v1.0.0

Mark package as deprecated

As part of our upcoming release of version 1 of BrainGlobe, the cellfinder-core and cellfinder-napari packages are merging into a single, unified, cellfinder package. You can read about this in our blog post.

As such, this will be the final release of a standalone cellfinder-core package. If you want to continue using the package, we recommend you follow the steps outlined in the blog post above, or head over to cellfinder and install version >=v1.0.0 in a clean environment.

What's Changed

• Set pre-commit autoupdate frequency to monthly by @adamltyson in #217
• Prepare for retirement by @willGraham01 in #226

Full Changelog: v0.5.1...v1.0.0

v0.5.1

What's Changed

• Update CHANGELOG with 0.5.0 changes by @willGraham01 in #192
• MANIFEST only necessary files for package install by @willGraham01 in #195
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #196
• possible fix for mac error by @alessandrofelder in #200
• CI Check against tensorflow include guard by @willGraham01 in #204
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #205
• ensure cellfinder-core can run on single cpu by @alessandrofelder in #198
• asv benchmarks for imports and tools modules by @sfmig in #184
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #210
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #211
• Update links by @adamltyson in #212

New Contributors

• @sfmig made their first contribution in #184

Full Changelog: v0.5.0...v0.5.1

v0.5.0

cellfinder-core 0.5.0

What's Changed

• Fix mypy type checking by @dstansby in #180
• Add typing to classification by @dstansby in #181
• Update dependency (imlib -> brainglobe-utils) by @adamltyson in #182
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #183
• Forbid import when tensorflow is not installed by @willGraham01 in #186
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #189
• Update README in light of possible noarch build by @willGraham01 in #191

Full Changelog: v0.4.1...v0.5.0

cellfinder-core 0.4.0

What's Changed

• Use standard pre-commit config by @dstansby in #77
• Use pyproject.toml by @dstansby in #79
• Remove print statment from 3D filter by @dstansby in #83
• Use random arrays for memory testing by @dstansby in #82
• Filter warnings in pytest by @dstansby in #80
• avoid using deprecated pkg_resources by @alessandrofelder in #93
• Fixture for programmatic creation of synthetic data by @alessandrofelder in #94
• Add macOS arm64 wheel building by @dstansby in #76
• Add connected component labelling unit tests by @dstansby in #97
• Filter setup typing by @dstansby in #78
• Test structure detection with different dtypes by @dstansby in #99
• Allow cellfinder tests to run on branches by @dstansby in #101
• Pin tensorflow to < 2.12.0 by @dstansby in #104
• Turn off codecov commenting by @dstansby in #107
• 3D filtering benchmark by @dstansby in #90
• Misc classification typing by @dstansby in #106
• Fix test coverage data collection by @dstansby in #117
• Convert CellDetector to numba by @dstansby in #112
• Merge benchmarking and numba work into main by @dstansby in #121
• Remove manifest file by @dstansby in #126
• Remove connect_eight() by @dstansby in #122
• Clean up structure_centre_wrapper by @dstansby in #123
• Clean and document 2D filter by @dstansby in #114
• Clean and document ball filter by @dstansby in #115
• Type ball filter by @dstansby in #133
• Remove some un-used code by @dstansby in #132
• Test for error when data dimensionality is wrong by @dstansby in #131
• Add some docs on how bright points are marked by @dstansby in #135
• Add docs to structure detection by @dstansby in #138
• Use "plane" instead of "layer" in detection by @dstansby in #142
• Add typing to structure splitting code by @dstansby in #147
• Collect coverage of numba decorated code by @dstansby in #124
• Only check unique neighbour IDs by @dstansby in #146
• Start a changelog for next version by @dstansby in #143
• Update README.md by @adamltyson in #156
• Add high level overview of cell detection stages by @dstansby in #151
• Use bool dtype for good tiles mask by @dstansby in #152
• Clip planes in-place by @dstansby in #153
• Remove cibuildwheel and build pure-Python wheel by @dstansby in #155
• Don't cast planes to uint64 in structure detection by @dstansby in #154
• Limit number of 2D filtering outputs stored in memory by @dstansby in #139
• Use nopython mode for all jitting by @dstansby in #165
• Force typing in detect sub-module by @dstansby in #161
• Fix typo in error message by @adamltyson in #164
• Add numpy to typing deps by @dstansby in #162
• Structure splitting: Smoke test and refactor for numba by @alessandrofelder in #167

Full Changelog: 0.3.1...0.4.0

v0.3.1

Bump version: 0.3.1-rc1 → 0.3.1