User documentation on different methods of benchmarking with SpatialData
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
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- Merged PRs (30d)
- 7
Description
Is your feature request related to a problem? Please describe.
A lot of documentation is focused on one dataset or method. Method developers need to benchmark multiple datasets or methods e.g.
Benchmarking functions
- compare two segmentation models creating a Labels element
- compare two methods outputting a SpatialData object
Benchmarking pipelines
- working towards larger benchmarks
- how to benchmark on large infrastructure, HPC
- link to openproblems.bio
Describe the solution you'd like
A tutorial documentation with just text on benchmarking pointing to the right resources or documentation for each type of benchmarking method.
Describe alternatives you've considered
A lot of existing material exists, but there is no overview or examples specifically using SpatialData.
Additional context
Benchmarking or performance analysis for developers contributing to SpatialData is out-of-scope for this issue.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No target file or test is named. Start by reviewing the existing benchmarking material and openproblems.bio, then create a SpatialData-focused tutorial covering function and pipeline benchmarking, including large-infrastructure and HPC guidance. Done means the overview points readers to the appropriate resources and examples.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100