Use the updated upload_pypi action #108
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #108 +/- ##
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Coverage 99.12% 99.12%
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Files 8 8
Lines 458 458
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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* 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: - 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[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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* added from_files() function * added from_files() function * Use the updated upload_pypi action (#108) * Bump action versions in upload_pypi workflow step * reuse the upload_pypi action instead of custom steps * adding code review suggestionas and tests * added log error * added from_files() function * added from_files() function * adding code review suggestionas and tests * added log error * formatted docstrign and added to API reference * added regex matching to ValueError test * documented new funciton in Getting started guide * use from_file() for fetching sample data --------- Co-authored-by: Niko Sirmpilatze <niko.sirbiladze@gmail.com>
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See neuroinformatics-unit/movement#108 Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com>
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* Fixed contents margins * Scaling of sample image added to adjust moving image dropdown * Added brainglobe-utils as dependency * Added error message when no images selected * Atlas rotation working using scipy * Pitch, yaw, roll implemented using one affine transform * Dask loading for both the reference atlas and the rotation * Added a 'Reset Atlas' button, blocked while dask computes the rotation to avoid race conditions * Rotate atlas button also greyed out while daks processes the rotation * Use the update upload_pypi action (#29) See neuroinformatics-unit/movement#108 * Added elastix Logs directory to .gitignore * Fixed tests * Moved run_registration to be imported just as run button is clicked to avoid long boot times * Atlas rotation works again (might relate to napari 0.4.19 * Added test for atlas_rotation_signal from AdjustMovingImage view * [pre-commit.ci] pre-commit autoupdate (#30) 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> * [pre-commit.ci] pre-commit autoupdate (#31) updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.5](astral-sh/ruff-pre-commit@v0.2.0...v0.3.5) - [github.com/psf/black: 24.1.1 → 24.3.0](psf/black@24.1.1...24.3.0) - [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](pre-commit/mirrors-mypy@v1.8.0...v1.9.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Import header from brainglobe-utils (#33) * import header from brainglobe-utils * split package name over two lines * remove brainglobe png from manifest * add brainglobe-utils dependency * Update requirements (#34) * import header from brainglobe-utils * split package name over two lines * remove brainglobe png from manifest * add brainglobe-utils dependency * Switched from bg-atlasapi to brainglobe-atlasapi * Added lxml_html_clean explicitly to requirements * Pinned itk to 5.4rc2 for now as 5.4rc3 cased a seg fault * Undo itk pin --------- Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * add codecov token (#35) * Added tests for calculate_rotated_bounding_box * Fixed docstrings for functions in utils.py * Keep track of napari layers for the atlas and atlas annotations in the napari widget class * Added tests for atlas rotation * Fixed pre-commit * Add test for reset_atlas in adjust_moving_image_view * Add caching * Update the function calls in test_adjust_moving_image_view * Apply suggestions from code review Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> * Applied suggestions from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Applied suggestions from code review --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com>
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* Moving from tabs to a dropdown style widget (#25) * Fixed contents margins * Added brainglobe-utils as dependency * Added min dependency version for brainglobe-utils * Add option to scale sample image (#26) * Fixed contents margins * Scaling of sample image added to adjust moving image dropdown * Added brainglobe-utils as dependency * Added error message when no images selected * Added tests for scaling * Added tests to check multiple scale_factors * Cache the moving image data to allow scaling image multiple times * Fixed tests by removing (0,0) case add guard in _on_scale_image in registration_widget.py * Fixed tests * Add docstring to _on_scale_moving_image * Replaced all curr_ variable names with current_ * Added units to pixel size selection, set max range to be 100 * Allow free rotation of the atlas (#36) * Fixed contents margins * Scaling of sample image added to adjust moving image dropdown * Added brainglobe-utils as dependency * Added error message when no images selected * Atlas rotation working using scipy * Pitch, yaw, roll implemented using one affine transform * Dask loading for both the reference atlas and the rotation * Added a 'Reset Atlas' button, blocked while dask computes the rotation to avoid race conditions * Rotate atlas button also greyed out while daks processes the rotation * Use the update upload_pypi action (#29) See neuroinformatics-unit/movement#108 * Added elastix Logs directory to .gitignore * Fixed tests * Moved run_registration to be imported just as run button is clicked to avoid long boot times * Atlas rotation works again (might relate to napari 0.4.19 * Added test for atlas_rotation_signal from AdjustMovingImage view * [pre-commit.ci] pre-commit autoupdate (#30) 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> * [pre-commit.ci] pre-commit autoupdate (#31) updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.5](astral-sh/ruff-pre-commit@v0.2.0...v0.3.5) - [github.com/psf/black: 24.1.1 → 24.3.0](psf/black@24.1.1...24.3.0) - [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](pre-commit/mirrors-mypy@v1.8.0...v1.9.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Import header from brainglobe-utils (#33) * import header from brainglobe-utils * split package name over two lines * remove brainglobe png from manifest * add brainglobe-utils dependency * Update requirements (#34) * import header from brainglobe-utils * split package name over two lines * remove brainglobe png from manifest * add brainglobe-utils dependency * Switched from bg-atlasapi to brainglobe-atlasapi * Added lxml_html_clean explicitly to requirements * Pinned itk to 5.4rc2 for now as 5.4rc3 cased a seg fault * Undo itk pin --------- Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * add codecov token (#35) * Added tests for calculate_rotated_bounding_box * Fixed docstrings for functions in utils.py * Keep track of napari layers for the atlas and atlas annotations in the napari widget class * Added tests for atlas rotation * Fixed pre-commit * Add test for reset_atlas in adjust_moving_image_view * Add caching * Update the function calls in test_adjust_moving_image_view * Apply suggestions from code review Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> * Applied suggestions from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Applied suggestions from code review --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> * Cleaned up a few things * Mark 'Advanced Settings' as optional (#48) * Info message when running BrainGlobe Registration plugin with no atlas installed (#46) * added error when no atlas found * added error when no atlas found * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * changes to info message * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * parent_widget * parent_widget --------- Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Clean up widget (#51) * Cleaned up rogue widget duplication * Added parent to parameters_tab * Fix slow plugin loading (#54) * Filter Images (#52) * work_in_progress * filter_images * filter_images * filter_images * filter_images * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/utils/utils.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Communicate napari layer deletions appropriately to the plugin (#49) * layer_deletion * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * layer_deletion_edits * Made pytest happy * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * Update brainglobe_registration/registration_widget.py Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated_layer * fixed manual vs automatic deletion * fixed manual vs automatic deletion * Refactored some old code to avoid duplication * add comments --------- Co-authored-by: Igor Tatarnikov <61896994+IgorTatarnikov@users.noreply.github.com> Co-authored-by: IgorTatarnikov <igor.tatarnikov@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Co-authored-by: Alessandro Felder <alessandrofelder@users.noreply.github.com> Co-authored-by: saarah815 <63860766+saarah815@users.noreply.github.com>
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Context
We recently, bumped the versions of many actions in the NIU actions repository, with the help of
dependabot. Among many other changes,actions/upload-artifactwas bumped tov4.This change is incompatible with older major versions of
actions/download-artifactwhich we use within this repo's GitHub workflow, specifically in the step that uploads the package to PyPI.Solution
The easy fix would be to also bump
actions/download-artifacttov4within the workflow, but we want to avoid having to do that for any future actions updates.Therefore, this PR modifies the PyPI upload logic of the workflow, so that it leverages our reusable upload_pypi action, which has also been updated to fulfill that purpose.
In this way, we should avoid having to modify the individual repo workflows. In the future, the relevant bumps will have to be implemented only upstream, in NIU actions.
How has this been tested
We made a new PyPI release of brainglobe-template-builder using this updated workflow, and it went down smoothly.