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Version 1 release 🥳 #146

Merged
merged 6 commits into from
Nov 6, 2023
Merged

Version 1 release 🥳 #146

merged 6 commits into from
Nov 6, 2023

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willGraham01
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@willGraham01 willGraham01 commented Oct 30, 2023 •
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Staging the changes for the upcoming release of v1.0.0 of brainreg along with v1 of BrainGlobe.

See brainglobe/BrainGlobe#38 for details.

Upon merging, we will:

willGraham01 and others added 4 commits October 27, 2023 16:46
@willGraham01 @stephenlenzi
@adamltyson @neuromusic @dstansby @paddyroddy @alessandrofelder @SimaoBolota-MetaCell @pre-commit-ci
Merge brainreg-napari into brainreg (#145)
5add675 
* initial commit

* adds gui

* removes deprecated folder

* Update README.md

* Update README.md

* adds brainreg to requirements

* renames gui label from register to brainreg

* renames register to brainreg-register

* adds brainglobe repo to setup.py

* Delete requirements.txt

* makes output destination selectable in GUI

* Update entry point

* removes sort_input_file option

* Update setup.py

* updates project urls in setup.cfg

* Update support link

* fixes output path to directory

* re adds sort_input_file as hardcoded variable

* adds atlas options as dropdown

* adds showing the results of registration

* removed a global declaration

* minor refactoring

* deleted commented code

* fixes logging output

* only loads relevant output data

* outputs scaled overlay of boundaries and atlas

* imports and groups segment plugin with register

* lowers requirements from python >=3.7 to >=3.6 and removes project url from setup.py

* removes superfluous pixel args from logging

* Update readme, setup.py & general reformatting (#16)

* update gitignore

* Update setup.py

* update readme

* format with black

* remove docs

* remove unused import

* delete tests for now

* format imports

* Release (#18)

* Update setup.py

* add bump2version config

* Bump version: 0.0.1 → 0.0.2-rc0

* remove reqs from manifest

* disable tests on GH actions for now

* fixes reset_defaults by ignoring atlas dropdown

* adds additional channels functionality

* Update OS compatibility & update use of napari API

* Bump (#23)

* Bump version: 0.0.2-rc1 → 0.0.2-rc2

* Bump version: 0.0.2-rc2 → 0.0.2-rc3

* Bump version: 0.0.2-rc3 → 0.0.3-rc0

* Add tooltips (#25)

* change default parameter names

* Add tooltips

* Bump version: 0.0.3-rc0 → 0.0.4-rc0

* Update README.md

* Update broken image URL

* Add categories and preview page workflow for the napari hub (#27)

* adds EDAM Bioimaging labels

* adds Action for napari hub preview service

* Update citation

* Update README.md

* Convert to npe2

* Add pyqt library setup

* Fix manifest

* Add basic smoke test

* Add link to contributing guide

* Add pre-commit

* Fix manifest

* Add sample data

* Add example script

* Fix pre-commit and manifest

* Use g-node.org for sample data

* Clean up example

Make noqa more specific

* Set plugin values from metadata

* Add a test for sample data

* Add pooch to requirements

Move pooch req comment

* Test loading sample data through napari

* Set sensible contrast limits

* pre-commit fixes

* Add Python 3.10 support, drop 3.7 support

* Add an integration test

Type block

* Fix getting additional layers

* Factor out add_image_layers function

* Remove arguments from run()

* Refactor blocking/non-blocking behaviour

* Store metadata in napari layers

* Use re-usable action for running tests

* Give better name to add_image_layers

* Add error if trying to load non-existent registration

* Return layers from add_registered_image_layers

* Bump version: 0.0.4-rc0 → 0.0.5-rc0

* Input orientation check (#44)

* Add many features:

- debug mode
- interactive way of checking input orientation
- brain geometry
- save annotations with original orientation

* add comments and docstring.

* Crop the reference atlas when using interactive orientation check with half brains.

* Fix a bug where run throw an error.

* Fix typo in docstrings

* format

* Add info to use if data not loaded before checking orientation

* Update docstrings

Co-authored-by: Jules Scholler <[email protected]>

* Update readme

* format readme

* Add codecov badge

* Added citation file (#45)

* Added citation file

* Changes according to PR comments

* Updated Citation file 

Updated citation file to have the preferred citation coming from the article/book when available

Co-authored-by: Simão sá <[email protected]>

* Update packaging (#46)

* update pre-commit config

* update args for new brainreg version

* lint

* update manifest

* Bump version: 0.0.5-rc0 → 0.0.5-rc1

* update testing

* update packaging

* update requirements

* update manifest

* move entry point to pyproject.toml

* update hub preview version

* update release for use with setuptools_scm

* migrate from BG to neuroinformatics actions

* add setuptools_scm to dev requirements

* reduce number of tested version

* update python versions tested

* update release

* [Napari HUB cli] Metadata enhancement suggestions (#47)

* Copy "Display Name" from secondary to primary file

Display Name was found in a secondary file and copied in the primary one:
* (found here)  "pyproject.toml"
* (copied here) "brainreg_napari/napari.yaml"

* Copy "Summary Sentence" from secondary to primary file

Summary Sentence was found in a secondary file and copied in the primary one:
* (found here)  "pyproject.toml"
* (copied here) ".napari/config.yml"

* Use standard pre-commit config (#51)

* Add standard pre-commit config

* Automated pre-commit fixes

* Testing clean (#50)

* Use composite test action

Fix use-xvfb argument

* Clean tox.ini

* Don't fail fast

* Remove old setup steps

* Clean up dev dependencies

Add pyqt5 back as a dev dep

* Try passing display env

Put back passenv in tox

* Use selected atlas to check orientation

* Add orientation check tests

* [pre-commit.ci] pre-commit autoupdate (#57)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.240 → v0.0.272](astral-sh/ruff-pre-commit@v0.0.240...v0.0.272)
- [github.com/psf/black: 23.1.0 → 23.3.0](psf/black@23.1.0...23.3.0)
- [github.com/pre-commit/mirrors-mypy: v0.991 → v1.3.0](pre-commit/mirrors-mypy@v0.991...v1.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update links (#56)

* Update README.md

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update dependency (imlib -> brainglobe-utils) (#58)

* [pre-commit.ci] pre-commit autoupdate (#59)

updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 → v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.4.1](pre-commit/mirrors-mypy@v1.3.0...v1.4.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#60)

updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 → v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#61)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.276 → v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#62)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.277 → v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278)
- [github.com/psf/black: 23.3.0 → 23.7.0](psf/black@23.3.0...23.7.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#63)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.278 → v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#65)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.280 → v0.0.281](astral-sh/ruff-pre-commit@v0.0.280...v0.0.281)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#66)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.281 → v0.0.282](astral-sh/ruff-pre-commit@v0.0.281...v0.0.282)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#67)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 → v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)
- [github.com/pre-commit/mirrors-mypy: v1.4.1 → v1.5.0](pre-commit/mirrors-mypy@v1.4.1...v1.5.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#68)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 → v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)
- [github.com/pre-commit/mirrors-mypy: v1.5.0 → v1.5.1](pre-commit/mirrors-mypy@v1.5.0...v1.5.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#70)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 → v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update .pre-commit-config.yaml (#71)

* [pre-commit.ci] pre-commit autoupdate (#72)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.286 → v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#74)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.287 → v0.0.292](astral-sh/ruff-pre-commit@v0.0.287...v0.0.292)
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Test on Python 3.11 (#49)

* Use composite test action

Fix use-xvfb argument

* Clean tox.ini

* Don't fail fast

* Remove old setup steps

* Clean up dev dependencies

Add pyqt5 back as a dev dep

* Try passing display env

Put back passenv in tox

* Test on Python 3.11

* Update Python versions

---------

Co-authored-by: Adam Tyson <[email protected]>

* Delete .github/workflows/plugin_preview.yml (#75)

* Write safe concat function

* Use safe concat of dataframes

* Fix logic of safe concat method

* pre-commit pass

* Add unit test to aplease codecov overlords

* Restructure as brainreg/core, adjust imports accordingly

* Make package installable again

* Fix test import

* Rework package structure to be compatible with brainreg-core

* Update example code with new structure

* Rename napari plugin to drop the -napari suffix

* Exclude the to-be-reconciled READMEs from the manifest

---------

Co-authored-by: stephen <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Adam Tyson <[email protected]>
Co-authored-by: Justin Kiggins <[email protected]>
Co-authored-by: David Stansby <[email protected]>
Co-authored-by: Patrick Roddy <[email protected]>
Co-authored-by: Alessandro Felder <[email protected]>
Co-authored-by: Jules Scholler <[email protected]>
Co-authored-by: Simão Bolota <[email protected]>
Co-authored-by: Simão sá <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@willGraham01 @adamltyson
Reconcile the core and napari READMEs (#147)
7b03341 
* Parse existing brainreg readme

* Incorporate plugin readme and update manifest

* Apply Adam's updates

Co-authored-by: Adam Tyson <[email protected]>

---------

Co-authored-by: Adam Tyson <[email protected]>
@willGraham01 @adamltyson
Reconcile the core and napari READMEs (#147)
d27f93d 
* Parse existing brainreg readme

* Incorporate plugin readme and update manifest

* Apply Adam's updates

Co-authored-by: Adam Tyson <[email protected]>

---------

Co-authored-by: Adam Tyson <[email protected]>
@willGraham01
Merge branch 'main' into bgv1-dev-branch.
c8ba83c 
Includes the move of safe_pandas_concat to brainglobe-utils.
@willGraham01 willGraham01 marked this pull request as ready for review November 2, 2023 14:31
@willGraham01 willGraham01 requested a review from a team November 2, 2023 14:31
@willGraham01 willGraham01 changed the title BrainGlobe V1 release Version 1 release 🥳 Nov 2, 2023
@adamltyson
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adamltyson commented Nov 2, 2023 •
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Is this going to break cellfinder? e.g. https://github.com/brainglobe/cellfinder/blob/21f724b46c84cf2c2489d1d4347c6c19f9277b45/cellfinder/main.py#L45

@willGraham01
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Is this going to break cellfinder? e.g. https://github.com/brainglobe/cellfinder/blob/21f724b46c84cf2c2489d1d4347c6c19f9277b45/cellfinder/main.py#L45

Yes (and the workflows repo dev branch too). Let me open a cellfinder PR to address the imminent breakage and add it to the list of things to update in during the breakage period. We won't be able to validate the fix until we get into the breakage-hour of course, but it should just be a substitution of brainreg -> brainreg.core.

alessandrofelder
alessandrofelder previously approved these changes Nov 2, 2023
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One tiny comment - and yes, we should make sure that we don't break cellfinder if possible :)

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@willGraham01 willGraham01 mentioned this pull request Nov 3, 2023
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@willGraham01
Update with brainreg-segment rename to brainglobe-segmentation (#149)
ab99d94 
* Update with brainreg-segment rename to brainglobe-segmentation

* Update pyproject.toml
@alessandrofelder alessandrofelder merged commit e91a132 into main Nov 6, 2023
12 of 14 checks passed
@alessandrofelder alessandrofelder deleted the bgv1-dev-branch branch November 6, 2023 12:09
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@willGraham01 @adamltyson @alessandrofelder