Documentation fixes

[bclenet]

This Pull Request is related to issues :

• [BUG] Link to "testing.md" is wrong in "pipeline.md" #104
• [ENH] Test creation doc #107

Changes proposed in this Pull Request:

• fixing some broken links in the documentation

Checklist:

• Descriptive title
• Targets the main branch
• Changes are functional
• My code is explicit and comments were added to it
• Code conforms with PEP8
• Tests were added for the changes and they complete successfully
• Existing tests were updated (if needed) and they complete successfully
• Documentation was updated

[bclenet]

Hi @elodiegermani ! Please feel free to check if this PR answers what you suggested in the issues 🙂 Thanks !

PS: it may be easier to check the doc directly in my branch : https://github.com/bclenet/narps_open_pipelines/tree/documentation

[elodiegermani]

Hi @bclenet! Well, actually, that does not really answer my questions about the "pipeline_test".
Actually, it was because I had a pipeline that was functional, it passed all the tests except this one because it is not set as an "implemented pipeline" in the Pipeline class init file but when I tried to change this, it raised other errors due to tests you implemented regarding the number of implemented pipeline, etc.
So I was wondering, is this part already functional in the test?
If so, do you want to decide on your side if a pipeline is implemented or not? Or can we add it ourselves?
If we can add it ourselves, it would be nice to have a list of tests to modify to be able to pass this test :)

[bclenet]

Hi Elodie,

I understand your concern : the test you are talking about (test_utils() inside narps_open_pipelines/tests/pipelines/test_pipelines.py) is not relevant and should be changed. In fact, it is going to be changed soon, as part of one of my PRs.

Furthermore, i'll add something in the doc about modifying the implemented_pipelines dictionary, which you can do it by yourself of course, when starting a new pipeline reproduction.

Thanks !