| Commit message (Collapse) | Author | Age | Files | Lines |
|---|
| | |
|
| |
|
|
|
| |
* Improve test coverage for Kruskal & Prim
* Bug fix in prim_mst_edges()
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* lint and fix using ruff
* add flake8-pie lints
* remove useless import alias
* bump version
* bump deps
---------
Co-authored-by: daniel.eades <daniel.eades@hotmail.com>
|
| |
|
|
|
| |
* Fix_Typos
* Commit_Suggestions
|
| |
|
|
|
| |
* Add isort to pre-commit
* Run isort on all python files (except __init__.py ones)
|
| |
|
|
|
|
|
|
|
|
|
|
| |
Adds two new functions random_spanning_tree and
total_spanning_tree_weight to public networkx API, accessible
from the main namespace.
These functions had previously been defined, tested, and used internally
in the TSP package, but have now been added to the public API as they
are generally applicable.
Co-authored-by: Dan Schult <dschult@colgate.edu>
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
|
| |
|
| |
Co-authored-by: Dylan <dylan@200-18-80-eduroam-al.wlan.net.uc.cl>
|
| |
|
|
| |
A more descriptive variable name for exceptions. This reduces local var naming conflicts when
\`e\` is used e.g. to represent edges as a loop variable.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* Add greedy algorithm for solving TSP
Many problems of Combinational Optimization can be represented as
graphs.
These problems have enormous significance in many aspects of science,
but there are not any algorithms to solve some of them in polynomial
time.
However many, heuristic and metaheuristic algorithms have been published
over the past years in order to solve / approximate the solutions to
these problems.
The purpose of this commit is to add implementation of such algorithms
for solve one of the most famous problems of Combinational
Optimizations, Travelling Salesman Problem (TSP). A greedy algorithm has
been implemented at the moment for this reason.
"applications" package has been created which include modules that
represent a problem.
Each module contains several algorithms for solving the specific
problem.
At this commit, tsp.py module is added which contains greedy_tsp()
function; a implementation of a greedy algorithm.
* Fix example error
* Trivial changes
List of changes:
Removal of unnesecary _is_weighted() function
Improvements on documentation
* Add applications package to setup.py file
* Change output of greedy algorithm
Algorithm's output is a list of nodes now
* Add simulated annealing algorithm
Add a metaheuristic local search algorithm for solving TSP
* Minor changes
* Fix example doc errors
* Compatible with python 3
* Move tsp module to algorithms package
* Code improvements
* Handle small graphs and fix doc examples
* Documentation changes and rename variables
* Adds Threshold Accepting algorithm for TSP
* Implemented maximal matching of minimal weight and created test suite.
* Removed useless print
* Implemented Christofides.
* Coding was missing
* Add more general traveling_salesman_problem using christofides
Also reconfigure import structure and remove min_weight_matching from
module since it is now in matching.py
* Add new functions to the docs and minor typos
* pep8 fixes
* fix pep8 and change .gitignore
* Add tests of the approximation namespace
update docs in approximation/__init__.py
* Fix is_matching to check if edges in G. Other tweaks:
doc changes
and put not_implemented_for on find_matching functions
* Improve is_matching selfloop handling and expand tests
* Move tsp to approximation directory. Apply black.
* Move tsp tests to approximation tests folder
* Attempt to bring tsp up to current code.
* commit pep8 that my black didnt change, but pep8speaks did find. ??
* tweak a few things and run black
* combine #4083 and #3585 into traveling_salesman.py
* Match chistofides output to other tsp functions
and adjust calling syntax of tests
tweak docs
tweak see also section
* Put big-O complexity in in-line math env.
Prevents sphinx from trying to do variable substitution between
pipes.
* Minor touchups to christofides docstring.
* RST touchups to tsp module docstring.
* Rm extra string from tsp module.
* Docstring touchups for traveling_salesman_problem.
* rst fixups for greedy_tsp docstring.
* rst formatting for simulated annealing docstring.
* More math in-lining for simulated annealing docstring.
* rst and minor grammatical fixes to TA docstring.
* Fix path-finding and test all methods for tsp function
* the refactoring was incomplete. Now maybe is
- Add tests of TSP with all methods.
- Refactor tests to match simulated_annealing tests and threshold tests.
- Unify treatment of weight so unweighted edges use default weight 1.
weight now defaults to "weight" with a default value of 1.
- Rename tolerance to max_iterations (tolerance is used for error bound)
- Rename iterations to N_inner (each iteration takes this many inner loops)
- Introduce idioms like `pairwise` and `cycle.copy()` (over cycle[:])
- Allow passthrough of method kwargs for traveling_salesman_problem
Still need to:
- add test of case where path is more than one edge less that cycle
(incomplete_graph)
- require cycle input (maybe make default list(G)??)
- consider the complexity claims in the doc_strings
* More api changes to TSP functions
- `chritofides` now allows (and ignores) selfloops
- `move` can be a function as well as "1-1" and "1-0"
- `method` for traveling_salesman_problem must have 2 arguments
instead of passing kwargs. User must "curry" to set parameters
- changed doc_string typos in matching.py
* Add test to check that cycle=False can remove many edges
* Change init_cycle api to require input from user
The idea is to make the user specify the initial cycle to start from
rather than relying on the programmers default of a greedy algorithm.
To easy usage, I check for a string "greedy" as a shortcut.
* Update docs with more correct complexity info.
* Check for complete graph now more efficient and selfloops ignored
* merge is_matching changes
* Stub for Asadpour. Needed to create GSoC PR
* Update to integrate changes from main
* Added function stubs and draft docstrings for the Asadpour algorithm
* testing
* I'm not entirly sure how the commit hook works...
* Moved iterators into the correct files to maintain proper codebase visibility
* Including Black reformat
* Grabbing black reformats
* Working on debugging ascent method plus black reformats
* Ascent method terminating, but at non-optimal solution
* minor edits
* Fixed termination condition, still given non-optimal result
* Minor bugfix, still non-optimal result
* Fixed subtle bug in find_epsilon()
* Cleaned code and tried something which didn't work
* Modified the ArborescenceIterator to accept init partition
* Black formats
* Branch and bound returning optimal solution
* Working Ascent method, code needs cleaning
* black formatting changes
* Performance tweaks and testing fractional answers
* Fixed test bug, I hope
* Asadpour output for ascent method
* Fixed numpy imports crashing pypi tests
* Removed branch and bound method. One unit test misbehaving
* Added asymmetric fractional test for the ascent method
* Removed printn statements and tweaked final test to be more asymmetric
* Draft of spanning_tree_distribution
* Black changes
* Changed HK to only report on the support of the answer
* Fixed contraction bug by changing to MultiGraph. Problem with prob > 1
* Black reformats
* Fixed pypi test error
* Further testing of dist fix
* Can sample spanning trees
* Developing test for sampling spanning tree
* Changed sample_spanning_tree test to Chi squared test
* Tweaked signifiance level
* Found true minimum sample size
* fixed typo
* untested implementation of asadpour_tsp
* Fixed issue reading flow_dict
* Fixed runtime errors in asadpour_tsp
* black reformats
* Adding test cases
* documentation update
* Fixed rounding error with tests
* One new test and check
* Documentation update for the iterators
* Attempting to fix class documentation
* Reventing documentation changes
* Update mst.py to accept suggestion
Co-authored-by: Dan Schult <dschult@colgate.edu>
* Update branchings.py accept doc string edit
Co-authored-by: Dan Schult <dschult@colgate.edu>
* Review suggestions from dshult
* Cleaned code, merged functions if possible and opened partition functionality to all
* Fixed pypi test error
* Implemented review suggestions from rossbar
* review edits
added SpanningTreeIterator to algorithms/__init__.py
* Update __init__.py
ack, hasty / stupid change was meant to be a draft; github isn't letting me make a new branch to PR into this one
* fixed misspelling of Kirchhoff
* Implement suggestions from boothby
Co-authored-by: Thodoris Sotiropoulos <theosotr@windowslive.com>
Co-authored-by: Luca Cappelletti <cappelletti.luca94@gmail.com>
Co-authored-by: Dan Schult <dschult@colgate.edu>
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
Co-authored-by: Kelly Boothby <kelly.r.boothby@gmail.com>
Co-authored-by: Kelly Boothby <boothby@dwavesys.com>
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* Format code w/ black
* Format docstrings w/ black
* Manual cleanup
* Tell pytest to ignore planned deprecations
* Don't call plt.show during testing
* Another known deprecation
* DOC: rm duplicate line from docstring example
* Minor cleanup
Co-authored-by: Ross Barnowski <rossbar@berkeley.edu>
|
| | |
|
| | |
|
| |
|
|
|
|
|
|
|
| |
find -name "*py" | xargs grep -n '" % '
find -name "*py" | xargs grep -n '"\.format('
find -name "*py" | xargs grep -n "' %"
find -name "*py" | xargs grep -n 'msg % '
find -name "*py" | xargs grep -n ' %d '
find -name "*py" | xargs grep -n '\.format('
|
| |
|
|
| |
find networkx -name \*.py -exec pyupgrade --py36-plus {} \;
|
| |
|
|
|
|
|
|
|
| |
The copyright and author stuff is not necessary, out-of-date,
and inconsistent. It takes up visual space and is a pain to
police everyone doing the same thing on the top of the module.
Git handles authorship in a comprehensive and authoritative way.
The LICENSE.txt file applies to all project code.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
| |
* prim list to set data structure
* shorten set creation
* add sorting on examples in doc_strings to make it work with pypy
* change parens to square brackets for sorted output of example code
* Fix bug and add tests for order dependence on NaN checking in Prim
* pycodestyle fixup of my test additions.
|
| |
|
| |
Fixes small typos in the max. spanning tree docstring.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
* Simplify the Graphview and SubGraphView system
- add tests to show that extensions of base graph classes (only add new functions)
should be able to use the Graph.subgraph and Graph.copy methods easily
- Remove ReadOnlyGraph class in favor of existing freeze() function
- Switch all GraphView classes to generic_graph_view function
- Switch all SubGraph classes to subgraph_view function
- Introduce deprecated functions that act like the deprecated classes.
Still need to:
- add docs
- add tests
- make sure backward compatible and marked as deprecated
- remove GraphView and SubGraph construct from rest of codebase
- update release docs
Fixes #2889
Fixes #2793
Fixes #2796
Fixes #2741
* Ease subclassing for to_(un)directed
- add to_directed_class indicator functions to base classes
- start deprecating G.fresh_copy
- update function.to(un)directed
* Remove G.fresh_copy from code replace with __class__
Add deprecation warnings for GraphView classes, ReverseView and
SubGraph. Also for fresh_copy function.
|
| | |
|
| |
|
|
| |
isolated nodes with self-loops included in tree as isolated nodes.
Fixes #2667
|
| |
|
|
|
| |
Fixes #2648
Noticed hidden errors with G.name in operators.py
|
| |
|
|
|
|
|
|
|
|
| |
* move selfloop methods out of graph classes into function.py
* replace G.node with G.nodes. fix Pickle of views
* Replace G.edge with G.edges
* Add a few lines of docs for release realted to this PR.
|
| |
|
| |
Fixes #2164
|
| |
|
|
|
| |
The default argument could apply to either weight or data
so its confusing when there are two references. Looked at
two new default arguments and decided it wasn't an improvement.
|
| |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| |
(#2475)
* Dont assume iterators for nodes/edges/degrees (prep for views)
* Add graph view classes for nodes/edges/degree
* Add right set operations (not present in python3.3 KeysView
* Add nodes before adding edges so python36 tests work
By only adding edges, the nodes were added in order (0,1,3,2)
and with the ordered nature of python3.6 dicts the tests failed.
Could also fix by using nodelist on each call to to_convert_...
* weighted graph convert tests testing empty graphs
The edge iterator was exhausted for source before being used for dest
* allow DegreeView to include case of nbunch
* Make node/edge/degree properties of Graph
* View contains fix and Viewers can return self. More tests
* Add more tests including one for #2347
* Add nbunch tests and pep8
* Rename to EdgeView and EdgeDataView
* docs tweaks and pep8
* fix up nodeDataView contains. Add and clean up tests.
* Change the graph attributes to read-only properties
* Reframe views code and extend _node to all networkx (still need
examples)
* Clean up and pep8 for view changes
* ername AtlasViews, simplify code and add docstrings
* Make G[u] return a view, and catch some doc bugs
* Update views to use _node,_adj. Add len to EdgeDataView
* minor adjustments to example subclass/printgraph
|
| |
|
|
|
| |
This commit also simplifies the unit tests for the minimum spanning tree
functions while maintaining full test coverage.
|
| |
|
|
|
|
|
|
| |
Change double `` to single ` for all function arguments.
Remove double `` around True, False, None
Leave double `` when a literal python expression is intended.
I found a couple of places where math mode was intended.
Still need to look for those.
|
| |
|
|
|
|
| |
Before, the `minimum_spanning_edges()` function returned edges without
edge keys for multigraphs. This commit enables the user to choose to
return edge keys in addition to edges in a multigraph.
|
| |
|
