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Cellfinder merge #218

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Cellfinder merge #218

wants to merge 268 commits into from
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Commits on Apr 27, 2021

  1. update links

    @adamltyson
    adamltyson committed Apr 27, 2021
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  2. Update readme

    @adamltyson
    adamltyson committed Apr 27, 2021
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  3. Bump version: 0.0.6 → 0.0.7-rc0

    @adamltyson
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  4. Bump version: 0.0.7-rc0 → 0.0.7

    @adamltyson
    adamltyson committed Apr 27, 2021
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  5. Create cell layer metadata for I/O

    @adamltyson
    adamltyson committed Apr 27, 2021
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  6. Bump version: 0.0.7 → 0.0.8-rc0

    @adamltyson
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  7. Bump version: 0.0.8-rc0 → 0.0.8

    @adamltyson
    adamltyson committed Apr 27, 2021
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  8. tooltips

    @adamltyson
    adamltyson committed Apr 27, 2021
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  9. tooltip instruction

    @adamltyson
    adamltyson committed Apr 27, 2021
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  10. Bump version: 0.0.8 → 0.0.9-rc0

    @adamltyson
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  11. Bump version: 0.0.9-rc0 → 0.0.9

    @adamltyson
    adamltyson committed Apr 27, 2021
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Commits on Apr 28, 2021

  1. update readme

    @adamltyson
    adamltyson committed Apr 28, 2021
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Commits on May 7, 2021

  1. Update README.md

    @adamltyson
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Commits on May 8, 2021

  1. Add logo to manifest (#17)

    @adamltyson
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  2. Bump version: 0.0.10-rc5 → 0.0.10

    @adamltyson
    adamltyson committed May 8, 2021
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  3. update manifest

    @adamltyson
    adamltyson committed May 8, 2021
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Commits on Jun 10, 2021

  1. update supported python versions

    @adamltyson
    adamltyson committed Jun 10, 2021
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  2. update cellfinder-core version

    @adamltyson
    adamltyson committed Jun 10, 2021
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  3. update citation

    @adamltyson
    adamltyson committed Jun 10, 2021
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  4. Bump version: 0.0.10 → 0.0.11-rc0

    @adamltyson
    adamltyson committed Jun 10, 2021
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  5. Bump version: 0.0.11-rc0 → 0.0.11

    @adamltyson
    adamltyson committed Jun 10, 2021
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Commits on Jun 16, 2021

  1. Update use of deprecated napari API to viewer.layers.selection

    @adamltyson
    adamltyson committed Jun 16, 2021
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  2. allow overwrite of training data layers

    @adamltyson
    adamltyson committed Jun 16, 2021
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  3. Bump version: 0.0.11 → 0.0.12-rc0

    @adamltyson
    adamltyson committed Jun 16, 2021
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  4. Bump version: 0.0.12-rc0 → 0.0.12

    @adamltyson
    adamltyson committed Jun 16, 2021
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Commits on Jun 21, 2021

  1. run tests on PR

    @adamltyson
    adamltyson committed Jun 21, 2021
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Commits on Jun 22, 2021

  1. update twitter

    @adamltyson
    adamltyson committed Jun 22, 2021
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Commits on Jun 28, 2021

  1. Update URL

    @adamltyson
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Commits on Jun 29, 2021

  1. Bump version: 0.0.12 → 0.0.13-rc0

    @adamltyson
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  2. Bump version: 0.0.13-rc0 → 0.0.13

    @adamltyson
    adamltyson committed Jun 29, 2021
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  3. update setup.py

    @adamltyson
    adamltyson committed Jun 29, 2021
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  4. Bump version: 0.0.13 → 0.0.14-rc0

    @adamltyson
    adamltyson committed Jun 29, 2021
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  5. Bump version: 0.0.14-rc0 → 0.0.14

    @adamltyson
    adamltyson committed Jun 29, 2021
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  6. update license

    @adamltyson
    adamltyson committed Jun 29, 2021
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  7. Bump version: 0.0.14 → 0.0.15-rc0

    @adamltyson
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  8. Bump version: 0.0.15-rc0 → 0.0.15

    @adamltyson
    adamltyson committed Jun 29, 2021
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  9. update license

    @adamltyson
    adamltyson committed Jun 29, 2021
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  10. Bump version: 0.0.15 → 0.0.16-rc0

    @adamltyson
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  11. Bump version: 0.0.16-rc0 → 0.0.16

    @adamltyson
    adamltyson committed Jun 29, 2021
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  12. add user support

    @adamltyson
    adamltyson committed Jun 29, 2021
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  13. Bump version: 0.0.16 → 0.0.17-rc0

    @adamltyson
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  14. Bump version: 0.0.17-rc0 → 0.0.17

    @adamltyson
    adamltyson committed Jun 29, 2021
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  15. revert url changes

    @adamltyson
    adamltyson committed Jun 29, 2021
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  16. bump vesion

    @adamltyson
    adamltyson committed Jun 29, 2021
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  17. Bump version: 0.0.17 → 0.0.18-rc0

    @adamltyson
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  18. Bump version: 0.0.18-rc0 → 0.0.18

    @adamltyson
    adamltyson committed Jun 29, 2021
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Commits on Aug 4, 2021

  1. Fix tooltip typo

    @adamltyson
    adamltyson authored Aug 4, 2021
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Commits on Sep 22, 2021

  1. Update README.md

    @adamltyson
    adamltyson authored Sep 22, 2021
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  2. Update README.md

    @adamltyson
    adamltyson authored Sep 22, 2021
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  3. Fix typo

    @adamltyson
    adamltyson authored Sep 22, 2021
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  4. Update README.md

    @adamltyson
    adamltyson authored Sep 22, 2021
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  5. Update README.md

    @adamltyson
    adamltyson authored Sep 22, 2021
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Commits on Dec 21, 2021

  1. Add categories and preview page workflow for the napari hub (#30) 

    * adds EDAM Bioimaging labels

* adds Action for napari hub preview service
    @neuromusic
    neuromusic authored Dec 21, 2021
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Commits on Jan 20, 2022

  1. Migrate to napari plugin engine 2 (#33) 

    * yaml file added by automatic conversion

* apply instructions for manual part of migration
    @alessandrofelder
    alessandrofelder authored Jan 20, 2022
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Commits on Feb 2, 2022

  1. improve tooltip

    @alessandrofelder
    alessandrofelder committed Feb 2, 2022
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  2. Merge pull request #50 from brainglobe/improve-trained-model-tooltip 

    improve tooltip
    @alessandrofelder
    alessandrofelder authored Feb 2, 2022
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  3. include missing YAML files in sdist

    @alessandrofelder
    alessandrofelder committed Feb 2, 2022
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Commits on Feb 15, 2022

  1. Update README.md

    @adamltyson
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  2. reorder imports with isort 

    move TODOs to issues #52, #53
    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  3. move add_layers to separate python file

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  4. move threadworker to separate file

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  5. move default parameters to separate file

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  6. possible way to reduce number of arguments - dataclass for inputs

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  7. create detection input class to shorten code

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  8. pass data inputs as dict

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  9. restore defaults doesn't need event value argument

    @alessandrofelder
    alessandrofelder committed Feb 15, 2022
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  10. consistently use lowercase variable names internally

    @alessandrofelder
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Commits on Feb 17, 2022

  1. Merge pull request #51 from brainglobe/fix-manifest

    @dpshelio
    dpshelio authored Feb 17, 2022
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  2. add base class for inputs 

    - encapsulates persistent defaults
- widgets use defaults where needed
- customisable representation to pass inputs to cellfinder-core
    @alessandrofelder
    alessandrofelder committed Feb 17, 2022
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Commits on Feb 18, 2022

  1. Run pre-commit

    @paddyroddy
    paddyroddy committed Feb 18, 2022
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  2. Expand the pre-commit checks to other useful options

    @paddyroddy
    paddyroddy committed Feb 18, 2022
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  3. Add separate linting CI

    @paddyroddy
    paddyroddy committed Feb 18, 2022
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  4. Run pre-commit and fix besides mypy

    @paddyroddy
    paddyroddy committed Feb 18, 2022
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  5. Run future pre-commit hooks, mypy still fails

    @paddyroddy
    paddyroddy committed Feb 18, 2022
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  6. Merge pull request #60 from brainglobe/run-pre-commit 

    Run `pre-commit` and fix besides `mypy`
    @paddyroddy
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  7. Merge pull request #58 from brainglobe/expand-pre-commit-checks-add-ci 

    Expand pre commit checks and add ci
    @paddyroddy
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Commits on Feb 21, 2022

  1. Move badges (#61)

    @paddyroddy
    paddyroddy authored Feb 21, 2022
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Commits on Feb 23, 2022

  1. Merge main into reformat-structure branch (#64) 

    * include missing YAML files in sdist

* Expand the `pre-commit` checks to other useful options

* Add separate linting CI

* Run `pre-commit` and fix besides `mypy`

* Move badges (#61)

Co-authored-by: alessandrofelder <[email protected]>
Co-authored-by: David Pérez-Suárez <[email protected]>
    @paddyroddy @alessandrofelder @dpshelio
    3 people authored Feb 23, 2022
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  2. Change to linting, manifest, test (#66)

    @paddyroddy
    paddyroddy authored Feb 23, 2022
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Commits on Feb 25, 2022

  1. address review comments 

    - group widget sections in @magicgui arguments
- rename variables to match cellfinder_core keywords
- simplify logic to get defaults
- split functionality more meaningfully into files
    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  2. format with black

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  3. add some return types

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  4. make numerical widget rep private, and make step adapt to type if uns… 

    …pecified
    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  5. small stylistic improvements

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  6. fix small bug, fix step size for ints

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  7. Merge remote-tracking branch 'origin/reformat-restructure' into refor… 

    …mat-restructure
    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  8. fix botched merge

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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  9. Merge branch 'main' into reformat-restructure

    @alessandrofelder
    alessandrofelder committed Feb 25, 2022
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Commits on Mar 3, 2022

  1. Merge pull request #54 from brainglobe/reformat-restructure 

    Attempt at modularising/improving code legibility
    @alessandrofelder
    alessandrofelder authored Mar 3, 2022
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  2. Fix isort

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  3. Fix setuptools

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  4. Fix Optional[Path] typing

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  5. Fix missing Optional[Path]

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  6. Missed type in ClassificationInputs dataclass

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  7. Function has erroneous return type

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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  8. Ignore line due to mypy thinking its a list and a Path

    @paddyroddy
    paddyroddy committed Mar 3, 2022
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Commits on Mar 4, 2022

  1. Merge pull request #68 from brainglobe/fix-issue-59 

    Fix `mypy` now that the refactor PR has been merged
    @paddyroddy
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  2. Open error box if both images not specified

    @dstansby
    dstansby committed Mar 4, 2022
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Commits on Mar 8, 2022

  1. Add option to use pre-trained weights

    @dstansby
    dstansby committed Mar 8, 2022
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  2. Merge pull request #70 from dstansby/use-default-model 

    Add checkbox to use pre-trained weights
    @dstansby
    dstansby authored Mar 8, 2022
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  3. Merge pull request #69 from dstansby/no-data-error 

    Raise error box if no images specified
    @dstansby
    dstansby authored Mar 8, 2022
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Commits on Mar 9, 2022

  1. Add progress bar to detection

    @dstansby
    dstansby committed Mar 9, 2022
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Commits on Mar 11, 2022

  1. Update codecov action to v2

    @dstansby
    dstansby committed Mar 11, 2022
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  2. Merge pull request #73 from dstansby/progress-bars 

    Add a progress bar for detection
    @dstansby
    dstansby authored Mar 11, 2022
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  3. Merge pull request #78 from dstansby/codecov 

    Update codecov action to v2
    @paddyroddy
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  4. Add scroll bars to widget

    @dstansby
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  5. correct voxel size y default

    @alessandrofelder
    alessandrofelder committed Mar 11, 2022
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  6. Merge pull request #81 from brainglobe/correct-voxel-size-y 

    correct voxel size y default
    @paddyroddy
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Commits on Mar 15, 2022

  1. Merge pull request #79 from dstansby/scroll 

    Add scroll bars to widget
    @alessandrofelder
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  2. Add a basic widget test (#82) 

    * Add basic widget test

* Update comment on choosing a backend for tests

Co-authored-by: Alessandro Felder <[email protected]>

Co-authored-by: Alessandro Felder <[email protected]>
    @dstansby @alessandrofelder
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Commits on Mar 17, 2022

  1. Bump version: 0.0.18 → 0.0.19-rc0

    @adamltyson
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Commits on Mar 18, 2022

  1. Bump version: 0.0.19-rc0 → 0.0.19

    @adamltyson
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Commits on Mar 29, 2022

  1. Bump pre-commit black version to fix pre-commit (#89) 

    * Bump pre-commit black version to fix pre-commit

* Fix whitespace
    @dstansby
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  2. Update QT setup on github actions

    @dstansby
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  3. Merge pull request #90 from dstansby/qt-setup 

    Update QT setup on github actions
    @paddyroddy
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  4. Add sample data as plugin

    @dstansby
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  5. Move detection files to sub-folder

    @dstansby
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  6. Merge pull request #85 from dstansby/sample-data 

    Add sample data as plugin
    @paddyroddy
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  7. Merge pull request #91 from dstansby/detect-folder 

    Move detection files to sub-folder
    @paddyroddy
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Commits on Apr 5, 2022

  1. Add more docstrings and typing (#93) 

    * Add docstrings/typing to utils.py

* Add docstring to sample data

* Add docstrings/typing to thread_worker.py

* Add docstrings/typing to detect.py

* Add missing None return typing
    @dstansby
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Commits on Apr 6, 2022

  1. Use BrainGlobe composite actions to run tests (#94) 

    * Try using a re-usable action to run tests

* Use composite action to run linting

* Setup QT libraries

* Use composite action to run manifest check

* Use v1 of composite actions
    @dstansby
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  2. Add signature typing to curation.py (#101)

    @dstansby
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Commits on Apr 7, 2022

  1. Use napari show_info to communicate messages to users (#100) 

    * Use napari show_info to raise errors

* Renmove custom error/info box functions
    @dstansby
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Commits on Apr 11, 2022

  1. Add smoke test for curation widget (#102) 

    * Add simple curation widget test

* Rename detection test file

* Fix import order

* Convert comment to docstring in test

Co-authored-by: Patrick Roddy <[email protected]>

Co-authored-by: Patrick Roddy <[email protected]>
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Commits on Apr 22, 2022

  1. Drop Python 3.7 tests, add 3.10 tests

    @dstansby
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  2. Run linting and manifest jobs in parallel

    @dstansby
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  3. Fix os/platform variable name

    @dstansby
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  4. Add Python 3.10 to tox.ini

    @dstansby
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Commits on Apr 25, 2022

  1. Remove platform specific tox config

    @dstansby
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  2. Remove python 3.10 tests for now

    @dstansby
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  3. Merge pull request #104 from dstansby/test-py310 

    Drop Python 3.7 tests, add 3.9 tests
    @paddyroddy
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  4. Add simple smoke test for the main worker

    @dstansby
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  5. Bump cellfinder-core requirement

    @dstansby
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Commits on Apr 26, 2022

  1. Merge pull request #92 from dstansby/worker-test 

    Add simple smoke test for the main worker
    @paddyroddy
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  2. Update development dependencies

    @dstansby
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  3. Merge pull request #107 from dstansby/dev-dep 

    Update development dependencies
    @paddyroddy
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  4. Test adding new training layers for cell curation (#105) 

    * Test adding new training layers for cell curation

* Update cellfinder_napari/tests/test_curation.py

Co-authored-by: Patrick Roddy <[email protected]>

Co-authored-by: Patrick Roddy <[email protected]>
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Commits on Apr 28, 2022

  1. Test adding cells and non-cells during curation. (#106) 

    * Test that marking cells and non-cells works in curation

* Improve test variable names
    @dstansby
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Commits on Apr 29, 2022

  1. Add tests for cube extraction

    @dstansby
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  2. Speed up detection test

    @dstansby
    dstansby committed Apr 29, 2022
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  3. Remove old plugin engine v1 file

    @dstansby
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  4. De-duplicate widget header

    @dstansby
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  5. Swap order detection sample data is loaded

    @dstansby
    dstansby committed Apr 29, 2022
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  6. Add example to load napari and show detection sample data/widget

    @dstansby
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Commits on May 4, 2022

  1. Merge pull request #109 from dstansby/cube-extract-test 

    Cube extraction test
    @alessandrofelder
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  2. Merge pull request #110 from dstansby/detect-test-speed 

    Speed up detection test
    @alessandrofelder
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  3. Merge pull request #111 from dstansby/remove-npe1 

    Remove old plugin engine v1 file
    @alessandrofelder
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  4. Merge pull request #113 from dstansby/dedup-header 

    De-duplicate widget header
    @alessandrofelder
    alessandrofelder authored May 4, 2022
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Commits on May 5, 2022

  1. Update examples/show_detection_sample.py 

    Co-authored-by: Alessandro Felder <[email protected]>
    @dstansby @alessandrofelder
    dstansby and alessandrofelder authored May 5, 2022
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  2. Merge pull request #114 from dstansby/detect-example 

    Add example to load napari and show detection sample data/widget
    @alessandrofelder
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Commits on May 24, 2022

  1. separate abstract input class to own file 

    - detect widget dataclasses are now separate from abstract class
- custom_widget simplified and generalised to non-numerical types
    @alessandrofelder
    alessandrofelder committed May 24, 2022
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  2. implement training modularly

    @alessandrofelder
    alessandrofelder committed May 24, 2022
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  3. add training smoke test; update detection tests

    @alessandrofelder
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Commits on May 31, 2022

  1. Add link to contributing guide

    @adamltyson
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Commits on Jun 10, 2022

  1. Fix deprecated image saving function

    @dstansby
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  2. Add progress bar for saving curated data

    @dstansby
    dstansby committed Jun 10, 2022
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Commits on Jun 13, 2022

  1. Apply minor suggestions from review

    @dstansby
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  2. Merge pull request #103 from dstansby/curate-progress 

    Add progress bar when saving curated cells
    @dstansby
    dstansby authored Jun 13, 2022
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Commits on Jun 20, 2022

  1. Apply suggestions from code review 

    Co-authored-by: Patrick Roddy <[email protected]>
    @alessandrofelder @paddyroddy
    alessandrofelder and paddyroddy authored Jun 20, 2022
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  2. address more review comments 

    - add missing type annotations
- use show_info to display error message in GUI (instead of print)
- accept both .yml and .yaml files
- clarify intent of default for model_depth attribut of OptionalNetworkInputs
    @alessandrofelder
    alessandrofelder committed Jun 20, 2022
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Commits on Jun 21, 2022

  1. use FileDialogMode for clarity

    @alessandrofelder
    alessandrofelder committed Jun 21, 2022
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  2. Apply suggestions from second round code review 

    Co-authored-by: Patrick Roddy <[email protected]>
    @alessandrofelder @paddyroddy
    alessandrofelder and paddyroddy authored Jun 21, 2022
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  3. move import statement to top

    @alessandrofelder
    alessandrofelder committed Jun 21, 2022
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  4. enforce kwargs for html_label

    @alessandrofelder
    alessandrofelder committed Jun 21, 2022
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  5. enforce kwargs for html_label

    @alessandrofelder
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  6. Merge branch 'modularise-inputs' of https://github.com/brainglobe/cel… 

    …lfinder-napari into modularise-inputs
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  7. Merge pull request #121 from brainglobe/modularise-inputs 

    Modularise training widget inputs
    @alessandrofelder
    alessandrofelder authored Jun 21, 2022
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Commits on Jun 23, 2022

  1. Bump2version fix whitespace

    @paddyroddy
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  2. Merge pull request #123 from brainglobe/fix-issue-84 

    Bump2version fix whitespace
    @paddyroddy
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  3. Propagate errors from the worker to main thread

    @dstansby
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  4. Give the user more feedback when running detection

    @dstansby
    dstansby committed Jun 23, 2022
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  5. Merge pull request #125 from dstansby/propagate-errors 

    Propagate errors from the worker to main thread
    @paddyroddy
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Commits on Jun 24, 2022

  1. correct default model_depth value

    @alessandrofelder
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  2. add test for training reset button

    @alessandrofelder
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  3. Reset progress bar when setting up classification

    @dstansby
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  4. Merge pull request #126 from dstansby/detect-feedback 

    Give the user more feedback when running detection
    @dstansby
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Commits on Jun 27, 2022

  1. rename train() to training_widget() 

    to avoid confusion with file name and module name
    @alessandrofelder
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  2. add tests for reset and run buttons

    @alessandrofelder
    alessandrofelder committed Jun 27, 2022
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  3. add tests for training container core args

    @alessandrofelder
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  4. add docstrings to training tests

    @alessandrofelder
    alessandrofelder committed Jun 27, 2022
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  5. fix typo

    @alessandrofelder
    alessandrofelder committed Jun 27, 2022
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  6. rename detect() to detect_widget() 

    to avoid confusion with module and file name
    @alessandrofelder
    alessandrofelder committed Jun 27, 2022
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  7. increase detection test coverage

    @alessandrofelder
    alessandrofelder committed Jun 27, 2022
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  8. add smoke/unit tests for utils

    @alessandrofelder
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Commits on Jun 28, 2022

  1. remove debug print statement

    @alessandrofelder
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  2. add smoke tests for add_combobox and add_button utils

    @alessandrofelder
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  3. add test for show_info() in detect

    @alessandrofelder
    alessandrofelder committed Jun 28, 2022
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  4. add tests for some curation functionality

    @alessandrofelder
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  5. update renamed refs to detect_widget in YAML

    @alessandrofelder
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  6. add test widgets to viewer via napari.yaml names

    @alessandrofelder
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  7. additional test for show_info message

    @alessandrofelder
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  8. use set to check core_args are pass as expected.

    @alessandrofelder
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  9. remove explicit checks (now implicitly checked elsewhere)

    @alessandrofelder
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  10. add assertion to add_layers test

    @alessandrofelder
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  11. Simplify test parametrisation logic

    @alessandrofelder
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  12. Merge pull request #128 from brainglobe/expand-training-tests 

    Expand training tests
    @dstansby
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Commits on Jul 27, 2022

  1. Update website badge

    @adamltyson
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Commits on Oct 14, 2022

  1. Use official scrollable widget (#136) 

    * Use official scrollable widget

* lint

* revert deletion of pyqt QScrollArea()

* update supported python versions
    @adamltyson
    adamltyson authored Oct 14, 2022
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  2. Bump version: 0.0.19 → 0.0.20-rc0

    @adamltyson
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Commits on Oct 21, 2022

  1. Bump version: 0.0.20-rc0 → 0.0.20

    @adamltyson
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Commits on Oct 24, 2022

  1. Update requirements (#143)

    @adamltyson
    adamltyson authored Oct 24, 2022
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Commits on Dec 6, 2022

  1. Remove patch version of plugin preview action (#144)

    @adamltyson
    adamltyson authored Dec 6, 2022
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  2. Update .pre-commit-config.yaml (#145) 

    * Update .pre-commit-config.yaml

* Remove mypy
    @adamltyson
    adamltyson authored Dec 6, 2022
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Commits on Feb 3, 2023

  1. Fix tests (#149) 

    * Fix tox file

* Fix scikit-image dep

* Update pre-commit versions

* Don't fail fast

* Test with xvfb

* Use NI actions
    @dstansby
    dstansby authored Feb 3, 2023
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Commits on Feb 21, 2023

  1. Use standard pre-commit config (#150) 

    * Use standare pre-commit config

* Automated pre-commit fixes

* Make pre-commit happy
    @dstansby
    dstansby authored Feb 21, 2023
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Commits on Mar 9, 2023

  1. Update yaml filter 

    The "y?ml" syntax doesn't seem to be supported by napari.
    @adamltyson
    adamltyson authored Mar 9, 2023
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Commits on Mar 13, 2023

  1. Merge pull request #152 from brainglobe/update-yaml-filter 

    Update yaml filter
    @alessandrofelder
    alessandrofelder authored Mar 13, 2023
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Commits on Mar 14, 2023

  1. Use pyproject (#151) 

    * Use pyproject

* Remove pytest-xvfb from deps
    @dstansby
    dstansby authored Mar 14, 2023
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Commits on Apr 24, 2023

  1. Update README.md

    @adamltyson
    adamltyson authored Apr 24, 2023
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  2. Merge pull request #154 from brainglobe/readme-update 

    Update README.md
    @dstansby
    dstansby authored Apr 24, 2023
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Commits on Jun 19, 2023

  1. Update links (#156) 

    * Update links

* [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>
    @adamltyson @pre-commit-ci
    adamltyson and pre-commit-ci[bot] authored Jun 19, 2023
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Commits on Jun 20, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#158) 

    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>
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    pre-commit-ci[bot] authored Jun 20, 2023
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Commits on Jun 26, 2023

  1. Update dependency (imlib -> brainglobe-utils) (#159) 

    * Update dependency (imlib -> brainglobe-utils)

* dataclass

* Update cellfinder_napari/input_container.py

Co-authored-by: Alessandro Felder <[email protected]>

---------

Co-authored-by: Alessandro Felder <[email protected]>
    @adamltyson @alessandrofelder
    adamltyson and alessandrofelder authored Jun 26, 2023
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Commits on Jun 27, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#160) 

    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>
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    pre-commit-ci[bot] authored Jun 27, 2023
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Commits on Jul 4, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#161) 

    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-ci[bot] authored Jul 4, 2023
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Commits on Jul 11, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#162) 

    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-ci[bot] authored Jul 11, 2023
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Commits on Jul 13, 2023

  1. Update links (#163)

    @adamltyson
    adamltyson authored Jul 13, 2023
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Commits on Jul 18, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#164) 

    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-ci[bot] authored Jul 18, 2023
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Commits on Jul 25, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#165) 

    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-ci[bot] authored Jul 25, 2023
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Commits on Aug 1, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#166) 

    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-ci[bot] authored Aug 1, 2023
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Commits on Aug 8, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#167) 

    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-ci[bot] authored Aug 8, 2023
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Commits on Aug 17, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#169) 

    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>
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    pre-commit-ci[bot] authored Aug 17, 2023
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Commits on Aug 21, 2023

  1. Update CI deployment to use NI unit actions (#168) 

    * Update CI deployment to use NI unit actions

* [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>
    @willGraham01 @pre-commit-ci
    willGraham01 and pre-commit-ci[bot] authored Aug 21, 2023
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Commits on Aug 22, 2023

  1. [pre-commit.ci] pre-commit autoupdate (#170) 

    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>
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    pre-commit-ci[bot] authored Aug 22, 2023
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Commits on Aug 23, 2023

  1. Restructure under cellfinder umbrella

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  2. Rename most of the cellfinder_core to cellfinder.core

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  3. cellfinder_core tests now just in core

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  4. Separate cellfinder-core config files in prep for merge

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  5. Merge cellfinder-napari into cellfinder-core

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  6. Rename cellfinder-napari to cellfinder.napari

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  7. Move cellfinder.napari tests into test directory

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  8. Move cellfinder napari config files into temporary subdirectory

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  9. Reconcile licenses

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  10. Reconcile pre-commits

    @willGraham01
    willGraham01 committed Aug 23, 2023
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  11. Reconcile pyproject.tomls

    @willGraham01
    willGraham01 committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. Reconcile manifests

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  2. Reinstate cellfinder-core changelog

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  3. Reinstate .codedov

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  4. Reinstate plugin preview workflow

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  5. Reconcile tox

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  6. Reconcile READMEs temporarily

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  7. Reconcile CI workflows

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  8. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 24, 2023
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  9. mypy to ignore things

    @willGraham01
    willGraham01 committed Aug 24, 2023
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  10. Merge branch 'cellfinder-merge' of github.com:brainglobe/cellfinder-c… 

    …ore into cellfinder-merge
    @willGraham01
    willGraham01 committed Aug 24, 2023
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  11. Disable mypy for time being

    @willGraham01
    willGraham01 committed Aug 24, 2023
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Commits on Aug 29, 2023

  1. Fix plugin things by moving to non-flat directory struture

    @willGraham01
    willGraham01 committed Aug 29, 2023
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  2. Move to flat directory structure.

    @willGraham01
    willGraham01 committed Aug 29, 2023
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  3. Explicitly add napari.yaml to MANIFEST

    @willGraham01
    willGraham01 committed Aug 29, 2023
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Commits on Aug 31, 2023

  1. Make napari functionality optional

    @willGraham01
    willGraham01 committed Aug 31, 2023
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