Launch napari plugin with movement launch
#345
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## napari-dev #345 +/- ##
===========================================
Coverage 99.80% 99.81%
===========================================
Files 18 18
Lines 1051 1060 +9
===========================================
+ Hits 1049 1058 +9
Misses 2 2 ☔ View full report in Codecov by Sentry. 🚨 Try these New Features:
|
niksirbi
force-pushed
the
add-cli-entry-for-napari
branch
from
e45a171 to
7c7c02e
Compare
|
niksirbi
added a commit
that referenced
this pull request
Dec 16, 2024
niksirbi
added a commit
that referenced
this pull request
Dec 18, 2024
niksirbi
added a commit
that referenced
this pull request
Jan 28, 2025
sfmig
pushed a commit
that referenced
this pull request
Feb 24, 2025
sfmig
pushed a commit
that referenced
this pull request
Feb 25, 2025
niksirbi
added a commit
that referenced
this pull request
Feb 27, 2025
niksirbi
added a commit
that referenced
this pull request
Feb 28, 2025
niksirbi
added a commit
that referenced
this pull request
Mar 3, 2025
niksirbi
added a commit
that referenced
this pull request
Mar 3, 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 * Qt widget for loading pose datasets as napari Points layers (#253) * 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 <changhuan.lo@ucl.ac.uk> * [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 <changhuan.lo@ucl.ac.uk> * Remove print statement from test Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * 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 <changhuan.lo@ucl.ac.uk> * 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 <changhuan.lo@ucl.ac.uk> * fix typo Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * 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 <changhuan.lo@ucl.ac.uk> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> --------- Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * added `movement launch` CLI entrypoint (#345) * updated dimensions order in poses_to_napari_tracks conversion function * Document napari plugin (#393) * started user guide about napari plugin * added optional dependencies for napari-video and pyvideoreader * WIP expanding on the napari plugin user guide * add section on loading poses datasets * set maximum card columns to 2 in the user guide page * corrected grammar and spelling mistakes in the plugin guide * removed automatic setting of playback fps to tracking fps * update to v3 of pyvista/setup-headless-display-action * Apply suggestions from Sofia's code review Co-authored-by: sfmig <33267254+sfmig@users.noreply.github.com> * renamed napari guide and added clarifications * fps spinbox: make float, default 1, add tooltip * made image annotations more prominent * Apply suggestions from CH's code review Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * applied more suggestions from CH's review * documented known issues * renamed napari_plugin.md to gui.md * add link to github issues tagged with GUI + bug * Use movement-github link from myst-url-scheme Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> --------- Co-authored-by: sfmig <33267254+sfmig@users.noreply.github.com> Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * use updated pytest fixtures in napari convert tests * Replace bg-utils with qt-niu (#441) * update command for testing GUI in installation guide. * updated wording in v0.1 roadmap --------- Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: sfmig <33267254+sfmig@users.noreply.github.com>
niksirbi
added a commit
that referenced
this pull request
Apr 8, 2025
niksirbi
added a commit
that referenced
this pull request
Jun 17, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
What is this PR
Why is this PR needed?
This was brought up by @lochhh while reviewing #253.
What does this PR do?
Adds a new CLI entry point, called
movement launch, which aliases topython -m napari -w movement(i.e. launch napari with the movement plugin docked). I'm open to different names for this command.References
movement infoentry point Add CLI entrypoint #176How has this PR been tested?
I had troubles extending the existing unit test with parametrisation, so I added a separate test for the
movement launchcommand. Let me know if there's a better way.It would be nice to test if the command works as expected on Windows.
Is this a breaking change?
No.
Does this PR require an update to the documentation?
Yes, but this will be part of the upcoming user guide for the
napari plugin#283.Checklist: