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save_original_resolution breaks additional_image_downsample #50

Closed
npeschke opened this issue Dec 7, 2021 · 4 comments
Closed

save_original_resolution breaks additional_image_downsample #50

npeschke opened this issue Dec 7, 2021 · 4 comments

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@npeschke
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npeschke commented Dec 7, 2021

the save_original_orientation option is a great addition but it redefines atlas

brainreg/brainreg/backend/niftyreg/run.py

Lines 113 to 116 in 5164329

if save_original_orientation:
atlas = imio.load_any(niftyreg_paths.registered_atlas_path).astype(
np.uint32, copy=False
)

and thus, looses the atlas.resolution field which is needed later in additional_image_downsample

brainreg/brainreg/backend/niftyreg/run.py

Lines 189 to 193 in 5164329

save_nii(
downsampled_brain,
atlas.resolution,
tmp_downsampled_brain_path,
)

npeschke added a commit to npeschke/brainreg that referenced this issue Dec 7, 2021
@npeschke
fix brainglobe#50
d88ad2e 
renaming atlas in save_original_orientation
@npeschke npeschke mentioned this issue Dec 7, 2021
Merged
@adamltyson
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Thanks for this @npeschke, I released an RC with your fix (pip install brainreg==0.3.1rc0). Would you mind giving it a test before I make a full release?

@npeschke
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npeschke commented Dec 7, 2021

Just tested it and it ran fine with the following options

conda create -y -n test_brainreg -c conda-forge python=3.9 scipy && conda activate test_brainreg && pip install brainreg==0.3.1rc0
brainreg reg_file_paths.txt brainreg_test -d downsample_file_paths.txt -v 6 3.25 3.25 --debug --save-original-orientation --atlas allen_mouse_25um --orientation LPI

@adamltyson
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Great, thanks. I'll release 0.3.1 later today.

@npeschke
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npeschke commented Dec 7, 2021

Thanks for the quick response!

willGraham01 pushed a commit that referenced this issue Oct 27, 2023
@dstansby
Testing clean (#50)
9482efd 
* 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
alessandrofelder added a commit that referenced this issue Oct 27, 2023
@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)

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

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

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- [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)

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- [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>
alessandrofelder added a commit that referenced this issue Nov 6, 2023
@willGraham01 @stephenlenzi
@adamltyson @neuromusic @dstansby @paddyroddy @alessandrofelder @SimaoBolota-MetaCell @pre-commit-ci
Version 1 release 🥳 (#146)
e91a132 
* Merge `brainreg-napari` into `brainreg` (#145)

* 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>

* Reconcile the `core` and `napari` READMEs (#147)

* 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]>

* Reconcile the `core` and `napari` READMEs (#147)

* 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]>

* Update README.md

* Update with brainreg-segment rename to brainglobe-segmentation (#149)

* Update with brainreg-segment rename to brainglobe-segmentation

* Update pyproject.toml

---------

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>
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