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Merge cellfinder-core and cellfinder-napari into this package #262

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wants to merge 680 commits into from
Closed

Merge cellfinder-core and cellfinder-napari into this package #262

wants to merge 680 commits into from

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willGraham01
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@willGraham01 willGraham01 commented Nov 27, 2023 •
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brainglobe/BrainGlobe#46

Merges cellfinder-core and cellfinder-napari into this package, still called cellfinder.

  • Purges old cellfinder files. They're still in the history but are wiped when merging.

TODO:

  • Check that cellfinder-CLI tests from workflows are correctly found and run against

alessandrofelder and others added 30 commits March 10, 2023 11:23
@alessandrofelder
fix linting
da1dd7e
@dstansby
Merge pull request #93 from brainglobe/remove-pkg_resources
df1ea3b 
avoid using deprecated pkg_resources
@alessandrofelder
Fixture for programmatic creation of synthetic data (#94)
680ec0b 
* create a fixture for synthetic data generation

* add a test checking cell detection works on synthetic data

* fix linting

* fix line length
@alessandrofelder
Merge pull request #152 from brainglobe/update-yaml-filter
c1e62ea 
Update yaml filter
@dstansby
Basic working structure detection test
f5d90c2
@dstansby
Add parametrization to detection test
a17cd38
@dstansby
Add a two pixel structure test
5c7739d
@dstansby
Add some more connected test cases
e379aed
@dstansby
Move structure detection tests to existing file
0e0d320
@dstansby
Fix signal array typing
36ceaf9
@dstansby
Build wheels on macOS arm (#76)
b1b2f7d
@dstansby
Add a test for structure grouping
1e5f295
@dstansby
Use pyproject (#151)
d66f030 
* Use pyproject

* Remove pytest-xvfb from deps
@dstansby
Add two more test cases
ff1530b
@alessandrofelder
Merge pull request #97 from dstansby/connected-component-test
93e4b0d 
Add connected component labelling unit tests
@dstansby
Merge pull request #78 from dstansby/filter-setup-typing
c6b0493 
Filter setup typing
@dstansby
Test structure detection with different dtypes (#99)
212dced 
* Rename get_max_value > get_max_possible_value

* Add test for structure detection with different dtypes

* Fix uint8 structure detection

* Add comment about magic numbers

* Add a type hint
@dstansby
Allow cellfinder tests to run on branches (#101)
d60fc02 
* Fix cellfinder tests on main branch

* Prevent double running CI

* Use environment variable for repository name
@dstansby
Pin tensorflow to < 2.12.0
2a487dd
@alessandrofelder
Merge pull request #104 from dstansby/tensorflow-pin
23e1353 
Pin tensorflow to < 2.12.0
@alessandrofelder @dstansby
add a 2d filter benchmarking script
0e2dfbd
@alessandrofelder @dstansby
remove cython 2d filter extension
8add55d
@alessandrofelder @dstansby
move to a numba 2d filter
a0417e1
@alessandrofelder @dstansby
fix linting
83e75cf
@alessandrofelder @dstansby
random*65535 -> randint
036c2e3 
Co-authored-by: David Stansby <[email protected]>
@alessandrofelder @dstansby
add pyinstrument as dev dependency
d6a8bbd
@alessandrofelder @dstansby
spread too long line over several
3df702c
@dstansby
Isolate code that runs the 3D filter
9af4bc3
@dstansby
Add 3D filter benchmark
5a50970
@dstansby
Add pure Python structure detection
9bcc9e8
willGraham01 and others added 23 commits August 23, 2023 16:04
@willGraham01
Move cellfinder.napari tests into test directory
058eeb7
@willGraham01
Move cellfinder napari config files into temporary subdirectory
a57c5dd
@willGraham01
Reconcile licenses
7c32862
@willGraham01
Reconcile pre-commits
3263080
@willGraham01
Reconcile pyproject.tomls
f115785
@willGraham01
Reconcile manifests
52b872b
@willGraham01
Reinstate cellfinder-core changelog
b84bd24
@willGraham01
Reinstate .codedov
6075227
@willGraham01
Reinstate plugin preview workflow
0fdefea
@willGraham01
Reconcile tox
0dec9bc
@willGraham01
Reconcile READMEs temporarily
a14889f
@willGraham01
Reconcile CI workflows
d907858
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
1e7829b 
for more information, see https://pre-commit.ci
@willGraham01
mypy to ignore things
dfcedf7
@willGraham01
Merge branch 'cellfinder-merge' of github.com:brainglobe/cellfinder-c…
3627c62 
…ore into cellfinder-merge
@willGraham01
Disable mypy for time being
f18f840
@willGraham01
Fix plugin things by moving to non-flat directory struture
3bc4f4e
@willGraham01
Move to flat directory structure.
e276749
@willGraham01
Explicitly add napari.yaml to MANIFEST
67dec4c
@willGraham01
Make napari functionality optional
9fe13ff
@willGraham01
Remove napari plugin preview workflow (#251)
d086030
@willGraham01
Clean out cellfinder (old) to make way for merge
e6a5521
@willGraham01
Merge cellfinder-core and cellfinder-napari into this package.
7b29e91
@willGraham01 willGraham01 changed the base branch from main to prepare-for-migration November 27, 2023 14:33
@willGraham01 willGraham01 mentioned this pull request Nov 27, 2023
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Closing in favour of archiving the current main branch, rather than deleting the contents entirely.

@willGraham01 willGraham01 deleted the merge-core-and-plugin branch November 28, 2023 13:51
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5 participants
@willGraham01 @alessandrofelder @dstansby @adamltyson @sfmig