scverse / scverse/spatialdata

User documentation on how to setup jobs or run large analysis

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

Is your feature request related to a problem? Please describe.
Current documentation shows small examples. Working on real large datasets varies in some ways and has specific needs:

  • limiting Dask workers to limit memory usage
  • job-based instead of interactive
  • sometimes needs to use a specific HPC setup
  • requesting resources via SLURM or using workflow managers like Nextflow, Snakemake...
  • working with a distributed Dask cluster

Describe the solution you'd like
A documentation page should explain this and link to existing resources. It would also be interesting to gather existing documentation of executing large jobs with SpatialData.

Some resources:

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 reviewing the existing documentation and the Dask, HPC, SLURM, Hydra, Nextflow, and Snakemake resources linked in the issue. Done means adding a documentation page that explains job-based and distributed large-scale analysis, resource limits, HPC setup, and links to relevant SpatialData workflows.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
documentation, hpc
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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