Batch integration feature by danielStrobl · Pull Request #416 · openproblems-bio/openproblems

danielStrobl · 2022-05-18T15:11:50Z

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This submission adds a new dataset
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

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This submission was written on a forked copy of SingleCellOpenProblems
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If this pull request is not ready for review (including passing the "Run Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

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This submission follows the guidelines in our Contributing document
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)

… into openproblems-bio-main

This reverts commit f3f0f10.

This reverts commit 80bd50f.

This reverts commit 807c6d0.

This reverts commit 6180588.

…lOpenProblems into batch-integration

…ingleCellOpenProblems into batch-integration-feature

danielStrobl · 2022-10-01T11:25:50Z

I think this should be ready to merge now @LuckyMD

LuckyMD

This looks good to me. There is still one unanswered feature request above about computing PCA not only for scanorama input in the function, but also for ComBat output... but I think that might actually not be relevant. So fine to merge from my side. Maybe confirm this doesn't need to be addressed @danielStrobl

danielStrobl · 2022-10-04T14:11:33Z

This shouldn't matter for the results as we're using X_emb, so just a bit of unnecessary compute time

scottgigante-immunai · 2022-10-04T19:03:09Z

Tests are hanging, going ahead and re-triggering

…ingleCellOpenProblems into batch-integration-feature

scottgigante-immunai · 2022-10-05T16:10:32Z

Clear to merge? 🎉

scottgigante-immunai · 2022-10-05T16:11:10Z

I guess technically awaiting success of https://github.com/danielStrobl/SingleCellOpenProblems/actions/runs/3190561273

danielStrobl · 2022-10-05T16:28:53Z

Yes! clear to merge!

* lower bound scvi-tools, other fixes * add release notes * Refactor scvi without scib * remove comments * switch to pytorch_nvidia image * only output necessary data * add more arguments to component * add more params to scanvi * Apply suggestions from code review Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com> * Apply more suggestions from code review * Use counts --------- Co-authored-by: Kai Waldrant <kai@data-intuitive.com> Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* lower bound scvi-tools, other fixes * add release notes * Refactor scvi without scib * remove comments * switch to pytorch_nvidia image * only output necessary data * add more arguments to component * add more params to scanvi * Apply suggestions from code review Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com> * Apply more suggestions from code review * Use counts --------- Co-authored-by: Kai Waldrant <kai@data-intuitive.com> Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> Former-commit-id: 05cfabe

danielStrobl and others added 30 commits March 17, 2022 15:24

fix wrong desc import

539e7b6

install biocmanager python37-scgen container

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pre-commit

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Merge branch 'main' of https://github.com/openproblems-bio/openproblems…

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… into openproblems-bio-main

Merge branch 'openproblems-bio-main' into batch-integration

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fix r docker

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switch to separate r integration container

6180588

pre-commit

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gitignore

80bd50f

now with correct r extras container

f3f0f10

Revert "now with correct r extras container"

5befdbd

This reverts commit f3f0f10.

Revert "gitignore"

cf77ec7

This reverts commit 80bd50f.

Revert "pre-commit"

d6fdb90

This reverts commit 807c6d0.

Revert "switch to separate r integration container"

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This reverts commit 6180588.

deactivate desc

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pre-commit

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fastmnn dgcmatrix output

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Merge branch 'batch-integration' of github.com:danielStrobl/SingleCel…

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…lOpenProblems into batch-integration

transpose fastmnn matrix

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flake8 order

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pre-commit

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skip isort for import

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isort next try

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pre-commit

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clean up

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addressing changes requested

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pre-commit

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remove untested

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Merge branch 'batch-integration' of github.com:danielStrobl/SingleCel…

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…lOpenProblems into batch-integration

danielStrobl and others added 11 commits September 28, 2022 15:04

Merge branch 'batch-integration-feature' of github.com:danielStrobl/S…

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…ingleCellOpenProblems into batch-integration-feature

adapt embedding readme

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pre-commit

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Merge branch 'master' into bi-feature

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api fixes batch integration feature

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pre-commit

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readme and tests

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Merge branch 'batch-integration-feature' of github.com:danielStrobl/S…

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…ingleCellOpenProblems into batch-integration-feature

pre-commit

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Delete batch_integration_graph.py

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Import datasets directly from batch_integration_graph

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scottgigante-immunai reviewed Sep 30, 2022

View reviewed changes

Comment thread openproblems/tasks/_batch_integration/batch_integration_feature/__init__.py Outdated

danielStrobl added 2 commits October 1, 2022 13:16

change init py embed->feature

bfd02d9

remove unused import

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LuckyMD approved these changes Oct 4, 2022

View reviewed changes

Merge branch 'main' into batch-integration-feature

ccea443

scottgigante-immunai and others added 5 commits October 4, 2022 15:03

Merge branch 'main' into batch-integration-feature

4eb7c40

Merge branch 'main' into batch-integration-feature

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remove unused file

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Merge branch 'batch-integration-feature' of github.com:danielStrobl/S…

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…ingleCellOpenProblems into batch-integration-feature

Merge branch 'main' into batch-integration-feature

f73a4d5

danielStrobl merged commit b578c4f into openproblems-bio:main Oct 5, 2022

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Batch integration feature - #416

Batch integration feature#416
danielStrobl merged 524 commits into
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danielStrobl commented May 18, 2022

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