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Clarify repo purposes #33

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Dec 14, 2023
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Clarify repo purposes #33

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alessandrofelder Dec 14, 2023
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[skip ci] Flesh out secondary purposes of repo
alessandrofelder Dec 14, 2023
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11 changes: 11 additions & 0 deletions README.md
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Expand Up @@ -23,6 +23,17 @@ At present, the package offers the following workflows:

- [cellfinder](#cellfinder): Whole-brain detection, registration, and analysis.

These workflows should be representative of the most common use-cases and are meant to be easy to reuse. They also serve as an example of how to combine several BrainGlobe tools to achieve a goal, such as whole brain cell detection and atlas registration.
These workflows typically combine several BrainGlobe tools (possibly together with other tools) to achieve a goal,
such as whole brain cell detection and atlas registration.

## Secondary purposes of brainglobe-workflows, for developers

We also use these workflows to support code development. We do this by regularly benchmarking the time they take to complete to ensure performance is stable as the code changes.
* Developers can install these benchmarks locally via `pip install [dev]`. By executing `asv run`, the benchmarks will run with default parameters on a small dataset that is downloaded from [GIN](https://gin.g-node.org/G-Node/info/wiki). See [the asv docs](https://asv.readthedocs.io/en/v0.6.1/using.html#running-benchmarks) for further details on how to run benchmarks.
* Developers can also run these benchmarks on data available locally, by specifying the relevant paths in an input configuration file (JSON file).
* We additionally run and benchmark the workflows locally on a internal desktop machine with large example datasets. These benchmarks are run periodically and the results are made publicly available.

## Installation

If you want to install BrainGlobe workflows as a standalone tool, you can run `pip install` in your desired environment:
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