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Debug failing regression test #29
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willGraham01
changed the title
Add workflow dispatch to github workflows
Debug failing regression test
Jan 31, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #29 +/- ##
=======================================
Coverage 74.55% 74.55%
=======================================
Files 25 25
Lines 849 849
=======================================
Hits 633 633
Misses 216 216 ☔ View full report in Codecov by Sentry. |
alessandrofelder
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Jan 31, 2024
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OK, thanks @willGraham01
willGraham01
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Feb 9, 2024
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 <[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: - [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 <[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]>
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Noticed that some workflows over on #28 are failing due to a test that hasn't been touched, starting an investigation and fix here.
Conclusion
The data produced is identical, however the rows of the CSV come out in a different order - not sure of the reason why but I suspect this is a
pandas
speed-up that has been introduced that can't guarantee the writing order of rows.Fix that's implemented is to load the expected output and produced output as
DataFrames
and usepandas
to compare them, rather thanfilecmp
. This means we can order the CSV rows (by region) then assert that each row is identical throughDataFrame.equals()
.Other Misc Changes