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Use spatialdata_io.experimental.to_legacy_anndata #91

Merged
merged 11 commits into from
Oct 26, 2024
Merged

Use spatialdata_io.experimental.to_legacy_anndata #91

merged 11 commits into from
Oct 26, 2024

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cavenel
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@cavenel cavenel commented Oct 11, 2024

Replace the internal to_legacy_anndata by spatialdata_io.experimental.to_legacy_anndata and update to latest spatialdata, spatialdata-io and spatialadata-plot versions.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/spatialvi branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@cavenel cavenel mentioned this pull request Oct 11, 2024
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@fasterius fasterius linked an issue Oct 25, 2024 that may be closed by this pull request
Use to_legacy_anndata function from spatialdata_io instead of custom code #75
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github-actions bot commented Oct 25, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a510eec

+| ✅ 190 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialvi_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-26 10:52:18

@fasterius fasterius merged commit 0b1c35a into dev Oct 26, 2024
9 checks passed
@fasterius fasterius deleted the fix-legacy-anndata branch October 26, 2024 11:05
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@fasterius fasterius fasterius approved these changes

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Use to_legacy_anndata function from spatialdata_io instead of custom code
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@cavenel @fasterius