Add brainmapper analysis functionality #24

adamltyson · 2024-01-08T16:34:15Z

Follows on from #22, bringing more of brainmappers functionality into this package so it can be reused.
Part of brainglobe/brainglobe-workflows#73

for more information, see https://pre-commit.ci

codecov · 2024-01-08T16:54:31Z

Codecov Report

Attention: 76 lines in your changes are missing coverage. Please review.

Comparison is base (cb48329) 83.00% compared to head (b8b3d03) 75.87%.
Report is 1 commits behind head on main.

Files	Patch %	Lines
brainglobe_utils/brainreg/transform.py	0.00%	44 Missing ⚠️
brainglobe_utils/brainmapper/analysis.py	64.47%	27 Missing ⚠️
brainglobe_utils/brainmapper/export.py	0.00%	5 Missing ⚠️

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

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willGraham01

Not sure why CodeCov is unhappy if this is just a port from brainmapper, and the test file has come with it?

adamltyson · 2024-01-09T09:24:54Z

I think it's just the brainmapper code wasn't fully tested, so the coverage has dropped.

* 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 <[email protected]>

* 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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: - 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[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 <[email protected]> * 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 <[email protected]> Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Adam Tyson <[email protected]> Co-authored-by: Jaime Rodríguez-Guerra <[email protected]> Co-authored-by: Jules Scholler <[email protected]> Co-authored-by: Jules Scholler <[email protected]> Co-authored-by: David Stansby <[email protected]> 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 <[email protected]> Co-authored-by: Igor Tatarnikov <[email protected]>

adamltyson added 3 commits January 8, 2024 16:33

Add brainmapper analysis functionality

5870413

Merge branch 'main' into brainmapper-analysis

0553f10

Add atlas api to requirements

624eca2

adamltyson mentioned this pull request Jan 8, 2024

Move analysis functionality to brainglobe-utils brainglobe/brainglobe-workflows#76

Merged

adamltyson and others added 2 commits January 8, 2024 16:51

Add brainrender export

09fec95

[pre-commit.ci] auto fixes from pre-commit.com hooks

b8b3d03

for more information, see https://pre-commit.ci

adamltyson marked this pull request as ready for review January 8, 2024 16:55

adamltyson requested a review from a team January 8, 2024 16:55

willGraham01 approved these changes Jan 9, 2024

View reviewed changes

adamltyson merged commit d3a1a5f into main Jan 9, 2024
17 of 18 checks passed

adamltyson deleted the brainmapper-analysis branch January 9, 2024 09:25

This was referenced Jan 12, 2024

Add "Layer interpreters" as independent functionality and use them in BrainGlobe brainglobe/BrainGlobe#10

Open

Add misc functionality from brainmapper #25

Merged

willGraham01 mentioned this pull request Jan 31, 2024

Update dependency tree in light of brainglobe-utils depending on atla… brainglobe/brainglobe.github.io#145

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Add brainmapper analysis functionality #24

Add brainmapper analysis functionality #24

adamltyson commented Jan 8, 2024 •

edited

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adamltyson commented Jan 9, 2024

Add brainmapper analysis functionality #24

Add brainmapper analysis functionality #24

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adamltyson commented Jan 9, 2024

adamltyson commented Jan 8, 2024 •

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