openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics

MIT License

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Add ALRA preprocessing identical to literature #763

Closed wes-lewis closed 1 year ago

wes-lewis commented 1 year ago

Submission type

[ ] This submission adds a new dataset
[x] This submission adds a new method
[ ] This submission adds a new metric
[ ] This submission adds a new task
[ ] This submission adds a new Docker image
[ ] This submission fixes a bug (link to related issue: )
[ ] This submission adds a new feature not listed above

Testing

[x] This submission was written on a forked copy of openproblems
[ ] Nextflow test pipeline is passing on this base branch of this pull request (include link to passed test on NF Tower found in GitHub Actions summary: )
[ ] If this pull request is not ready for review (including passing the Nextflow test pipeline), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

Submission guidelines

[x] This submission follows the guidelines in our Contributing document
[x] I have checked to ensure there aren't other open Pull Requests for the same update/change

PR review checklist

This PR will be evaluated on the basis of the following checks:

[ ] The task addresses a valid open problem in single-cell analysis
[ ] The latest version of master is merged and tested
[ ] The methods/metrics are imported to __init__.py and were tested in the pipeline
[ ] Method and metric decorators are annotated with paper title, year, author, code version, and date
[ ] The README gives an outline of the methods, metrics and datasets in the folder
[ ] The README provides a satisfactory task explanation (for new tasks)
[ ] The sample test data is appropriate to test implementation of all methods and metrics (for new tasks)

wes-lewis commented 1 year ago

Seems some issues with docker images might be in the way--am re-running now https://github.com/wes-lewis/SingleCellOpenProblems/actions/runs/3850077442/jobs/6559813810

wes-lewis commented 1 year ago

Was getting an error with tocsr(). Local testing showed using scipy to cast as csr worked, but I continued to get image build issues, and it seemed scipy was not included in openproblems base image, R base, or R extras (unless I overlooked/was absent from README's). I created another PR to add scipy to r-extras in the meantime.

However, tocsr() was working in the merged version of alra.py, so I may just have to check output types from the normalizations prior to the tocsr() line.

scottgigante-immunai commented 1 year ago

Scipy is a core dependency of openproblems and is installed in all images. See https://github.com/openproblems-bio/openproblems/blob/main/setup.py

scottgigante-immunai commented 1 year ago

This, on the other hand, is a flake. Worth rerunning it and seeing what the error is.

scottgigante-immunai commented 1 year ago

Switching back to draft as nextflow tests haven't passed yet (see issue template in first comment.)

wes-lewis commented 1 year ago

Switching back to draft as nextflow tests haven't passed yet (see issue template in first comment.)

I'm a bit confused about what the 'issue template' refers to?

scottgigante-immunai commented 1 year ago

https://github.com/openproblems-bio/openproblems/pull/763#issue-1517865094

You should convert from draft only after you include the link to the passed test run

scottgigante-immunai commented 1 year ago

Tests at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/4l0dEfrCB00jgp

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.78% // Head: 94.93% // Increases project coverage by +0.15% :tada:

Coverage data is based on head (86b1af8) compared to base (3d8964a). Patch coverage: 99.36% of modified lines in pull request are covered.

Additional details and impacted files

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