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Add napari-btrack-reader to this package #115

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merged 14 commits into from
May 30, 2022

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dstansby
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@dstansby dstansby commented Apr 19, 2022

This adds the napari reader as an optional napari plugin to this package. This is entireley optional, and I've configured most of the tests to check that the btrack can still be run fine without napari installed. To check that the optional napari bits work there is now an extra tox environment that runs the tests with napari installed. I've also added some docs on how users can install the dependencies needed for the napari plugin.

I anticipate we will add btrack-napari in a similar way in a separate PR in the future.

Fixes https://github.com/lowe-lab-ucl/napari-btrack/issues/7
Fixes lowe-lab-ucl/napari-btrack-reader#3

@dstansby dstansby force-pushed the napari-reader branch 4 times, most recently from ae47ad5 to 4653d22 Compare April 20, 2022 13:45
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codecov-commenter commented Apr 20, 2022

Codecov Report

Merging #115 (842c9a0) into main (443f984) will decrease coverage by 0.08%.
The diff coverage is 76.66%.

@@            Coverage Diff             @@
##             main     #115      +/-   ##
==========================================
- Coverage   80.79%   80.71%   -0.09%     
==========================================
  Files          13       14       +1     
  Lines        1432     1462      +30     
==========================================
+ Hits         1157     1180      +23     
- Misses        275      282       +7     
Impacted Files Coverage Δ
btrack/napari/reader.py 76.66% <76.66%> (ø)

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dstansby commented May 9, 2022

@quantumjot could you install the napari-hub preview app on this repository, so we can get the preview comments: https://github.com/apps/napari-hub ?

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could you install the napari-hub preview app on this repository

Should be done now.

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deprecated-napari-hub-preview-bot bot commented May 10, 2022

Preview page for your plugin is ready here:
https://preview.napari-hub.org/quantumjot/BayesianTracker/115
Updated: 2022-05-25T11:57:47.278623

@dstansby dstansby changed the title First pass at adding napari reader Add napari-btrack-reader to this package May 10, 2022
@dstansby dstansby marked this pull request as ready for review May 10, 2022 13:39
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@alessandrofelder alessandrofelder left a comment

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Looks largely good!
Some very minor points that I think were there before this PR in the other repo.
Variable names could be improved a bit, I think? (but as part of a separate PR)

btrack/napari/reader.py Outdated Show resolved Hide resolved
tests/napari/test_reader.py Outdated Show resolved Hide resolved
tests/napari/test_reader.py Outdated Show resolved Hide resolved
tests/napari/test_reader.py Show resolved Hide resolved
btrack/napari/reader.py Outdated Show resolved Hide resolved
dstansby and others added 2 commits May 23, 2022 12:51
Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
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@paddyroddy paddyroddy left a comment

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Nothing critical but some suggestions which should improve the code quality

.github/workflows/napari-hub-preview.yml Outdated Show resolved Hide resolved
btrack/napari/reader.py Outdated Show resolved Hide resolved
btrack/napari/reader.py Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
tests/conftest.py Outdated Show resolved Hide resolved
tests/napari/test_reader.py Show resolved Hide resolved
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I have addressed the comments in the PR since I've reviewed so going to merge

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deprecate this in favour of adding reader to napari-btrack plugin?
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