This PR will wait to be rebased after #80 merges before further testing to avoid having to solve conflicts in notebooks due to the pre-commit hook.

@hanayik I sent you an email at your ndcn.ox.ac.uk address but I am not sure if you received it. If not, let me know. It is about adding a codecov token to the ipyniivue project. I am not part of the NiiVue organization so I cannot do it myself.

@bcalford That's cool. The CI is now running the notebooks and the tests flag any crashing notebook. It allowed us to find that two of our notebooks were broken! One was just missing an import, but the other was due to a change in the API. This will make it easier for us to maintain everything in working order!

@christian-oreilly I received the email, thanks! We can keep the conversation on here though since it's in context with the PR.

I don't think it's necessary to give the coverage service access to the entire Niivue github organisation.

I have instead modified the CI workflow to use pytest-cov and upload the coverage summary as artifacts and show the coverage as markdown tables in the workflow summary page.

see: https://github.com/niivue/ipyniivue/actions/runs/13050900236?pr=105

Let me know if this is ok for your use case. The first table is the src code summary, and the second table is the notebook coverage summary (per matrix combination in your test runners).

@hanayik Thank for your feedback. I am not sure I get where this report is uploaded. I relaunched the jobs to check the result I don't see the report added to the PR. I am trying to have the report added to the PR as can be seen in this PR lina-usc/pylossless#214 for example. My understanding is that it is done through this

https://github.com/lina-usc/pylossless/blob/d835e404b5a213eea1352e4fcb200e2f631cd480/.github/workflows/test_pipeline.yml#L46-L48

which requires a token for codecov. I does not require giving the coverage access to the whole organization, just to ipyniivue repo. I would have done it myself, but I can't because I am not a member of the NiiVue organization.

Thanks for the review @bcalford