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0.2.0 integration PR #219

Merged
merged 41 commits into from
Oct 6, 2022
Merged

0.2.0 integration PR #219

merged 41 commits into from
Oct 6, 2022

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talonchandler
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Please excuse this hodge-podge PR full of integration fixes found during integration testing and debugging.

talonchandler and others added 19 commits October 1, 2022 11:18
@talonchandler
Merge branch 'small-swing-fix' into 0.2.0-integration
8b7d018
@talonchandler
Fix tab order
fa56851
@talonchandler
Fix typos
9c7f2b3
@talonchandler
Format 4-state in the same way as 5-state
a7beef0
@talonchandler
Remove fluorescence from README figure
3d765cb
@talonchandler
Merge branch '0.2.0-integration' of https://github.com/mehta-lab/recO…
6bfcede 
…rder into 0.2.0-integration
@talonchandler
Misc automation scripts
7d728b1
@ziw-liu
avoid overriding recorder
6f82340
@ziw-liu
semi-automate stage movement
0419c72
@talonchandler
Merge branch '0.2.0-integration' of https://github.com/mehta-lab/recO…
16aa166 
…rder into 0.2.0-integration
@talonchandler
Merge branch 'bg-stage-move' into 0.2.0-integration
2701537
@talonchandler
Merge branch 'main' into 0.2.0-integration
bae9611
@talonchandler
Remove unneeded scripts
f2a4fac
@talonchandler
Remove pre-processing from reconstruction worker
29a33e0
@talonchandler
Typo
f0070e6
@talonchandler
Comment typo
b6c7b26
@ziw-liu
fix set xy position call
df32669
@ziw-liu
address pycromanager Java object issue
92d9816
@talonchandler
Warn user if MM config is misconfigured
37a8816
@codecov-commenter
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codecov-commenter commented Oct 4, 2022 •
edited
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Codecov Report

Merging #219 (870935f) into main (f7946b9) will decrease coverage by 0.16%.
The diff coverage is 0.00%.

@@            Coverage Diff             @@
##             main     #219      +/-   ##
==========================================
- Coverage   10.17%   10.00%   -0.17%     
==========================================
  Files          39       40       +1     
  Lines        5190     5278      +88     
==========================================
  Hits          528      528              
- Misses       4662     4750      +88
Impacted Files Coverage Δ
recOrder/calib/Calibration.py 0.00% <0.00%> (ø)
recOrder/io/utils.py 0.00% <0.00%> (ø)
recOrder/plugin/widget/main_widget.py 0.00% <0.00%> (ø)
recOrder/plugin/workers/reconstruction_workers.py 0.00% <ø> (ø)
recOrder/scripts/repeat-cal-acq-rec.py 0.00% <0.00%> (ø)
recOrder/scripts/repeat-calibration.py 0.00% <0.00%> (ø)

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deprecated-napari-hub-preview-bot bot commented Oct 4, 2022 •
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Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/219
Updated: 2022-10-05T22:00:25.297728

@ziw-liu ziw-liu added bug Something isn't working enhancement New feature or request labels Oct 4, 2022
@ziw-liu ziw-liu added this to the 0.2.0 milestone Oct 4, 2022
@talonchandler
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I just tested the fixes for #217 and they're working as I expect. I will link that issue and move to testing the automation scripts.

@talonchandler talonchandler linked an issue Oct 4, 2022 that may be closed by this pull request
[BUG] Check that LF States are defined correctly for the given calibration mode #217
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@talonchandler
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The automation script is working well. Great job, Ziwen.

I'm going to write up the docs for the new installation, then let's merge this.

talonchandler and others added 16 commits October 4, 2022 14:34
@talonchandler
Remove unused import
0b3f4db
@ziw-liu
remove unused import
aec186f
@ziw-liu
clean dir info
f98cae7
@talonchandler
Reduce "Value" in default overlay
765a263
@mattersoflight
fixed bugs ret_ori_overlay method
960976a
@mattersoflight
updated calls to ret_ori_overlay
81a6a75
@ziw-liu
Fix 'Load Default Config' in offline mode (#226)
fd56dae 
* load default config from file

* fix file path

* fix config loading
@ziw-liu
fix accidental syntax error
a78a17c
@mattersoflight
Merge branch 'rescale-hsv' of https://github.com/mehta-lab/recOrder i…
eeececd 
…nto rescale-hsv
@talonchandler
Merge pull request #223 from mehta-lab/rescale-hsv
870935f 
Reduce "Value" in default overlay
@talonchandler
Add "Phase2D" to QLIPP pipeline label
7012084
@ziw-liu
remove microscope params from calibration metadata
1fbbb18
@talonchandler
Comment _microscope_params as candidate for deletion
e9da838
@talonchandler
Merge pull request #227 from mehta-lab/rm-microscope-params
e932954 
Remove microscope parameters from calibration metadata
@talonchandler
Remove "Optional" text from calibration_metadata field
8bd940f
@talonchandler
Merge branch '0.2.0-integration' of https://github.com/mehta-lab/recO…
00460a3 
…rder into 0.2.0-integration
@talonchandler
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@ziw-liu and I just finished a final round of testing. We are merging this branch and releasing its HEAD as 0.2.0.

@talonchandler talonchandler merged commit 7cbda15 into main Oct 6, 2022
@talonchandler talonchandler deleted the 0.2.0-integration branch October 6, 2022 17:07
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@ziw-liu ziw-liu ziw-liu left review comments

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@talonchandler talonchandler

@ziw-liu ziw-liu

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bug Something isn't working enhancement New feature or request
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0.2.0
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Successfully merging this pull request may close these issues.

[BUG] Check that LF States are defined correctly for the given calibration mode
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@talonchandler @codecov-commenter @ziw-liu @mattersoflight