Janelia-Trackathon-2023 / traccuracy

Utilities for computing common accuracy metrics on cell tracking challenge solutions with ground truth
https://traccuracy.readthedocs.io
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Add written documentation for errors and metrics #116

Closed msschwartz21 closed 2 weeks ago

msschwartz21 commented 10 months ago

I'm opening this as a draft so that we can take a look at the RTD preview while we are working on it.

Pages to write:

msschwartz21 commented 10 months ago

@cmalinmayor I took a stab at the division errors page. I just used super simple text based diagrams like we use in the docstrings for tests. We may want to upgrade to something fancier in the future, but I don't want the plotting to become a blocker to writing.

https://traccuracy--116.org.readthedocs.build/en/116/track_errors/divisions.html

codecov-commenter commented 10 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (27da5a7) 83.01% compared to head (b1f4e49) 83.64%. Report is 50 commits behind head on main.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #116 +/- ## ========================================== + Coverage 83.01% 83.64% +0.62% ========================================== Files 18 19 +1 Lines 848 899 +51 ========================================== + Hits 704 752 +48 - Misses 144 147 +3 ```

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cmalinmayor commented 10 months ago

Ooh I like it a lot!! I think if we should implement this for all metrics and then we can make it fancier later if we have time and inclination, but this is so much better than nothing.

msschwartz21 commented 10 months ago

@DragaDoncila Caroline and I started this branch to work towards closing #77 by adding pages in the sidebar for each error annotation type and downstream metrics. Can you take a stab at the ctc related pages which I think would be docs/track_errors/nodes.rst, docs/track_errors/edges.rst, and docs/metrics/ctc.rst when you have some time?

DragaDoncila commented 10 months ago

@msschwartz21 would you like me to PR into this branch for these docs, or review this PR independently and make another for the CTC docs

msschwartz21 commented 10 months ago

@msschwartz21 would you like me to PR into this branch for these docs, or review this PR independently and make another for the CTC docs

I'd prefer to get all of the docs changes in place before we merge into main so let's do a PR or direct push to this branch.

DragaDoncila commented 9 months ago

@msschwartz21 I merged some additions to the CTC docs!

msschwartz21 commented 2 weeks ago

Since we are starting to get a few more eyes on traccuracy, I'm leaning towards a mindset of some incomplete documentation is better than no documentation at all. To that end, I added a note block to the pages we haven't written yet saying "Coming soon!"

@DragaDoncila @cmalinmayor Does this sound ok to you? I'll open up an issue to keep track of the remaining pages that we need to write.

cmalinmayor commented 2 weeks ago

I very much agree. Some docs better than no docs!