[WIP] Migration from pytest to nf-test.

[gagnonanthony]

This is the first attempt to migrate a module from the pytest framework to nf-test. Here is a list of changes made to make it work:

Configs (@AlexVCaron feel free to make changes to how I did things, it sure isn't perfect!):

• Added a nf-test.config file in the root directory.
• Added a nf-test.config file in tests/config/ specifying the profiles, parameters, etc. (similar to the nextflow.config file).
• Added nf-test installation in the Dockerfile.
• Updated nf-core to the latest version (2.13.1).
• Changed the in-project creation of poetry virtualenv to false. Having it to true made nf-test fetching the nf-core template as a test to run which was falling each time.
• Added nf-test testing section to the test_modules.yml GitHub action (not sure if it works as is). UPDATE: nf-test setup action isn't authorized to be used in workflows.

Steps to convert pytest to nf-test (@ThoumyreStanislas I'll make it cleaner so you can add it to the workflow doc soon.):

1. Create an environment.yml file within the module's folder. The conversion crashes if this file isn't available.
2. Run nf-core modules create --migrate-pytest <tool/subtool> and fill out the prompts.
3. Replace the input in the new main.nf.test file with the one in your previous test file. Those inputs are positional, so it is mandatory to keep the structure input[0] = file(....
4. To generate the snapshot, run nf-core modules --git-remote https://github.com/scilus/nf-scil.git test segmentation/fastseg. In the latest nf-core, using --git-remote solves the previous issue of the hardcoded nf-core directory structure.

114 #116 #117

[gagnonanthony]

Thanks @AlexVCaron ! Yes, the tests passed locally. I think once we figure out the actions/etc., the switch between pytest and nf-test will be fairly easy.

[AlexVCaron]

Thanks @AlexVCaron ! Yes, the tests passed locally. I think once we figure out the actions/etc., the switch between pytest and nf-test will be fairly easy.

I'm super happy ! I'll give a look on the action framework, make sure everything is run correctly, with the right workflow versions. There may be something to modify in the checks.yml workflow, it think the nf-test modules are not fetched in the failing-modules step.

[gagnonanthony]

Yeah, that's exactly what I was looking at! I'll go through the nf-core/modules repo to see what they are doing over there.

Update: I've added the fetching of nf-test modules and a separate workflow to test them (to avoid using pytest when it is an nf-test module). That way, it shouldn't mess up other modules that are still using pytest. Two minor issues: nf-test action isn't set up in the workflow, not sure why and the module's linting requires the environment-schema.json which I added, but can't be used until the PR is merged. @AlexVCaron, I'm not sure the environment.yml file is really necessary in our case since we do not really use environments, should we just remove it?

[AlexVCaron]

You're a rockstar :metal: I'll add the schema for the environment file to the main, I'll keep you updated. Also, I opened an issues for the setup action for nf-test, waiting on it, it'll fix the current test step failure !

Waiting on nf-core/setup-nf-test#6

[AlexVCaron]

I trickled a bit in the action. Can you try AlexVCaron/setup-nf-test@main instead of the one from nf-core, see if it fixes our problem ?

[gagnonanthony]

Done, seems like it returned a different error message this time: Error: File not found: '/home/runner/_work/_actions/AlexVCaron/setup-nf-test/main/dist/index.js'

[AlexVCaron]

Allright. The setup-nf-test action is working correctly. The environment-schema file is also available on the main. There seems to still be a problem with the testing. It doesn't look like the tests are run inside the docker container, even with the PROFILE=docker supplied to nf-test. Is there a missing configuration ?