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.

Sign up for GitHub

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

Jump to bottom

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

Closed
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

Conversation

willGraham01
Copy link
Collaborator

@willGraham01 willGraham01 commented Nov 27, 2023 •
edited
Loading

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 <dstansby@gmail.com>
@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
Closed
47 tasks
@willGraham01
Copy link
Collaborator Author

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
5 participants
@willGraham01 @alessandrofelder @dstansby @adamltyson @sfmig