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pip dev(deps-dev): update scirpy requirement from <=0.16.1 to <=0.17.0 #385

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merged 1 commit into from
Jun 3, 2024

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@dependabot dependabot bot commented on behalf of github May 20, 2024

Updates the requirements on scirpy to permit the latest version.

Release notes

Sourced from scirpy's releases.

v0.17.0

See the release notes for more details.

Changelog

Sourced from scirpy's changelog.

v0.17.0

Additions

  • Add "TCRdist" as new metric (#502)

Fixes

  • Fix issue with detecting the number of available CPUs on MacOD (#518)

v0.16.1

Fixes

  • Fix default value for n_jobs in ir.tl.ir_query that could lead to an error (#498).
  • Update description of D50 diversity metric in documentation (#499).
  • Fix clonotype_modularity not being able to store result in MuData in some cases (#504).
  • Fix issue with creating sparse matrices from generators with the latest scipy version (#504)

v0.16.0

Backwards-incompatible changes

  • Use the umi_count field instead of duplicate_count to store UMI counts. The field umi_count has been added to the AIRR Rearrangement standard in version 1.4 (#487). Use of duplicate_count for UMI counts is now discouraged. Scirpy will use umi_count in all scirpy.io functions. It will not change AIRR data that is read through scirpy.io.read_airr that still uses the duplicate_count column. Scirpy remains compatible with datasets that still use duplicate_count. You can update your dataset using

    adata.obsm["airr"]["umi_count"] = adata.obsm["airr"]["duplicate_count"]

Other

  • the io.to_dandelion and io.from_dandelion interoperability functions now rely on the implementation provided by Dandelion itself (#483).

v0.15.0

Fixes

  • Fix incompatibility with scipy 1.12 (#484)
  • Fix incompatibility with adjustText 1.0 (#477)
  • Reduce overall importtime by deferring the import of the airr package until it is actually used. (#473)

New features

  • Speed up alignment distances by pre-filtering. There are two filtering strategies: A (lossless) length-based filter and a heuristic based on the expected penalty per mismatch. This is implemented in the FastAlignmentDistanceCalculator class which supersedes the AlignmentDistanceCalculator class, which is now deprecated. Using the "alignment" metric

... (truncated)

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Updates the requirements on [scirpy](https://github.com/scverse/scirpy) to permit the latest version.
- [Release notes](https://github.com/scverse/scirpy/releases)
- [Changelog](https://github.com/scverse/scirpy/blob/main/CHANGELOG.md)
- [Commits](scverse/scirpy@v0.1...v0.17.0)

---
updated-dependencies:
- dependency-name: scirpy
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels May 20, 2024
@zktuong zktuong merged commit 1c90542 into master Jun 3, 2024
15 checks passed
@dependabot dependabot bot deleted the dependabot/pip/scirpy-lte-0.17.0 branch June 3, 2024 13:13
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