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Adding Directionality #120

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merged 50 commits into from
Dec 3, 2023
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af6a590
documented research per algorithm as docstrings per class for the alg…
ntalluri Aug 23, 2023
3f173b5
added directionality for generate inputs
ntalluri Aug 29, 2023
a214cc8
Merge branch 'master' of github.com:ntalluri/spras into direction
ntalluri Aug 30, 2023
1e7fef9
added in parse_output directionality
ntalluri Aug 30, 2023
4fdaadb
removed directed from config file, testing with analysis all false
ntalluri Aug 30, 2023
cae057a
made updates to code and attempted to add testing for interactome
ntalluri Sep 4, 2023
319a5d3
precommit formatting
ntalluri Sep 5, 2023
bb55ee0
cleaned up code and finished interactome test
ntalluri Sep 5, 2023
7aed4ee
updated util to deal with the idea if someone is using an old config …
ntalluri Sep 5, 2023
0e15534
current ml repairs
ntalluri Sep 5, 2023
75be8b8
ml post processing pre-commit and config file
ntalluri Sep 6, 2023
550614a
fixed testing
ntalluri Sep 12, 2023
760b1b7
Merge branch 'master' into direction
ntalluri Sep 18, 2023
9e29ceb
updated summary.py/associated files and tests. updated interactome.py
ntalluri Sep 18, 2023
0b47bd9
Merge branch 'direction' of github.com:ntalluri/spras into direction
ntalluri Sep 18, 2023
713279a
pre-commit
ntalluri Sep 18, 2023
1198c9a
added generate inputs test, cleaned up code
ntalluri Sep 19, 2023
39b4748
Resolve merge conflicts
agitter Sep 22, 2023
af1b849
Update EGFR network with edge directions
agitter Sep 22, 2023
a34f832
added back graphspace to work for directed and undirected graphs only
ntalluri Sep 26, 2023
9b551d6
precommit
ntalluri Sep 26, 2023
b314751
automate test_prepare_inputs
ntalluri Sep 29, 2023
32be496
renamed the tests for creating the inputs
ntalluri Oct 4, 2023
57599f7
fix break in test
ntalluri Oct 4, 2023
e991e0a
added parse_output tests and still fixing generate inputs
ntalluri Oct 4, 2023
dd6c899
precommit
ntalluri Oct 4, 2023
ae276f5
added more information to step 5 of contributing guide
ntalluri Oct 4, 2023
df7da32
add cytoscape into workflow
ntalluri Oct 4, 2023
e5be5a0
cleaning up generate inputs/parse outputs test suites
ntalluri Oct 17, 2023
09c2913
clean up gen inputs and prase outputs
ntalluri Oct 17, 2023
8dd0990
Merge with master
agitter Oct 18, 2023
d9b0f0b
Fix ruff errors on GitHub actions
agitter Oct 18, 2023
6f631ef
made changes based on review
ntalluri Oct 26, 2023
f651376
made more changes based on review
ntalluri Oct 26, 2023
b764129
fixed error
ntalluri Oct 27, 2023
8eb9ebb
some of the comments
ntalluri Nov 27, 2023
5c0939f
more comments
ntalluri Nov 27, 2023
884fe4f
precommit
ntalluri Nov 27, 2023
19a4ad4
more comments
ntalluri Nov 27, 2023
99e6e6f
more comments resolved
ntalluri Nov 28, 2023
e8735ea
resolving parse output comments
ntalluri Nov 29, 2023
96c0482
precommit
ntalluri Nov 29, 2023
83262c7
add check to dataset.py
ntalluri Dec 1, 2023
7bc9e3e
Rename .csv to .txt in test directory
agitter Dec 3, 2023
d918c00
Add tests for invalid 4th edge column
agitter Dec 3, 2023
cd625d4
Remove self-edges from EGFR data
agitter Dec 3, 2023
ee58069
Update Cytoscape wrapper for directed edges
agitter Dec 3, 2023
da655b3
Remove directed from EGFR config and run more algs
agitter Dec 3, 2023
b4d6e1c
Systematic proofreading and formatting
agitter Dec 3, 2023
cccf5ce
Bump Cytoscape image version in workflow
agitter Dec 3, 2023
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add cytoscape into workflow
ntalluri committed Oct 4, 2023
commit df7da322490c4e41d27a8c6e1c4103dd7b0e461c
2 changes: 1 addition & 1 deletion config/config.yaml
Original file line number Diff line number Diff line change
@@ -124,7 +124,7 @@
include: true
# Create Cytoscape session file with all pathway graphs for each dataset
cytoscape:
include: false
include: true
# Machine learning analysis (e.g. clustering) of the pathway output files for each dataset
ml:
include: true