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Documentation for starfiles #470

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jojoelfe
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@jojoelfe jojoelfe commented Apr 1, 2024

This should add the starfile node to the documentation. I am still working on the tutorial, but figured I open the PR to see if the CI for the docs works correctly.

ALso included are some small fixes for relion import that I noticed while making a tutorial.

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codecov bot commented Apr 1, 2024

Codecov Report

Attention: Patch coverage is 37.50000% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 77.66%. Comparing base (e18b144) to head (5f6b596).
Report is 17 commits behind head on main.

Current head 5f6b596 differs from pull request most recent head 5f11a4d

Please upload reports for the commit 5f11a4d to get more accurate results.

Files Patch % Lines
molecularnodes/io/parse/star.py 37.50% 5 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #470      +/-   ##
==========================================
+ Coverage   75.70%   77.66%   +1.95%     
==========================================
  Files          41       40       -1     
  Lines        3742     3617     -125     
==========================================
- Hits         2833     2809      -24     
+ Misses        909      808     -101     

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@BradyAJohnston
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The docs build OK on my machine - I need to look into why they aren't auto-triggering a build for the PR.

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BradyAJohnston commented Apr 2, 2024

Now changed so that the docs will build & deploy on every PR :)

EDIT:
OK I remember why I disabled this - because there was an error with deploying to netlify from PRs that weren't mine. Will look into it

fix deployments

maybe fix

maybe fix
@BradyAJohnston
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OK for security reasons we can't have a preview deployment unless the PR is from me - but the docs now at least still build & report if successful.

@BradyAJohnston
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no rush on this - but I will be giving a tutorial to some CryoEM and CryoET people in a couple of weeks and would love to have a written tutorial for the starfile importing :)

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jojoelfe commented May 7, 2024

Hey, I am slowly coming back to things after traveling.

I think the tutorial for cryo-EM SPA is in fairly good shape. It would be great to have something similar for cryo-ET, but there the problem is to find good datasets. An new choice would be some data from the CZI portal (https://cryoetdataportal.czscience.com/), but they don't use starfiles, but a json format. Maybe thats trivial to implement, but I haven't looked at it carefully yet.

@BradyAJohnston
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Just put together an initial .ndjson parser in #493 if you wanted to take a look. If you can point out some good datasets to use as testing on that portal (I've had a look, but this isn't my field of expertise).

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