Path Complex

[quang-truong]

This pull request contains source code to implement the Path Complex based on simple paths, which is inspired from the original Path Complex.

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +1.70% 🎉

Comparison is base (7f4235a) 87.89% compared to head (ef27662) 89.59%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #238      +/-   ##
==========================================
+ Coverage   87.89%   89.59%   +1.70%     
==========================================
  Files          26       28       +2     
  Lines        2858     3326     +468     
==========================================
+ Hits         2512     2980     +468     
  Misses        346      346              

Files Changed	Coverage Δ
toponetx/algorithms/spectrum.py	100.00% <100.00%> (ø)
toponetx/classes/__init__.py	100.00% <100.00%> (ø)
toponetx/classes/path.py	100.00% <100.00%> (ø)
toponetx/classes/path_complex.py	100.00% <100.00%> (ø)
toponetx/classes/reportviews.py	83.93% <100.00%> (+1.70%)	⬆️

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[mhajij]

Please add the following methods :

(1) to_other_complex()

where other_complex is any more general of path complex. e.g colored HG and combinatorial complex.

(2) restrict_to_nodes

(3) restrict to paths

(4) set attrs and get attrs (similar to

TopoNetX/toponetx/classes/cell_complex.py

Line 957 in da155df

def get_edge_attributes(self, name: str) -> dict[tuple, Any]:

)

(5) add hodge_laplacian_spectrum methods in the file :

https://github.com/pyt-team/TopoNetX/blob/main/toponetx/algorithms/spectrum.py

(6) add tutorial on path complex demonstrating the main methods.

[mhajij]

@quang-truong Finally for adj/incidence/laplacian matrices please add weight parameter to make the signature consistent across the package #242. Also please do not forget to cite the paper https://arxiv.org/pdf/1207.2834.pdf along your paper in the documentation for PathComplex.

[quang-truong]

Please add the following methods :

(1) to_other_complex()

where other_complex is any more general of path complex. e.g colored HG and combinatorial complex.

(2) restrict_to_nodes

(3) restrict to paths

(4) set attrs and get attrs (similar to

TopoNetX/toponetx/classes/cell_complex.py

Line 957 in da155df

def get_edge_attributes(self, name: str) -> dict[tuple, Any]:

)
(5) add hodge_laplacian_spectrum methods in the file :

https://github.com/pyt-team/TopoNetX/blob/main/toponetx/algorithms/spectrum.py

(6) add tutorial on path complex demonstrating the main methods.

Regarding (1), the current implementation of CombinatorialComplex prevents me from generalizing PathComplex, because paths take into account order sequence, while CombinatorialComplex converts all inputs to frozenset.

Besides that, all of the above methods are implemented. I am working on (6), which will take a while.

[mhajij]

@ffl096 can you please take a look at this one when you get a chance, give your comments ? Thanks!

[mhajij]

@ninamiolane @michaelschaub any high level comments?

[ffl096]

Some things I didn't notice before, sorry! Other than that, this pull request looks good to me :)

[mhajij]

@quang-truong we are aiming to publish the package soon and the publisher requires almost 100% code coverage, can you try to increase the code coverage of path complex to its maximal ? thank you

[quang-truong]

@quang-truong we are aiming to publish the package soon and the publisher requires almost 100% code coverage, can you try to increase the code coverage of path complex to its maximal ? thank you

@mhajij I just add more test cases to cover all possible if statements and errors.

[ninamiolane]

Excellent, thank you very much for this contribution!