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Recent Releases of brainglobe-utils

brainglobe-utils - v0.7.0

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/109
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/110
  • bump pyvista action version 2->3 by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/111
  • Replaced NIU upload action with separate steps by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/112
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/113
  • Use pypa/gh-action-pypi-publish stable release v1 by @lochhh in https://github.com/brainglobe/brainglobe-utils/pull/114
  • Remove qt elements migrated to qt-niu by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/118
  • Update Python versions to adhere to SPEC 0 and remove Intel testing on macOS by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/119
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/120
  • Updates shape calculation in brainreg/transform.py by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/121

New Contributors

  • @lochhh made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/114

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.6.3...v0.7.0

- Python
Published by adamltyson over 1 year ago

brainglobe-utils - v0.6.3

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/100
  • Change cache path by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/101
  • Schedule tests to run weekly by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/102
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/103
  • use log10 for zero padding tiffs by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/104
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/105
  • Notify slack on scheduled test failure by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/106
  • Accept both .tif and .tiff files in directories by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/108

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.6.2...v0.6.3

- Python
Published by adamltyson over 1 year ago

brainglobe-utils - v0.6.2

What's Changed

  • Conform to new linting rules by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/97
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/96
  • improve readwithdask docs, ignore OME metadata by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/98

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.6.1...v0.6.2

- Python
Published by alessandrofelder almost 2 years ago

brainglobe-utils - v0.6.1

What's Changed

  • handle nii.gz correctly by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/93
  • Export cells to brainrender from brainmapper widget by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/95

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.6.0...v0.6.1

- Python
Published by alessandrofelder almost 2 years ago

brainglobe-utils - v0.6.0

v0.6.0

Adds a new brainmapper napari widget to transform points to atlas space

What's Changed

  • Changed collapsed icon for CollapsibleWidget by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/78
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/80
  • Remove nrrd IO by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/82
  • Update supported python versions by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/81
  • Add cell matching support by @matham in https://github.com/brainglobe/brainglobe-utils/pull/74
  • Provide optional dependencies for qt instead of napari by @niksirbi in https://github.com/brainglobe/brainglobe-utils/pull/84
  • Numpy 2.0 compliance by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/85
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/86
  • Standardise contact information in readme by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/87
  • Add transform widget by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/88

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.5.0...v0.6.0

- Python
Published by adamltyson almost 2 years ago

brainglobe-utils - v0.5.0

What's Changed

  • Run CI on both types of Mac by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/71
  • Support single z-stack tif file for input by @matham in https://github.com/brainglobe/brainglobe-utils/pull/67
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/72
  • Add image IO loading code from cellfinder & create image IO submodule within IO by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/73
  • Be permissive about tiff axis metadata by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/75

New Contributors

  • @matham made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/67

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.4.3...v0.5.0

- Python
Published by adamltyson about 2 years ago

brainglobe-utils - v0.4.3

What's Changed

  • Add tests for cells sub-module by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/61
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/62
  • Add tests for qtpy sub-module by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/64
  • Convert remaining docstrings to numpydoc style by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/66
  • Add docstrings and expand tests for IO sub-module by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/65
  • Update Pathlib usage and docstrings by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/68
  • Expand header_widget to include doc path, citation and help text by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/70

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.4.2...v0.4.3

- Python
Published by K-Meech about 2 years ago

brainglobe-utils - v0.4.2

What's Changed

  • add tests for transforming to atlas space function by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/38
  • Fix test that is still importing bg-atlasapi by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/40
  • Convert image_io docstrings to numpydoc style by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/43
  • Add minisblack photometric to tiff writing by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/46
  • Tests for the image_io sub-module by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/48
  • Add saveany function to imageio by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/51
  • Convert general submodule docstrings to numpydoc by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/53
  • Add tests for brainmapper sub-module by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/52
  • Handle str and pathlib.Path consistently in image_io by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/54
  • Use codecov token in testanddeploy by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/55
  • Use data path and fixtures consistently by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/58
  • Refactor ImageIOLoadException by @K-Meech in https://github.com/brainglobe/brainglobe-utils/pull/59

New Contributors

  • @K-Meech made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/43

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.4.1...v0.4.2

- Python
Published by K-Meech about 2 years ago

brainglobe-utils - v0.4.1

Bump to brainglobe-atlasapi dependency

bg-atlasapi has been renamed to brainglobe-atlasapi, so we now depend on the new package.

What's Changed

  • bg-atlasapi -> brainglobe-atlasapi by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/39

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.4.0...v0.4.1

- Python
Published by willGraham01 over 2 years ago

brainglobe-utils - v0.4.0

Incorporate imio functionality

What's Changed

  • Debug failing regression test by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/29
  • Update testanddeploy.yml by @alessandrofelder in https://github.com/brainglobe/brainglobe-utils/pull/30
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/31
  • Add manifest to ci by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/32
  • Merge imio in as image_io submodule by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/33
  • Add citation tool by @willGraham01 in https://github.com/brainglobe/brainglobe-utils/pull/28

New Contributors

  • @alessandrofelder made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/30

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.6...v0.4.0

- Python
Published by willGraham01 over 2 years ago

brainglobe-utils - v0.3.6

What's Changed

  • Move qtpy functionality from brainglobe-segmentation & cellfinder by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/27

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.5...v0.3.6

- Python
Published by adamltyson over 2 years ago

brainglobe-utils - v0.3.5

What's Changed

  • Add misc functionality from brainmapper by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/25

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.4...v0.3.5

- Python
Published by adamltyson over 2 years ago

brainglobe-utils - v0.3.4

What's Changed

  • Collapsible Widget API v1.1 by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/23
  • Add brainmapper analysis functionality by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/24

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.3...v0.3.4

- Python
Published by adamltyson over 2 years ago

brainglobe-utils - v0.3.3

Refactor heatmap generation functionality

Refactors the ability to generate heatmaps from brainglobe-heatmap into this package. We will be using this functionality across multiple packages.

What's Changed

  • Brainmapper utils by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/22

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.2...v0.3.3

- Python
Published by willGraham01 over 2 years ago

brainglobe-utils - v0.3.2

What's Changed

  • Add slurmio back to dependencies by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/20

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.1...v0.3.2

- Python
Published by adamltyson over 2 years ago

brainglobe-utils - v0.3.1

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/brainglobe-utils/pull/14
  • Update pre-commit monthly by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/15
  • Simplify slurmio dependency by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/16
  • Add slurmio to dev dependencies by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/17
  • Delete unused code & add tests by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/18

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/14

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.3.0...v0.3.1

- Python
Published by adamltyson over 2 years ago

brainglobe-utils -

What's Changed

  • Added napari as optional dependency by @niksirbi in https://github.com/brainglobe/brainglobe-utils/pull/10
  • Qt based utilities for BrainGlobe by @IgorTatarnikov in https://github.com/brainglobe/brainglobe-utils/pull/13

New Contributors

  • @niksirbi made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/10
  • @IgorTatarnikov made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/13

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.2.7...v0.3.0

- Python
Published by alessandrofelder over 2 years ago

brainglobe-utils - v0.2.7

What's Changed

  • Add safe_pandas_concat function by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/8
    • This fixes an issue with pandas.DataFrame.append being stricter in >=v2 of pandas.

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.2.6...v0.2.7

- Python
Published by willGraham01 over 2 years ago

brainglobe-utils - v0.2.6

What's Changed

  • Limit n processes on Windows to 61 by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/5
  • Remove Python 3.8 support by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/7

Full Changelog: https://github.com/brainglobe/brainglobe-utils/compare/v0.2.5...v0.2.6

- Python
Published by adamltyson over 2 years ago

brainglobe-utils - v0.2.4

- Python
Published by adamltyson about 3 years ago

brainglobe-utils - v0.2.3

- Python
Published by adamltyson about 3 years ago

brainglobe-utils - v0.2.2

- Python
Published by adamltyson about 3 years ago

brainglobe-utils - v0.2.1

Main changes

brainglobe-utils is a fork of imlib but brought under the BrainGlobe umbrella for ease of maintenance. Gradually all imlib dependencies will be changed to brainglobe-utils.

What's Changed

  • Update tooling and remove unused functions by @adamltyson in https://github.com/brainglobe/brainglobe-utils/pull/1

New Contributors

  • @adamltyson made their first contribution in https://github.com/brainglobe/brainglobe-utils/pull/1

Full Changelog: https://github.com/brainglobe/brainglobe-utils/commits/v0.2.1

- Python
Published by adamltyson about 3 years ago