`bsb audit` command

[Helveg]

I've often encountered situations where I wasn't sure to throw an error, warn or do nothing because the warning would spam too much.

I introducing: audits. You can run the pluggable bsb audit command or bsb audit --fix command to check your entire project (#123 ) for mistakes or suboptimal practices.

[AliceGem]

Is it like a test?

[Helveg]

Not like the "testing" we do to validate the function of our code no. It's something that a modeller can run to make sure they aren't doing strange things. Like for example they could run an audit that warns you when there's an empty morphology in your repository:

• It could be a valid generated morphology that you intend or need to have there and if we always warn for it you would get spammed thousands of times with warnings when you use it!
• But, more likely, it could be an error with importing or something and it might be nice to have this audit warn you about it :)

So they are basically "overly sensitive" warnings that you can run on-demand so that we don't have to worry too much about the insensitivity of our regular warnings.

[Helveg]

Audit ideas

• [ ] Audit cell id continuity: Most things go faster if the data is continuous (fix by taking avg id of PS to sort PSs, then assign new continuous IDs)
• [ ] Audit virtualenv: Check if the project is in a virtual env with a small amount of dependencies so that a small pip freeze is generated (or use pygar?)
• [ ] Audit morphology repository for empty morphos
• [ ] Audit that morpho repo is empty

[Helveg]

Simone Torsello inspired me for a bsb audit hdf5 command that could check the integrity of HDF5 files!