protected]>

… and ignored isolated nodes in `panther_similarity` (networkx#7110) * ignoring isolated nodes in panther_similarity * added NodeNotFound in simrank_similarity * added NodeNotFound in _apply_prediction * bug fix * added Raises sec to all funcs and updated error msg * added Raises sec to simrank_similarity * added tests to test_similarity.py and updated simrank_similarity docs * updated link_prediction.py * updated and added tests in test_link_prediction.py * bug : updated NodeNotFound tests of simrank_similarity * bug : updated test_simrank_target_not_found and style fixes * added NetworkXUnfeasible to panther_similarity * bug fix * added NodeNotFound for panther_similarity * style fix * list() -> set()

…ilar functions. (networkx#7171) * Fixes networkx#7147 * Word documentation change properly based on PR review Co-authored-by: Ross Barnowski <[email protected]> * Update walk_type documentation in laplacian_centrality function * Update walk_type documentation in _transition_matrix and directed_combinatorial_laplacian matrix functions --------- Co-authored-by: Ross Barnowski <[email protected]>

* DOC: Add plots to classic graph generators docs * Update conf.py * make pre-commit happy

networkx#7182) * Add tests for NotImplementedError for is_regular. * Fix NetworkXNotImplemented for is_regular and related fns. * Handle similar instances in maxcut. * Handle similar case for asyn_fluid. * Handle similar case for tree_isomorphism.

… where no d-separators exist (networkx#7019) * add check that minimal d-separating set is valid sepset * make api change note * add edge case where proposed sepset is not empty but does not separate * fix typo in test * improve efficiency of d_sep check * finish fixing failing unit tests * remove xml * use existing ancestors function * check non disjoint node sets raise error * enforce disjoint node sets for d-separation * add test for nondisjoint sets raising error * fix test errors. allow `i` and `r` to be nodes instead of sets. * add keyword-only indicators * rename u -> x and v -> y; fix docs quotations * rename i -> included and r -> restricted * docstrings * allow `included`, `restricted` to be nodes * fix raise error for nondisjoint sets * added nondisjoint test for `minimal_d_separated` * added test of `included` and `restricted` * add test of `included` and `restricted`; found bug * rebase on main * update func sigs according to dschult's suggestion * updated docs with new func sig; ref new algorithm * update `find_min...` to new alg; outline 2 helper funcs * Designate 3.2 release * implemented reachable; tests pass * typo * updated `find_minimal_d_separator` docs * finish implement new alg for `is/find_min_d_sep..` * reworking and adding to docs for d-separation * remove release note * cleanup extra files * updated input checking and doc_strings * deprecate d_separated and minimal_d_separator * change stacklevel of deprecations --------- Co-authored-by: Jaron Lee <[email protected]> Co-authored-by: Alex Markham <[email protected]> Co-authored-by: Alex Markham <[email protected]>

* Fix for complete graphs case in all_node_cuts * Check node_connectivty in complete graph * test for broken cuts. add fix --------- Co-authored-by: Dan Schult <[email protected]>

…etworkx#7198) Update structuralholes.py Fix a tiny typo in local_constraint docstring.

…docs (networkx#7197) issue7170

* Fix online docs for `_dispatch` * whatcha talkin bout mypy?

…networkx#7192) Use `"networkx.backends"` and `"networkx.backend_info"` instead. Version 3.2 supported both options. The next release can drop "plugin".

* DOC : Updated panther_similarity * style fix * removed eg * Update similarity.py

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Rm deprecated_call filter from strongly connected raises test. * Replace deprecated pytest.warns(None) with catch_warnings.

…etworkx#7204) * Un-xfail pydot tests. * Pin pydot minver to 2.0. * Rm deprecation bullet from devdocs. * Back out deprecation warnings for nx_pydot. --------- Co-authored-by: Jarrod Millman <[email protected]>

* Fix intermittent doctest failures for expanders with seeding. * Rm deprecated asftype. * Fix warnings filter for join. * Prepare for pandas copy-on-write.

…nce (networkx#7328) * Rm 3d animation from spectral clustering example. * Add xref to 3D examples to illustrate how to animate 3D viz. * Vastly improves (>100x) example runtime. * Add sphinx-gallery config to allow xrefs.

networkx#7335) fix linprog method, add new test result

Co-authored-by: Dan Schult <[email protected]>

peijenburg and others added 30 commits December 9, 2023 17:49

DOC: fix URL econded links and doc references (networkx#7152)

d85f3a4

Changed return types of shortest path methods to improve consistency (n…

dd6d68e

…etworkx#6584) * Fixed return types and modified tests * Resolved check failures in centrality\reaching.py * Fixed doc_str examples * Minor edit

adding test coverage for isomorphism when using digraphs (networkx#6417)

7abde00

Co-authored-by: Mridul Seth <[email protected]> Co-authored-by: Ross Barnowski <[email protected]>

Remove usage of __networkx_plugin__ (use __networkx_backend__ ins…

1dade0d

…tead) (networkx#7157) Backends should have had enough time to update by now.

DOC: consistent spelling of neighbor and rename vars (networkx#7162)

1c2fa4b

* DOC: consistent spelling of neighbor and rename vars * rename more vars

DOC: add reference to fast_label_propagation_communities (networkx#7167)

c0f5918

MAINT: use ruff format instead of black (networkx#7160)

6ad7842

* use ruff format instead of black * Rm pylint comment guards. --------- Co-authored-by: Ross Barnowski <[email protected]>

updated See also sec of argmap class (networkx#7163)

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* updated See also sec of argmap class * Update decorators.py

Modify GML test to fix invalid octal character warning. (networkx#7159)

f34dda2

* Modify GML test to fix invalid octal character warning. * Switch to unicode char. * Rm extra unicode string indicators.

DOC : updated examples in mincost.py (networkx#7169)

483ea9a

Ensure warnings related to changes in shortest_path returns are visib…

d68caf6

…le to users (networkx#7161) * Update shortest_path warning. * Update single_target_shortest_path_length futurewarning. * Update warnings filters in conftest. * Update developer docs.

Sync up behavior of is_{type} for empty graphs (networkx#5849)

92afda9

Improve consistency of property-checking functions (i.e. is_something) for empty graph inputs. Tend towards NetworkXPointlessConcept exceptions for consistency. Co-authored-by: Ross Barnowski <[email protected]>

DOC: Add plots to classic graph generators docs (networkx#7114)

d042db5

* DOC: Add plots to classic graph generators docs * Update conf.py * make pre-commit happy

Fix all_node_cuts output for complete graphs (networkx#6558)

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* Fix for complete graphs case in all_node_cuts * Check node_connectivty in complete graph * test for broken cuts. add fix --------- Co-authored-by: Dan Schult <[email protected]>

Fix a tiny typo in structuralholes.py::local_constraint docstring (n…

0762b7f

…etworkx#7198) Update structuralholes.py Fix a tiny typo in local_constraint docstring.

Added subgraph_is_monomorphic and subgraph_monomorphisms_iter in …

6109e10

…docs (networkx#7197) issue7170

Fix online docs for _dispatch (networkx#7194)

e755ea7

* Fix online docs for `_dispatch` * whatcha talkin bout mypy?

Remove "networkx.plugins" and "networkx.plugin_info" entry-points (…

3a98973

…networkx#7192) Use `"networkx.backends"` and `"networkx.backend_info"` instead. Version 3.2 supported both options. The next release can drop "plugin".

DOC : Updated docs for panther_similarity (networkx#7175)

ad92646

* DOC : Updated panther_similarity * style fix * removed eg * Update similarity.py

Fix warnings when building docs (networkx#7195)

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Update test suite for Pytest v8 (networkx#7203)

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* Rm deprecated_call filter from strongly connected raises test. * Replace deprecated pytest.warns(None) with catch_warnings.

Undeprecate nx_pydot now that pydot is actively maintained again (n…

5d2f19b

…etworkx#7204) * Un-xfail pydot tests. * Pin pydot minver to 2.0. * Rm deprecation bullet from devdocs. * Back out deprecation warnings for nx_pydot. --------- Co-authored-by: Jarrod Millman <[email protected]>

Future-proofing and improve tests (networkx#7209)

f573004

* Fix intermittent doctest failures for expanders with seeding. * Rm deprecated asftype. * Fix warnings filter for join. * Prepare for pandas copy-on-write.

Drop old dependencies per SPEC 0 (networkx#7217)

f52696e

rossbar and others added 2 commits March 6, 2024 11:37

Add new test result to test_asadpour_tsp and change linprog method (

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networkx#7335) fix linprog method, add new test result

rossbar force-pushed the adding-broadcasting branch from b0379a2 to 3b59ba5 Compare March 7, 2024 06:47

Transurgeon and others added 27 commits March 6, 2024 22:48

adding tree broadcast algorithm

e31af67

adding steps and more tests

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adding citation and assertion

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applying first set of suggestions

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updating docstrings for tree broadcast

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Apply suggestions from code review

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Co-authored-by: Dan Schult <[email protected]>

removing self-loop check

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cleaning update to avoid dict instance

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adding test case for star graph

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updating docstrings for constraints

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applying some theoretical changes

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adding broadcast center implementation and tests

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completing tree broadcast algorithm and tests

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adding first set of changes round 2

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adding optimization for broadcast time of the tree

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copying code to new location

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Update networkx/algorithms/approximation/broadcasting.py

f4cdc9e

Co-authored-by: Dan Schult <[email protected]>

Update networkx/algorithms/approximation/broadcasting.py

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Co-authored-by: Dan Schult <[email protected]>

changing all instances of vertices to nodes

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fixing up some formatting issues

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removing two previous files from implementation

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adding broadcsting to index reference file

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Update networkx/algorithms/broadcasting.py

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Co-authored-by: Dan Schult <[email protected]>

Update networkx/algorithms/broadcasting.py

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Co-authored-by: Dan Schult <[email protected]>

Update networkx/algorithms/broadcasting.py

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Co-authored-by: Dan Schult <[email protected]>

Update networkx/algorithms/broadcasting.py

c349423

Minor touchups.

3b59ba5

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