Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update README and sample contribution #440

Merged
merged 14 commits into from
Oct 6, 2023

Conversation

talonchandler
Copy link
Collaborator

@talonchandler talonchandler commented Sep 27, 2023

This PR adds:

  • A reconfigured README following @mattersoflight's suggestions. The README now leads with a link to our comms video and dataset examples (zebrafish and zebrafish embryo examples).
  • A new ~100 MB sample contribution of the zebrafish embryo (retardance and orientation reconstructions only, center z plane, every fifth time point to keep the file size reasonable)
  • The phase reconstruction from the the Kazansky sample contribution.

I will move this from draft to full when it fixes #433. We still need to:

  • Upload zebrafish embryo sample contribution to zenodo
  • Test zenodo sample contribution from fresh installation

When this merges I will release 0.4.1.

@talonchandler talonchandler marked this pull request as ready for review September 29, 2023 16:05
@ziw-liu
Copy link
Contributor

ziw-liu commented Oct 3, 2023

One open question is whether we should delete the old version to prevent ever-increasing storage usage on client systems.

talonchandler and others added 4 commits October 5, 2023 17:29
Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
@talonchandler talonchandler requested a review from ziw-liu October 6, 2023 00:45
Copy link
Member

@mattersoflight mattersoflight left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've reviewed the README and it looks great!

How should I test the sample contribution? pip install from this branch?

@talonchandler
Copy link
Collaborator Author

👍 yep pip install from this branch will let you test the sample contributions (they’ll download from Zenodo). PS if you have the recorder widget open, you’ll get birefringence overlays.

Copy link
Contributor

@ziw-liu ziw-liu left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Code looks good!

@talonchandler
Copy link
Collaborator Author

I just tried an installation from scratch, and everything looks good to me.

I'll shoot to merge this and release 0.4.1 around the end of the day. @mattersoflight we can demo the sample contributions at our desks anytime for you if you'd like to take a look.

@codecov
Copy link

codecov bot commented Oct 6, 2023

Codecov Report

Merging #440 (4837af3) into main (ff996ba) will decrease coverage by 0.03%.
The diff coverage is 2.85%.

@@           Coverage Diff            @@
##            main    #440      +/-   ##
========================================
- Coverage   8.86%   8.83%   -0.03%     
========================================
  Files         29      29              
  Lines       4547    4561      +14     
========================================
  Hits         403     403              
- Misses      4144    4158      +14     
Files Coverage Δ
...er/tests/widget_tests/test_sample_contributions.py 100.00% <100.00%> (ø)
recOrder/scripts/samples.py 0.00% <0.00%> (ø)

@talonchandler talonchandler added this pull request to the merge queue Oct 6, 2023
Merged via the queue into main with commit 7f33e5d Oct 6, 2023
@talonchandler talonchandler deleted the update-sample-contrib-and-readme branch October 6, 2023 21:18
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

[DOCS] Biological sample contribution
3 participants