[pre-commit.ci] pre-commit autoupdate #338
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updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50)
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #338 +/- ##
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Coverage 99.77% 99.77%
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Files 14 14
Lines 878 878
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Hits 876 876
Misses 2 2 ☔ View full report in Codecov by Sentry. |
niksirbi
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Nov 4, 2024
niksirbi
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Nov 19, 2024
updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
niksirbi
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Nov 20, 2024
* initialise napari plugin development * Create skeleton for napari plugin with collapsible widgets (#218) * initialise napari plugin development * initialise napari plugin development * create skeleton for napari plugin with collapsible widgets * add basic widget smoke tests and allow headless testing * do not depend on napari from pip * include napari option in install instructions * make meta_widget module private * pin atlasapi version to avoid unnecessary dependencies * pin napari >= 0.4.19 from conda-forge * switched to pip install of napari[all] * seperation of concerns in widget tests * add pytest-mock dev dependency * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * Added loader widget for poses * update widget tests * simplify dependency on brainglobe-utils * consistent monospace formatting for movement in public docstrings * get rid of code that's only relevant for displaying Tracks * enable visibility of napari layer tooltips * renamed widget to PosesLoader * make cmap optional in set_color_by method * wrote unit tests for napari convert module * wrote unit-tests for the layer styles module * linkcheck ignore zenodo redirects * move _sample_colormap out of PointsStyle class * small refactoring in the loader widget * Expand tests for loader widget * added comments and docstrings to napari plugin tests * refactored all napari tests into separate unit test folder * added napari-video to dependencies * replaced deprecated edge_width with border_width * got rid of widget pytest fixtures * remove duplicate word from docstring * remove napari-video dependency * include napari extras in docs requirements * add test for _on_browse_clicked method * getOpenFileName returns tuple, not str * simplify poses_to_napari_tracks Co-authored-by: Chang Huan Lo <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#338) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Implement `compute_speed` and `compute_path_length` (#280) * implement compute_speed and compute_path_length functions * added speed to existing kinematics unit test * rewrote compute_path_length with various nan policies * unit test compute_path_length across time ranges * fixed and refactor compute_path_length and its tests * fixed docstring for compute_path_length * Accept suggestion on docstring wording Co-authored-by: Chang Huan Lo <[email protected]> * Remove print statement from test Co-authored-by: Chang Huan Lo <[email protected]> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <[email protected]> * adapt warning message match in test * change 'any' to 'all' * uniform wording across path length docstrings * (mostly) leave time range validation to xarray slice * refactored parameters for test across time ranges * simplified test for path lenght with nans * replace drop policy with ffill * remove B905 ruff rule * make pre-commit happy --------- Co-authored-by: Chang Huan Lo <[email protected]> * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * avoid redefining duplicate attributes in child dataclass * modify test case to match poses_to_napari_tracks simplification * expected_log_messages should be a subset of captured messages Co-authored-by: Chang Huan Lo <[email protected]> * fix typo Co-authored-by: Chang Huan Lo <[email protected]> * use names for Qwidgets * reorganised test_valid_poses_to_napari_tracks * parametrised layer style tests * delet integration test which was reintroduced after conflict resolution * added test about file filters * deleted obsolete loader widget file (had snuck back in due to conflict merging) * combine tests for button callouts Co-authored-by: Chang Huan Lo <[email protected]> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <[email protected]> --------- Co-authored-by: Chang Huan Lo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
niksirbi
added a commit
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Dec 16, 2024
* initialise napari plugin development * Create skeleton for napari plugin with collapsible widgets (#218) * initialise napari plugin development * initialise napari plugin development * create skeleton for napari plugin with collapsible widgets * add basic widget smoke tests and allow headless testing * do not depend on napari from pip * include napari option in install instructions * make meta_widget module private * pin atlasapi version to avoid unnecessary dependencies * pin napari >= 0.4.19 from conda-forge * switched to pip install of napari[all] * seperation of concerns in widget tests * add pytest-mock dev dependency * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * Added loader widget for poses * update widget tests * simplify dependency on brainglobe-utils * consistent monospace formatting for movement in public docstrings * get rid of code that's only relevant for displaying Tracks * enable visibility of napari layer tooltips * renamed widget to PosesLoader * make cmap optional in set_color_by method * wrote unit tests for napari convert module * wrote unit-tests for the layer styles module * linkcheck ignore zenodo redirects * move _sample_colormap out of PointsStyle class * small refactoring in the loader widget * Expand tests for loader widget * added comments and docstrings to napari plugin tests * refactored all napari tests into separate unit test folder * added napari-video to dependencies * replaced deprecated edge_width with border_width * got rid of widget pytest fixtures * remove duplicate word from docstring * remove napari-video dependency * include napari extras in docs requirements * add test for _on_browse_clicked method * getOpenFileName returns tuple, not str * simplify poses_to_napari_tracks Co-authored-by: Chang Huan Lo <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#338) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Implement `compute_speed` and `compute_path_length` (#280) * implement compute_speed and compute_path_length functions * added speed to existing kinematics unit test * rewrote compute_path_length with various nan policies * unit test compute_path_length across time ranges * fixed and refactor compute_path_length and its tests * fixed docstring for compute_path_length * Accept suggestion on docstring wording Co-authored-by: Chang Huan Lo <[email protected]> * Remove print statement from test Co-authored-by: Chang Huan Lo <[email protected]> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <[email protected]> * adapt warning message match in test * change 'any' to 'all' * uniform wording across path length docstrings * (mostly) leave time range validation to xarray slice * refactored parameters for test across time ranges * simplified test for path lenght with nans * replace drop policy with ffill * remove B905 ruff rule * make pre-commit happy --------- Co-authored-by: Chang Huan Lo <[email protected]> * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * avoid redefining duplicate attributes in child dataclass * modify test case to match poses_to_napari_tracks simplification * expected_log_messages should be a subset of captured messages Co-authored-by: Chang Huan Lo <[email protected]> * fix typo Co-authored-by: Chang Huan Lo <[email protected]> * use names for Qwidgets * reorganised test_valid_poses_to_napari_tracks * parametrised layer style tests * delet integration test which was reintroduced after conflict resolution * added test about file filters * deleted obsolete loader widget file (had snuck back in due to conflict merging) * combine tests for button callouts Co-authored-by: Chang Huan Lo <[email protected]> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <[email protected]> --------- Co-authored-by: Chang Huan Lo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
niksirbi
added a commit
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Dec 18, 2024
* initialise napari plugin development * Create skeleton for napari plugin with collapsible widgets (#218) * initialise napari plugin development * initialise napari plugin development * create skeleton for napari plugin with collapsible widgets * add basic widget smoke tests and allow headless testing * do not depend on napari from pip * include napari option in install instructions * make meta_widget module private * pin atlasapi version to avoid unnecessary dependencies * pin napari >= 0.4.19 from conda-forge * switched to pip install of napari[all] * seperation of concerns in widget tests * add pytest-mock dev dependency * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * Added loader widget for poses * update widget tests * simplify dependency on brainglobe-utils * consistent monospace formatting for movement in public docstrings * get rid of code that's only relevant for displaying Tracks * enable visibility of napari layer tooltips * renamed widget to PosesLoader * make cmap optional in set_color_by method * wrote unit tests for napari convert module * wrote unit-tests for the layer styles module * linkcheck ignore zenodo redirects * move _sample_colormap out of PointsStyle class * small refactoring in the loader widget * Expand tests for loader widget * added comments and docstrings to napari plugin tests * refactored all napari tests into separate unit test folder * added napari-video to dependencies * replaced deprecated edge_width with border_width * got rid of widget pytest fixtures * remove duplicate word from docstring * remove napari-video dependency * include napari extras in docs requirements * add test for _on_browse_clicked method * getOpenFileName returns tuple, not str * simplify poses_to_napari_tracks Co-authored-by: Chang Huan Lo <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#338) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Implement `compute_speed` and `compute_path_length` (#280) * implement compute_speed and compute_path_length functions * added speed to existing kinematics unit test * rewrote compute_path_length with various nan policies * unit test compute_path_length across time ranges * fixed and refactor compute_path_length and its tests * fixed docstring for compute_path_length * Accept suggestion on docstring wording Co-authored-by: Chang Huan Lo <[email protected]> * Remove print statement from test Co-authored-by: Chang Huan Lo <[email protected]> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <[email protected]> * adapt warning message match in test * change 'any' to 'all' * uniform wording across path length docstrings * (mostly) leave time range validation to xarray slice * refactored parameters for test across time ranges * simplified test for path lenght with nans * replace drop policy with ffill * remove B905 ruff rule * make pre-commit happy --------- Co-authored-by: Chang Huan Lo <[email protected]> * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * avoid redefining duplicate attributes in child dataclass * modify test case to match poses_to_napari_tracks simplification * expected_log_messages should be a subset of captured messages Co-authored-by: Chang Huan Lo <[email protected]> * fix typo Co-authored-by: Chang Huan Lo <[email protected]> * use names for Qwidgets * reorganised test_valid_poses_to_napari_tracks * parametrised layer style tests * delet integration test which was reintroduced after conflict resolution * added test about file filters * deleted obsolete loader widget file (had snuck back in due to conflict merging) * combine tests for button callouts Co-authored-by: Chang Huan Lo <[email protected]> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <[email protected]> --------- Co-authored-by: Chang Huan Lo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
niksirbi
added a commit
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Jan 28, 2025
* initialise napari plugin development * Create skeleton for napari plugin with collapsible widgets (#218) * initialise napari plugin development * initialise napari plugin development * create skeleton for napari plugin with collapsible widgets * add basic widget smoke tests and allow headless testing * do not depend on napari from pip * include napari option in install instructions * make meta_widget module private * pin atlasapi version to avoid unnecessary dependencies * pin napari >= 0.4.19 from conda-forge * switched to pip install of napari[all] * seperation of concerns in widget tests * add pytest-mock dev dependency * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * Added loader widget for poses * update widget tests * simplify dependency on brainglobe-utils * consistent monospace formatting for movement in public docstrings * get rid of code that's only relevant for displaying Tracks * enable visibility of napari layer tooltips * renamed widget to PosesLoader * make cmap optional in set_color_by method * wrote unit tests for napari convert module * wrote unit-tests for the layer styles module * linkcheck ignore zenodo redirects * move _sample_colormap out of PointsStyle class * small refactoring in the loader widget * Expand tests for loader widget * added comments and docstrings to napari plugin tests * refactored all napari tests into separate unit test folder * added napari-video to dependencies * replaced deprecated edge_width with border_width * got rid of widget pytest fixtures * remove duplicate word from docstring * remove napari-video dependency * include napari extras in docs requirements * add test for _on_browse_clicked method * getOpenFileName returns tuple, not str * simplify poses_to_napari_tracks Co-authored-by: Chang Huan Lo <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#338) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Implement `compute_speed` and `compute_path_length` (#280) * implement compute_speed and compute_path_length functions * added speed to existing kinematics unit test * rewrote compute_path_length with various nan policies * unit test compute_path_length across time ranges * fixed and refactor compute_path_length and its tests * fixed docstring for compute_path_length * Accept suggestion on docstring wording Co-authored-by: Chang Huan Lo <[email protected]> * Remove print statement from test Co-authored-by: Chang Huan Lo <[email protected]> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <[email protected]> * adapt warning message match in test * change 'any' to 'all' * uniform wording across path length docstrings * (mostly) leave time range validation to xarray slice * refactored parameters for test across time ranges * simplified test for path lenght with nans * replace drop policy with ffill * remove B905 ruff rule * make pre-commit happy --------- Co-authored-by: Chang Huan Lo <[email protected]> * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * avoid redefining duplicate attributes in child dataclass * modify test case to match poses_to_napari_tracks simplification * expected_log_messages should be a subset of captured messages Co-authored-by: Chang Huan Lo <[email protected]> * fix typo Co-authored-by: Chang Huan Lo <[email protected]> * use names for Qwidgets * reorganised test_valid_poses_to_napari_tracks * parametrised layer style tests * delet integration test which was reintroduced after conflict resolution * added test about file filters * deleted obsolete loader widget file (had snuck back in due to conflict merging) * combine tests for button callouts Co-authored-by: Chang Huan Lo <[email protected]> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <[email protected]> --------- Co-authored-by: Chang Huan Lo <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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