Update requirements #34
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Out of interest, why do we depend on an itk release candidate here? |
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From what I understand https://github.com/InsightSoftwareConsortium/ITKElastix/blob/main/setup.py#L51-L53 |
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Looks like the segfault has been fixed! I've removed |
adamltyson
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Apr 22, 2024
IgorTatarnikov
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Jul 26, 2024
* 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>
alessandrofelder
added a commit
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Aug 16, 2024
* 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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Description
What is this PR
Why is this PR needed?
Cleaned up and added some requirements.
What does this PR do?
Explicitly add lxml_html_clean to requirements for now to avoid napari/napari#6799.
Replace all mentions of
bg-atlasapiwithbrainglobe-atlasapiReferences
Closes #32
How has this PR been tested?
All tests pass locally.
Is this a breaking change?
No
Does this PR require an update to the documentation?
No
Checklist: