feat: direction support on apsp #223

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tristan-f-r wants to merge 11 commits into Reed-CompBio:main from tristan-f-r:apsp-directed

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tristan-f-r commented May 22, 2025 •

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closes #121. This PR also:

updates the Python and networkx version associated to the AllPairsShortestPaths algorithm.
Uses Path unsparingly (should we encourage this throughout the codebase?)

tristan-f-r added 5 commits

May 22, 2025 16:22


          feat: direction support on apsp

0b5830b

don't merge, untested; will test once I figure out where good directed data lays

closes Reed-CompBio#121


          fix: don't void command

877bd91


          style: use append instead of ternary extend

ea53715

???


          fix: have directed argument act as a boolean flag

25309e7


          test: apsp directed

3bf25a2

tristan-f-r marked this pull request as ready for review

May 23, 2025 17:27

ntalluri reviewed

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tristan-f-r added 5 commits

May 27, 2025 08:16


          chore: rm domino-network.txt.pkl

b40a1af

???


          refactor: explicit use of nx.Graph

482bad1

readability fix


          docs: better comment on has_direction

6309dee

hopefully this avoids further confusion


          style: lint

35dbcaa


          style: rm extraneous spaces

e665cdc

tristan-f-r mentioned this pull request

fix: let raw_pathway_df handle present headers but no data #236

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tristan-f-r added the algorithm label


          fix: use correct empty call

d7adf7c

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tristan-f-r commented Jun 11, 2025

Note that the CI fails because the --directed flag is not present inside the published docker container.

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