scverse / scverse/spatialdata

Harmonize artifical dataset creation

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Dominant language
Python
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394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

Is your feature request related to a problem? Please describe.
There are multiple artificial dataset creation functions. It should be clear which ones are most useful and when.

Describe the solution you'd like
Merge or document the different artificial dataset implementations. Ideally, the default one and the benchmarking one are merged and the ones from libraries using SpatialData can reuse some functionality to make more specific artificial datasets.

Additional context
Here is a list of some implementations:

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by comparing spatialdata.datasets.blobs in src/spatialdata/datasets.py with benchmarks/utils.py and the linked SOPA and Harpy implementations. Identify the overlapping capabilities and differences, then clarify whether the expected outcome is a shared dataset API, merged implementations, documentation, or some combination; completion criteria are not defined in the issue.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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