Code

Adding Directionality#120

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agitter merged 50 commits intoReed-CompBio:masterReed-CompBio/spras:masterfrom ntalluri:directionntalluri/spras:directionCopy head branch name to clipboardDec 3, 2023

+162,957-162,458

Commits

Commits on Aug 23, 2023

• documented research per algorithm as docstrings per class for the algorithms in master

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  af6a590

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Commits on Aug 29, 2023

• added directionality for generate inputs

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Commits on Aug 30, 2023

• Merge branch 'master' of github.com:ntalluri/spras into direction

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  a214cc8

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• added in parse_output directionality

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• removed directed from config file, testing with analysis all false

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Commits on Sep 4, 2023

• made updates to code and attempted to add testing for interactome

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Commits on Sep 5, 2023

• precommit formatting

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  319a5d3

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• cleaned up code and finished interactome test

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  bb55ee0

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• updated util to deal with the idea if someone is using an old config file

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• current ml repairs

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Commits on Sep 6, 2023

• ml post processing pre-commit and config file

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Commits on Sep 12, 2023

• fixed testing

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Commits on Sep 18, 2023

• Merge branch 'master' into direction

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• updated summary.py/associated files and tests. updated interactome.py

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  9e29ceb

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• Merge branch 'direction' of github.com:ntalluri/spras into direction

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• pre-commit

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Commits on Sep 19, 2023

• added generate inputs test, cleaned up code

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Commits on Sep 22, 2023

• Resolve merge conflicts

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• Update EGFR network with edge directions

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Commits on Sep 26, 2023

• added back graphspace to work for directed and undirected graphs only

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• precommit

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Commits on Sep 29, 2023

• automate test_prepare_inputs

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Commits on Oct 4, 2023

• renamed the tests for creating the inputs

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  32be496

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• fix break in test

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  57599f7

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• added parse_output tests and still fixing generate inputs

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  e991e0a

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• precommit

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  dd6c899

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• added more information to step 5 of contributing guide

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  ae276f5

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• add cytoscape into workflow

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Commits on Oct 17, 2023

• cleaning up generate inputs/parse outputs test suites

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  e5be5a0

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• clean up gen inputs and prase outputs

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Commits on Oct 18, 2023

• Merge with master

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  8dd0990

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• Fix ruff errors on GitHub actions

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  d9b0f0b

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Commits on Oct 26, 2023

• made changes based on review

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• made more changes based on review

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  f651376

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Commits on Oct 27, 2023

• fixed error

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Commits on Nov 27, 2023

• some of the comments

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• more comments

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• precommit

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  884fe4f

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• more comments

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  19a4ad4

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Commits on Nov 28, 2023

• more comments resolved

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  99e6e6f

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Commits on Nov 29, 2023

• resolving parse output comments

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• precommit

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Commits on Dec 1, 2023

• add check to dataset.py

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Commits on Dec 3, 2023

• Rename .csv to .txt in test directory

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  7bc9e3e

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• Add tests for invalid 4th edge column

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  d918c00

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• Remove self-edges from EGFR data

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  cd625d4

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• Update Cytoscape wrapper for directed edges

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• Remove directed from EGFR config and run more algs

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• Systematic proofreading and formatting

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  b4d6e1c

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• Bump Cytoscape image version in workflow

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