Add brainmapper analysis functionality #24
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #24 +/- ##
==========================================
- Coverage 83.00% 75.87% -7.13%
==========================================
Files 20 23 +3
Lines 606 742 +136
==========================================
+ Hits 503 563 +60
- Misses 103 179 +76 ☔ View full report in Codecov by Sentry. |
willGraham01
approved these changes
Jan 9, 2024
|
I think it's just the brainmapper code wasn't fully tested, so the coverage has dropped. |
This was referenced Jan 12, 2024
willGraham01
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Feb 9, 2024
* docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com>
adamltyson
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Feb 9, 2024
* Initial commit * bump * bump * bump * add bump2version * Bump version: 0.0.2 → 0.0.3 * add pre commit hooks * update testing * reorder ci * fix non-istropic loading error * Bump version: 0.0.3 → 0.0.4 * Gh actions (#3) * add gh actions * Update testing * update testing * add lint * coveralls * coveralls * deploy * Bump version: 0.0.4 → 0.0.5 * update readme * transfer to brainglobe * run tests on PR * update coverage * support python 3.9 * Bump version: 0.0.5 → 0.0.6 * update bump2version * Bump version: 0.0.6 → 0.1.0-rc0 * Bump version: 0.1.0-rc0 → 0.1.0 * Update setup.py * add missing import * Update README.md * fix linting * Exclude tests from packaged distributions (#6) * Update pre commit * reformat * Python 3.10 compatibility * Bump version: 0.1.0 → 0.2.0-rc0 * update GH actions * Bump version: 0.2.0-rc0 → 0.2.0-rc1 * Bump version: 0.2.0-rc1 → 0.2.0 * Revert older changes * Fix deprecation of tifffile.imsave replaced by tifffile.imwrite. (#8) Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch> * Bump version: 0.2.1 → 0.2.2-rc0 * Bump version: 0.2.2-rc0 → 0.2.2 * Add link to contributing guide * Add tox and use brainglobe/actions (#10) * Add tox and use brainglobe actions for testing * Update pre-commit * run pre-commit * Update tox.ini * Bump version: 0.2.2 → 0.2.3-rc0 * Bump version: 0.2.3-rc0 → 0.2.3 * Long description (#11) * Add long description for PyPI * Bump version: 0.2.3 → 0.2.4-rc0 * Bump version: 0.2.4-rc0 → 0.2.4 * Change coverage badge to codecov. * Test on recent python versions (#13) * Test on recent python versions * Bump pre-commit versions * Fix dtype issue * Remove straggling mention of 3.7 * Replace brainglobe > NI actions (#14) * Use standard pre-commit config (#15) * Add standard pre-commit config * pre-commit fixes * Use pyproject.toml (#16) * Filter warnings in pytest (#17) * Filter warnings in pytest * Filter nptyping warnings * Add all-contributors * Update README.md Co-authored-by: David Stansby <dstansby@gmail.com> * docs: add crousseau as a contributor for code, ideas, and test (#25) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Remove badge --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com> * Don't skip CI for all-contrbutors-bot * Update .all-contributorsrc * docs: add jaimergp as a contributor for code (#23) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com> * docs: add JulesScholler as a contributor for code (#22) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md * Update .all-contributorsrc * Update .all-contributorsrc --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com> * docs: add dstansby as a contributor for test, code, and 3 more (#21) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com> * docs: add adamltyson as a contributor for code, infra, and 2 more (#24) * docs: update README.md [skip ci] * docs: create .all-contributorsrc [skip ci] * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * Update README.md --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Adam Tyson <code@adamltyson.com> * Update doc links (#27) * [pre-commit.ci] pre-commit autoupdate (#28) 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 dependency (imlib -> brainglobe-utils) (#29) * [pre-commit.ci] pre-commit autoupdate (#31) 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> * remove all contributors (#32) * [pre-commit.ci] pre-commit autoupdate (#33) 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 (#34) 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> * Update CI workflow to use NIU actions (#35) * [pre-commit.ci] pre-commit autoupdate (#36) 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 (#37) 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 (#38) 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 (#39) 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 (#40) 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 (#41) 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 (#42) 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> * Set pre-commit autoupdate frequency to monthly (#43) * [pre-commit.ci] pre-commit autoupdate (#44) 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 (#45) 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> * [pre-commit.ci] pre-commit autoupdate (#48) updates: - [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0) - [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.1.4](astral-sh/ruff-pre-commit@v0.0.292...v0.1.4) - [github.com/psf/black: 23.9.1 → 23.10.1](psf/black@23.9.1...23.10.1) - [github.com/pre-commit/mirrors-mypy: v1.5.1 → v1.6.1](pre-commit/mirrors-mypy@v1.5.1...v1.6.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#49) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.4 → v0.1.6](astral-sh/ruff-pre-commit@v0.1.4...v0.1.6) - [github.com/psf/black: 23.10.1 → 23.11.0](psf/black@23.10.1...23.11.0) - [github.com/pre-commit/mirrors-mypy: v1.6.1 → v1.7.1](pre-commit/mirrors-mypy@v1.6.1...v1.7.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#50) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.6 → v0.1.9](astral-sh/ruff-pre-commit@v0.1.6...v0.1.9) - [github.com/psf/black: 23.11.0 → 23.12.1](psf/black@23.11.0...23.12.1) - [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](pre-commit/mirrors-mypy@v1.7.1...v1.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update GH actions badge (#51) * Update test_and_deploy.yml (#52) See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Add manifest (#54) * Update CI workflows with manifest * Allow workflow to be dispatchable * Add pyarrow dependency to prevent future pandas failures * [pre-commit.ci] pre-commit autoupdate (#53) updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.9...v0.2.0) - [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@23.12.1...24.1.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * refactor image_io as submodule * Deprecated alias warning is still present * Fix an actual circular import because of wildcard import * Fix buggy html logo - wrong escape backslash --------- Co-authored-by: crousseau <c.rousseau@ucl.ac.uk> Co-authored-by: Adam Tyson <adam.tyson@ucl.ac.uk> Co-authored-by: Adam Tyson <code@adamltyson.com> Co-authored-by: Jaime Rodríguez-Guerra <jaimergp@users.noreply.github.com> Co-authored-by: Jules Scholler <jules.scholler@gmail.com> Co-authored-by: Jules Scholler <jules.scholler@wysscenter.ch> Co-authored-by: David Stansby <dstansby@gmail.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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Follows on from #22, bringing more of
brainmappersfunctionality into this package so it can be reused.Part of brainglobe/brainglobe-workflows#73