Sync changes from development into main
#772
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Sync changes from `main` with `dev`
Delete duplicate layer in AnnData objects
This reverts commit 74527c8.
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Use new, slimmer sometimes, containers
…r-images Test new docker image and add test samples to profile config
…blishdir Move bulk output to separate bulk directory
updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.5.0](astral-sh/ruff-pre-commit@v0.4.5...v0.5.0) - [github.com/pre-commit/mirrors-prettier: v3.1.0 → v4.0.0-alpha.8](pre-commit/mirrors-prettier@v3.1.0...v4.0.0-alpha.8)
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
for more information, see https://pre-commit.ci
[pre-commit.ci] pre-commit autoupdate
…a-to-reports Add sample metadata tables to reports
Change version to v0.8.2
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Just adding all the changes into
mainfor the release.Note that I did to another test run and everything completed as expected.