gustaveroussy/sopa: v2.0.0

Sopa version 2.0.0

This version introduces many new API features but also some breaking changes; check our migration guide to smoothly update your code base.

Added

• Full Visium HD support (including, notably, bins aggregation)
• Dask parallelization backend for faster segmentation (useful for API users). This can be done via sopa.settings.parallelization_backend = 'dask'. More details in the FAQ.
• Support for one-line segmentation, e.g. sopa.segmentation.cellpose(sdata, ...) or sopa.segmentation.baysor(sdata, ...). This will implicitly use the selected parallelization backend.
• Spatial elements keys are saved in sdata.attrs so that Sopa knows automatically which element should be used in which function. It is still possible to precise image_key / points_key / shapes_key if needed. More details in the FAQ.
• Allows changing the auto-save settings (i.e. decide if spatial elements are saved on-disk automatically or not). This can be done via sopa.settings.auto_save_on_disk = False.
• Can recover a failed/stopped segmentation when using the API (and also force a segmentation, for Baysor)
• Better cache handling (invisible to API users)
• New tissue segmentation for non-H&E data (sopa.segmentation.tissue)
• Full support for baysor>=0.7.0
• Added Stardist segmentation (mainly used for H&E data)
• Added support for Python 3.12

Changes

• The sopa.io.uniform dataset is now deprecated (use sopa.io.toy_dataset instead)
• API: The image patches are now called sdata["image_patches"] instead of sdata["sopa_patches"]

Breaking changes

• Drop support for Python 3.9
• API: sopa.segmentation.Patches2D is deprecated. Instead, use the functions sopa.make_image_patches or sopa.make_transcript_patches
• API: Use sopa.overlay_segmentation instead of sopa.segmentation.overlay_segmentation
• API: The Aggregator class has been replaced by a simple function wrapper: sopa.aggregate
• API: The annotations methods are moved to the utils. For instance, use sopa.utils.higher_z_score instead of sopa.annotation.higher_z_score
• CLI: sopa read has been renamed sopa convert to avoid confusion.
• CLI: during segmentation, use --cache-dir-name instead of --patch-dir
• Drop support for Python 3.9

Fixes

• Snakemake path issue on Windows (#64)
• Issues related to incompatible versions of Baysor