Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Cell type annotation: scGPT workflow #832

Open
wants to merge 51 commits into
base: main
Choose a base branch
from
Open

Cell type annotation: scGPT workflow #832

wants to merge 51 commits into from

Commits on Jul 9, 2024

  1. scgpt cell type annotation workflow

    @dorien-er
    dorien-er committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    bf671cc View commit details
    Browse the repository at this point in the history

  2. update changelog

    @dorien-er
    dorien-er committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    c7f2553 View commit details
    Browse the repository at this point in the history

Commits on Jul 23, 2024

  1. update annotation component

    @dorien-er
    dorien-er committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    45ca460 View commit details
    Browse the repository at this point in the history

  2. update annotation subworkflow

    @dorien-er
    dorien-er committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    d4ca247 View commit details
    Browse the repository at this point in the history

  3. elevate integration test permissions

    @dorien-er
    dorien-er committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    70961ce View commit details
    Browse the repository at this point in the history

Commits on Sep 4, 2024

  1. Merge remote-tracking branch 'origin/main' into scgpt-annotation-work… 

    …flow
    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    77da8af View commit details
    Browse the repository at this point in the history

  2. remove temp scgpt annotation component

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    04987c4 View commit details
    Browse the repository at this point in the history

  3. scgpt cell type annotation workflow

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    949937e View commit details
    Browse the repository at this point in the history

  4. remove temp scgpt annotation component

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    864364e View commit details
    Browse the repository at this point in the history

  5. update scgpt test resources

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    f8ba860 View commit details
    Browse the repository at this point in the history

  6. update scgpt test resources

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    b83be7e View commit details
    Browse the repository at this point in the history

  7. update scgpt test resources

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    6c34c59 View commit details
    Browse the repository at this point in the history

  8. update to viash 9

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    538bff1 View commit details
    Browse the repository at this point in the history

  9. add test workflow

    @dorien-er
    dorien-er committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    4b59667 View commit details
    Browse the repository at this point in the history

Commits on Sep 5, 2024

  1. fix multi-processing

    @dorien-er
    dorien-er committed Sep 5, 2024
    Configuration menu
    Copy the full SHA
    5d6f526 View commit details
    Browse the repository at this point in the history

Commits on Sep 6, 2024

  1. expand test workflow

    @dorien-er
    dorien-er committed Sep 6, 2024
    Configuration menu
    Copy the full SHA
    bea7c9e View commit details
    Browse the repository at this point in the history

  2. refactorings

    @dorien-er
    dorien-er committed Sep 6, 2024
    Configuration menu
    Copy the full SHA
    6f09dc2 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'main' into scgpt-annotation-workflow

    @dorien-er
    dorien-er authored Sep 6, 2024
    Configuration menu
    Copy the full SHA
    ff7fc82 View commit details
    Browse the repository at this point in the history

  4. update test workflow

    @dorien-er
    dorien-er committed Sep 6, 2024
    Configuration menu
    Copy the full SHA
    1b2a160 View commit details
    Browse the repository at this point in the history

Commits on Sep 10, 2024

  1. cleanup

    @dorien-er
    dorien-er committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    7ff7b38 View commit details
    Browse the repository at this point in the history

  2. update changelog

    @dorien-er
    dorien-er committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    a9fcfa7 View commit details
    Browse the repository at this point in the history

Commits on Nov 18, 2024

  1. Add checkout back to integration test CI

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    6aae494 View commit details
    Browse the repository at this point in the history

  2. CI: add missing checkout when syncing s3

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    cf8c0ea View commit details
    Browse the repository at this point in the history

  3. Update description for concatenate_h5mu component (#880) 

    * update description concat component

* Update src/dataflow/concatenate_h5mu/config.vsh.yaml

Co-authored-by: Dries Schaumont <[email protected]>

---------

Co-authored-by: Dries Schaumont <[email protected]>
    @dorien-er @DriesSchaumont
    dorien-er and DriesSchaumont committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    aa28cd2 View commit details
    Browse the repository at this point in the history

  4. Leftover updates for viash 0.9 (#882)

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    aa865cb View commit details
    Browse the repository at this point in the history

  5. Add LSI (#552) 

    Co-authored-by: Vladimir Shitov <[email protected]>
    @SarahOuologuem @VladimirShitov @dorien-er
    2 people authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    dc38e15 View commit details
    Browse the repository at this point in the history

  6. Update random_forrest_annotation component (#878)

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    7c9a8cb View commit details
    Browse the repository at this point in the history

  7. Add copy var component (#877)

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    1b5e8f2 View commit details
    Browse the repository at this point in the history

  8. Add TF-IDF normalization (#870) 

    Co-authored-by: DriesSchaumont <[email protected]>
    @VladimirShitov @DriesSchaumont @dorien-er
    2 people authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    458e3fc View commit details
    Browse the repository at this point in the history

  9. SVM annotation component (#845)

    @jakubmajercik @dorien-er
    jakubmajercik authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    9ab9893 View commit details
    Browse the repository at this point in the history

  10. CI: avoid components being tested twice

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    aee759d View commit details
    Browse the repository at this point in the history

  11. CI: Only build containers once

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    e52f528 View commit details
    Browse the repository at this point in the history

  12. Onclass annotation component (#844)

    @jakubmajercik @dorien-er
    jakubmajercik authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    5adab08 View commit details
    Browse the repository at this point in the history

  13. add metrics to uns slot after conversion to h5mu

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    c4af8e1 View commit details
    Browse the repository at this point in the history

  14. update changelog

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    6516f32 View commit details
    Browse the repository at this point in the history

  15. update changelog

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    16e906a View commit details
    Browse the repository at this point in the history

  16. Remove uses of auto: [publish: true] (#886) 

    * Remove uses of auto: [publish: true]

* Undo removal of publish component

* Fix integration test
    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    5ff83fb View commit details
    Browse the repository at this point in the history

  17. Add component to subset obsp (#888) 

    * add component to subset obsp

* update changelog

* update descriptions

* fix tests

* add comment
    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    90475c1 View commit details
    Browse the repository at this point in the history

  18. Accept pre-calculated distances in knn component (#890) 

    * update knn component

* update changelog

* update changelog

* address pr comments

* fix tests

* fix tests
    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    84ddecb View commit details
    Browse the repository at this point in the history

  19. scANVI updates (#892) 

    * update scanvi

* typo

* update changelog
    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    374c10c View commit details
    Browse the repository at this point in the history

  20. Update CHANGELOG.md (#895)

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    c32a877 View commit details
    Browse the repository at this point in the history

  21. Fix ingestion components not working when optional arguments are unset ( 

    #894)

* Fix ingestion components not working when optional arguments are unset

* update changelog

* fix test
    @rcannood @dorien-er
    rcannood authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    90ffa51 View commit details
    Browse the repository at this point in the history

  22. Fix location of CHANGELOG entry from PR #823 (#896)

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    73a8401 View commit details
    Browse the repository at this point in the history

  23. Fix missing dependency in from_cellranger_multi_to_h5mu (#897)

    @DriesSchaumont @dorien-er
    DriesSchaumont authored and dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    5ceefbe View commit details
    Browse the repository at this point in the history

  24. scgpt cell type annotation workflow

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    349a82e View commit details
    Browse the repository at this point in the history

  25. Merge branch 'main' into scgpt-annotation-workflow

    @dorien-er
    dorien-er committed Nov 18, 2024
    Configuration menu
    Copy the full SHA
    22e3787 View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2024

  1. Merge branch 'main' into scgpt-annotation-workflow

    @dorien-er
    dorien-er committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    e511ed3 View commit details
    Browse the repository at this point in the history

  2. cleanup

    @dorien-er
    dorien-er committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    7ffcf50 View commit details
    Browse the repository at this point in the history

  3. cleanup

    @dorien-er
    dorien-er committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    a1701f5 View commit details
    Browse the repository at this point in the history

  4. cleanup

    @dorien-er
    dorien-er committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    6e5b306 View commit details
    Browse the repository at this point in the history

  5. cleanup

    @dorien-er
    dorien-er committed Nov 22, 2024
    Configuration menu
    Copy the full SHA
    bd8253b View commit details
    Browse the repository at this point in the history