Merge `recOrder` into `waveorder` by talonchandler · Pull Request #183 · mehta-lab/waveorder

talonchandler · 2025-02-21T21:16:00Z

This PR merges recOrder into waveorder.

TODO before this branch merges into main:

Merge recOrder's commit history into waveorder
Address merge conflicts sensibly, but without testing
Fix installation of CLI and plugin
Non-example tests passing on GH
Remove image references to recOrder
Clean up README and docs (~~WIP here~~ now merged)
Transfer issues from recOrder to waveorder
Transfer active PRs from recOrder to waveorder (all remaining PRs are stale and/or very small)
Test calibration on microscopes

TODO after this branch merges into main:

Update dependencies see Dependencies on iohub, pydantic, and micromanager are getting stale #197, and test.
First post-merge release of waveorder
Mark the recOrder repository as archived, and point to waveorder, see this recOrder draft PR

Bump napari-hub-preview-action version to fix CI

) * unpin recorder version * Revert "unpin recorder version" This reverts commit 838e9a1bb49ac5256c876cbad12c12d48da102c7. * add waveorder co-dev guide & fix markdown syntax * fix markdown syntax * bump napari-hub-preview-action version to fix CI * add waveorder co-dev guide & fix markdown syntax * Revert "Merge branch 'waveorder-co-dev' of https://github.com/mehta-lab/recOrder into waveorder-co-dev" This reverts commit 3e09466c4b94828da557c8fe0d25a7eb69f0db0d, reversing changes made to b399c36cae7cdbb1bf0c4bbc08d2888fe4237a87. Co-authored-by: Talon Chandler <talonchandler@gmail.com>

* Pol offset checkbox * apply +90 degree offset when box is checked * remove debug message Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

Import `qtpy` instead of `PyQt5` in autogenerated `gui.py`

…into recon-scripts

* ignore waveorder/_version.py * update recOrder README figure * updates plugin logo

* update main README, README per method to summarize hardware * move `/examples` to `/docs/examples` * `/examples/documentation` -> `/examples/deprecated` * update link * remove [examples] installation * fix tests * cleaning up `/docs` * fix .toml typo * clean development-guide.md * fix typo * update `recorder` -> `waveorder` throughout docs --------- Co-authored-by: Talon Chandler <talonchandler@gmail.com>

talonchandler · 2025-03-08T01:10:29Z

The major TODOs are complete, and branch is nearly ready to merge. I successfully installed and calibrated on falcon, and I ran successful GUI and CLI reconstructions on bruno.

@mattersoflight feel free to make additional README edits on this branch directly.

mattersoflight · 2025-04-01T00:05:40Z

@talonchandler I finally got around to finalizing the README. I like the current structure (overview, summary of methods with illustrations and references, links to examples).

I started an issue to collect images/videos that we can link: [DOCS] Images and videos for README #443
Please add the new logo at the top of the README.

This branch can be merged after this.

Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

talonchandler · 2025-04-02T18:49:49Z

Ready to merge IMO. Re-requesting review from @ziw-liu. Thanks all!

ziw-liu

Thanks! @talonchandler do you want to bump the current head of main as v2.2.1 (we have a v2.2.1b0) before merging?

talonchandler · 2025-04-02T20:36:33Z

Good idea! Just bumped and released 2.2.1. Merging. Thanks @ziw-liu.

talonchandler and others added 30 commits November 3, 2022 15:32

Improve documentation

dccceed

Delete examples/__init__.py

fce4e62

TC + ZL script improvements

87efe8d

bump napari-hub-preview-action version to fix CI

bc88dd0

Merge pull request #251 from mehta-lab/napari-hub-action-fix

5c4e91a

Bump napari-hub-preview-action version to fix CI

Remove unsupported calibration notebook

71c4591

Replace defunct notebooks with working scripts

403aa61

Document script workflows

869525e

Remove unused import

245014a

Improve documentation

cd6d519

Delete examples/__init__.py

5501ea6

TC + ZL script improvements

7566ce5

Import qtpy in gui.py

e4105bb

Add documentation for changing the file in place

1742c8a

90 degree orientation offset checkbox (#248)

fe847f1

* Pol offset checkbox * apply +90 degree offset when box is checked * remove debug message Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

Merge branch 'main' into PyQt5-to-qtpy

4f154eb

human-readable time stamp and open in napari

7af5af3

suppress markdown linter complaints

81577ac

add gnu sed hint

cc8d89c

Fix typo

5cf4af2

Merge pull request #252 from mehta-lab/PyQt5-to-qtpy

97fc4cf

Import `qtpy` instead of `PyQt5` in autogenerated `gui.py`

Merge branch 'recon-scripts' of https://github.com/mehta-lab/recOrder …

9c35edd

…into recon-scripts

Remove hidden characters in plugin guide

ef92a34

Improve readability of timestamps

5f6f0d0

Fix mismatched bold

61615c6

🇺🇸 focussing -> focusing

5898a9a

Improve create_preset_voltage.png

8a61133

Typo

119c29a

Remove extra background info

b947e93

talonchandler and others added 5 commits March 6, 2025 14:59

Remove recorder image references (#189)

b5a7a25

* ignore waveorder/_version.py * update recOrder README figure * updates plugin logo

don't save recorder version

bfe8741

clean "recOrder" from docs

6849375

minor docs fix

bd40f79

talonchandler marked this pull request as ready for review March 8, 2025 01:25

talonchandler mentioned this pull request Mar 26, 2025

Move biahub deconvolve to waveorder czbiohub-sf/biahub#63

Open

ziw-liu reviewed Mar 26, 2025

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Comment thread .github/workflows/test.yml

ziw-liu reviewed Mar 26, 2025

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Comment thread setup.py Outdated

mattersoflight added 2 commits March 31, 2025 16:43

update README: phase from defocus

7cb5453

add refs for fluorescence reconstruction

c7090ca

talonchandler added 3 commits April 2, 2025 10:54

logo as top-level headline

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remove setup.py

f5d9b7f

75%-size logo

10ac8d1

ziw-liu reviewed Apr 2, 2025

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Comment thread README.md Outdated

talonchandler and others added 4 commits April 2, 2025 11:16

smaller

bb2e157

Add quotes to pip install "waveorder[all]"

34938df

Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>

try again w/ <img> attributes

c2d4528

even smaller

f2852a5

talonchandler requested a review from ziw-liu April 2, 2025 18:49

ziw-liu reviewed Apr 2, 2025

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Comment thread README.md Outdated

remove mention of confocal fluorescence reconstruction

394e442

ziw-liu approved these changes Apr 2, 2025

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talonchandler merged commit 8315e00 into main Apr 2, 2025
8 checks passed

ziw-liu added this to the waveOrder v3 milestones milestone May 22, 2025

talonchandler deleted the recorder-merge branch April 20, 2026 21:10

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Merge `recOrder` into `waveorder` #183

Merge `recOrder` into `waveorder` #183
talonchandler merged 1377 commits intomainfrom
recorder-merge

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