please provide functional test suite.

[EricDeveaud]

Hello,

we usualy set up a functional test suite to check after installation that the tools we manage on our cluster are correctly installed and working as expected.

for that purpose can you provide some small data set and associated command lines.
--help is fine, but lacks some functionalities ;-)

regards

Eric

[asarnow]

What specifically do you want to test?

Tests are run as part of the conda-forge compilation pipeline (and yes...right now it is --help), so I would start by adding more there, which would serve as the example.

[EricDeveaud]

Hello,

I would like to be able to have basic tests for each tools.
with real or forged data as input.

testing with --help is just testing for argparse

regards

Eric

[asarnow]

That is not accurate, in the more-or-less traditional way these programs are written --help is actually testing the environment with respect to the CLI programs. The issue for me is triangulating "tests" that add value and are worth the effort to implement (and wait on, every time the conda-forge release is updated). I won't be adding unit tests, because there is simply too much effort involved to write tests for every function, especially numerical functions where unit testing requires both sufficient binary data and appropriate definitions of accuracy. I also don't think it's worthwhile to add things like star.py --info test.star, it adds very little over --help (i.e. just checking that starfile hasn't totally changed its API). There are also very many functions, so more comprehensive test commands would quickly become as bad as a professional unit test suite.

Now, looking back I see that you didn't really care about tests that integrate into the release build. It's also clear that the primary use of the software by others is to export particles from cryoSPARC using csparc2star.py. Would a /example/ directory in the repo containing a small .cs file and a result, to compare with the output of csparc2star.py example.cs example.star, be enough?

[EricDeveaud]

don't get me wrong I'm not asking for a complete unittest suite (that's your code you manage it the way you want)
yes the example directoy you mention is the kind of things I wish. as a complete ignorant in this cryo* field. I just whish to have some data file, associated commands and to feed the tools

nb about

testing with --help is just testing for argparse

when using -h//--help no other code than argparse itself is run

[asarnow]

As I said, that isn't the case. In my CLI programs all the code in the module scope runs (in particular, all the imports statements, and unfortunately this is why startup is rather slow even with --help).

I'll add some example files to the repo plus some example commands in the readme, that will encompass a few of the most common uses. Thanks for the prod to do that.

[EricDeveaud]

great. many thanks for that