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Add Method SCOT to Multi-modal data Integration Task #298
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Looks good to me. Matches the API and is fully metadata annotated.
…Problems into method-scot-atong
I broke some strings into multiline strings and added a |
let's wait for tests and then merge. |
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## master #298 +/- ##
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- Coverage 91.67% 89.23% -2.44%
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Files 70 71 +1
Lines 1465 1505 +40
Branches 89 89
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Hits 1343 1343
- Misses 94 134 +40
Partials 28 28
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* master: fix region fix nf wkdir use env.BRANCH rm echo BRANCH -> WKDIR for s3 set branch variable in S3 setup job Fix s3 bucket clash Dimred methods preprocessing (openproblems-bio#301) Add trustworthiness score for dimred task (openproblems-bio#258) Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298) Update README.md Update README.md Update README.md
* master: fix region fix nf wkdir use env.BRANCH rm echo BRANCH -> WKDIR for s3 set branch variable in S3 setup job Fix s3 bucket clash Dimred methods preprocessing (openproblems-bio#301) Add trustworthiness score for dimred task (openproblems-bio#258) Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298) Update README.md Update README.md Update README.md
* master: fix region fix nf wkdir use env.BRANCH rm echo BRANCH -> WKDIR for s3 set branch variable in S3 setup job Fix s3 bucket clash Dimred methods preprocessing (openproblems-bio#301) Add trustworthiness score for dimred task (openproblems-bio#258) Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298) Update README.md Update README.md Update README.md
…ction * dimred-methods: (34 commits) Update alra.py (openproblems-bio#304) updated template for PR with PR evaluation checks (openproblems-bio#314) pre-commit Fix preprocessing Fix preprocessing Add new preprocessing Add new preprocessing fix region fix nf wkdir use env.BRANCH rm echo BRANCH -> WKDIR for s3 set branch variable in S3 setup job Fix s3 bucket clash Dimred methods preprocessing (openproblems-bio#301) Add trustworthiness score for dimred task (openproblems-bio#258) Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298) Change batch size to 1k cells for aff. matrix Add preprocessing Fix some small bugs ...
* Add nf-tower cli for dataset loader * add mising directive labels for dataset loader * add missing directive labels process datasets * remove space in file name
* Add nf-tower cli for dataset loader * add mising directive labels for dataset loader * add missing directive labels process datasets * remove space in file name Former-commit-id: 6ed72c7
This PR adds the Single-cell Optimal Transport method to the multimodal integration task.
Some potential questions:
flake8
test, this is useful for documenting where these parameters came from.balanced
option, which is quite important (as it represents separate but important variants of the Gromov-Wasserstein distance).SCOT
via my forked repository. I have submitted a PR on the SCOT GitHub, if this is merged up there it should be a quick fix. Not sure how we want to support these not quite fully packaged methods in the future.Submission type
Testing
Submission guidelines