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Update Viash to 0.9.0-RC7 #796

Merged
merged 77 commits into from
Aug 30, 2024
Merged

Update Viash to 0.9.0-RC7 #796

merged 77 commits into from
Aug 30, 2024

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jakubmajercik
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@jakubmajercik jakubmajercik commented Apr 26, 2024 •
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Changelog

Refactored component configs:

  • the platforms field into runners and engines
  • remove the functionality field
  • make sure all tests pass

Branched out from main and develop - certain new components might not be included

All components passed the tests apart from the interactive namespace due to issues with ports as specified in docker_run_args

Issue ticket number and link

Closes #776

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributor's guide

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

  • Proposed changes are described in the CHANGELOG.md

  • CI tests succeed!

VladimirShitov and others added 18 commits March 25, 2024 11:35
@VladimirShitov
Add ATAC demux (#726)
9ccc4a3
@DriesSchaumont
Remove muon as test dependency for concatenate_h5mu. (#773)
41b60be
@dorien-er @DriesSchaumont
scGPT binning component (#765)
7ec3ba4 
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
@jakubmajercik @DriesSchaumont
Cellranger Multi: output stdout/err on when cellranger failed (#766)
a169145 
* stdout/err stored on fail

Co-authored-by: Dries Schaumont <DriesSchaumont@users.noreply.github.com>

* changelog entry added + minor fixes

---------

Co-authored-by: Dries Schaumont <DriesSchaumont@users.noreply.github.com>
@jakubmajercik
config mods + report/mermaid refactored
fac74cd
@jakubmajercik
files/make_params refactored
e5e0426
@jakubmajercik
interactive/run_cellxgene and compression/compress_h5mu refactored
70c1130
@jakubmajercik
compression, interactive, process namespaces refactored
ee8273d
@jakubmajercik
interactive namespace refactored
9ba4f55
@jakubmajercik
10xt_to_h5mu changed config
0bb1f18
@jakubmajercik
cluster - dimred namespaces (alphabetically) refactored and tested
baeac77
@jakubmajercik
all components refactored and tested
29481d8
@jakubmajercik
annotate/popv fix
1cf9b34
@jakubmajercik @DriesSchaumont
Implement cellranger mkgtf (#771)
0cae088 
* cellranger mkgtf component working and tested

* removed comments

* changelog entry added

* test unique attribute in result

* multiple attribute par added

* removed unused packages

* use pytest, multiple attributes tested

---------

Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into develop
39dedf2
@jakubmajercik
Merge branch 'main' of github.com:openpipelines-bio/openpipeline into…
ee2c71d 
… 776-refactor-config-new-viash
@jakubmajercik
Merge branch 'develop' of github.com:openpipelines-bio/openpipeline i…
f1fde6f 
…nto 776-refactor-config-new-viash
@jakubmajercik
removed viashpy from cellbender_remocve_background
2c598d9
Base automatically changed from develop to main June 12, 2024 14:20
DriesSchaumont and others added 21 commits August 13, 2024 12:19
@DriesSchaumont
Adjust some new components
45ebd6e
@DriesSchaumont
Fix some meta variables
7bf0cef
@DriesSchaumont
Bump viash
6aa72c8
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into 776-refactor-config-n…
992a1b1 
…ew-viash
@DriesSchaumont
Fix some components
67efba5
@DriesSchaumont
Fix some more components
c64af4d
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into 776-refactor-config-n…
8938ec0 
…ew-viash
@DriesSchaumont
Update split_h5mu_train_test
2957702
@DriesSchaumont
Update densmap
ecc8570
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into 776-refactor-config-n…
7fec4d1 
…ew-viash
@DriesSchaumont
Update split_h5mu component
ee90b9f
@DriesSchaumont
Remove symlink of qc workflow in root of repo.
f2644eb
@DriesSchaumont
Remove references to functionality.name
1984218
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into 776-refactor-config-n…
43a5178 
…ew-viash
@DriesSchaumont
Fix cellxgene_census component
ce6f26c
@DriesSchaumont
Remove run_cellxgene and run_cirrocumulus
afa3bc0
@rcannood
Merge remote-tracking branch 'origin/main' into 776-refactor-config-n…
4beab88 
…ew-viash
@rcannood
fix typo
3b94fd2
@rcannood
update config
4ab92f6
@DriesSchaumont
Fix some components
b0f4fb9
@DriesSchaumont
Fix config syntax problems
96db003
@DriesSchaumont DriesSchaumont changed the title 776 refactor config new viash Update Viash to 0.9.0-RC7 Aug 23, 2024
@jakubmajercik jakubmajercik linked an issue Aug 23, 2024 that may be closed by this pull request
Refactor components to use new Viash version >= 0.9.0 #776
Closed
@DriesSchaumont DriesSchaumont merged commit 331d655 into main Aug 30, 2024
106 checks passed
@DriesSchaumont DriesSchaumont deleted the 776-refactor-config-new-viash branch August 30, 2024 07:08
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Refactor components to use new Viash version >= 0.9.0
5 participants
@jakubmajercik @DriesSchaumont @VladimirShitov @dorien-er @rcannood