chore: refactor and simplify menu bar creation, add workaround for macOS numpy problem #1124

Czaki · 2024-07-05T14:21:35Z

Summary by CodeRabbit

Refactor
- Improved code readability and maintainability by moving menu bar setup logic to a dedicated method in the main window classes of the ROI Analysis and ROI Mask modules.
Bug Fixes
- Added conditional logic to manage thread usage based on the numpy version and macOS arm64 architecture in the napari image view.
Chores
- Simplified dependencies in pyproject.toml by combining them into a single string "PartSeg[accelerate,pyqt5]".

move creation of menu bar to separate function

sourcery-ai · 2024-07-05T14:21:43Z

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coderabbitai · 2024-07-05T14:21:45Z

Walkthrough

The recent changes improve code organization and functionality in the PartSeg package by refactoring menu bar setup into separate methods, introducing conditional thread usage in napari_image_view.py based on the numpy version and macOS arm64 architecture, and consolidating dependencies in pyproject.toml for better management.

Changes

File	Change Summary
`package/PartSeg/_roi_analysis/main_window.py`	Refactored `MainWindow` class to move menu bar setup to `_setup_menu_bar` method.
`package/PartSeg/_roi_mask/main_window.py`	Refactored `MainWindow` class to move menu setup logic into `_setup_menu_bar` method.
`package/PartSeg/common_gui/napari_image_view.py`	Introduced conditional thread usage for `USE_THREADS` and adjusted `_prepare_layers` method.
`pyproject.toml`	Consolidated dependencies into a single combined dependency string `"PartSeg[accelerate,pyqt5]"`.

Poem

In the land of code, changes bloom bright,
Menu bars refactored, threads take flight.
Dependencies now simpler, all in one bind,
PartSeg evolves, oh how entwined.
A rabbit’s joy in the lines we write,
For maintainability and speed, in the tranquil night.
🐇✨🌙

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sourcery-ai

We've reviewed this pull request using the Sourcery rules engine. If you would also like our AI-powered code review then let us know.

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 2e64542 and 4bab6f6.

Files selected for processing (4)

package/PartSeg/_roi_analysis/main_window.py (2 hunks)
package/PartSeg/_roi_mask/main_window.py (3 hunks)
package/PartSeg/common_gui/napari_image_view.py (3 hunks)
pyproject.toml (1 hunks)

Files skipped from review due to trivial changes (1)

pyproject.toml

Additional comments not posted (6)

package/PartSeg/_roi_analysis/main_window.py (2)

580-581: LGTM! Ensure _setup_menu_bar is correctly implemented.

The call to _setup_menu_bar in the __init__ method looks good. Ensure that the _setup_menu_bar method is correctly implemented and performs the necessary menu bar setup.

611-637: LGTM! Menu bar setup is clear and well-organized.

The _setup_menu_bar method correctly sets up the menu bar and connects actions to their respective methods.

package/PartSeg/_roi_mask/main_window.py (2)

894-895: LGTM! Ensure _setup_menu_bar is correctly implemented.

The call to _setup_menu_bar in the __init__ method looks good. Ensure that the _setup_menu_bar method is correctly implemented and performs the necessary menu bar setup.

950-973: LGTM! Menu bar setup is clear and well-organized.

The _setup_menu_bar method correctly sets up the menu bar and connects actions to their respective methods.
package/PartSeg/common_gui/napari_image_view.py (2)
48-61: Verify the conditional logic for USE_THREADS assignment.

The logic conditionally assigns USE_THREADS based on numpy version and platform details. Ensure that this logic correctly handles all relevant cases and doesn't introduce any unintended side effects.

735-747: Verify the conditional implementation of _prepare_layers.

The method implementation varies based on the USE_THREADS flag. Ensure that both implementations (threaded and non-threaded) are correct and handle all relevant cases.

Verification successful

The conditional implementation of _prepare_layers is correct.

Both the threaded and non-threaded implementations handle image preparation correctly. The threaded implementation creates a worker, connects signals, and starts the worker, while the non-threaded implementation directly calls _prepare_layers.

Threaded implementation: Lines 735-742 in package/PartSeg/common_gui/napari_image_view.py

Non-threaded implementation: Lines 744-746 in package/PartSeg/common_gui/napari_image_view.py
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify the correctness of the conditional implementation of `_prepare_layers`.

# Test: Ensure both implementations (threaded and non-threaded) handle all relevant cases.
rg --type python $'_prepare_layers'
Length of output: 65

Script:
#!/bin/bash
# Description: Verify the correctness of the conditional implementation of `_prepare_layers`.

# Test: Ensure both implementations (threaded and non-threaded) handle all relevant cases.
rg --glob '*.py' '_prepare_layers'
Length of output: 1078

Script:
#!/bin/bash
# Extract the full implementations of `_prepare_layers` from the identified files

# Extract from napari_image_view.py
ast-grep --lang python --pattern $'def _prepare_layers($_, $_, $_):\n    $$$' package/PartSeg/common_gui/napari_image_view.py

# Extract from conftest.py
ast-grep --lang python --pattern $'def _prepare_layers($_, $_, $_):\n    $$$' package/tests/test_PartSeg/conftest.py
Length of output: 242

Script:
#!/bin/bash
# Extract the full implementations of `_prepare_layers` from the identified files

# Extract from napari_image_view.py
ast-grep --lang python --pattern $'def _prepare_layers($_, $_, $_):\n    $$$' package/PartSeg/common_gui/napari_image_view.py

# Extract from conftest.py
ast-grep --lang python --pattern $'def _prepare_layers($_, $_, $_):\n    $$$' package/tests/test_PartSeg/conftest.py
Length of output: 242

Script:
#!/bin/bash
# Extract the full implementations of `_prepare_layers` from the identified files

# Extract from napari_image_view.py
rg --glob '*.py' -A 20 -B 5 'def _prepare_layers' package/PartSeg/common_gui/napari_image_view.py

# Extract from conftest.py
rg --glob '*.py' -A 20 -B 5 'def _prepare_layers' package/tests/test_PartSeg/conftest.py
Length of output: 3037

codecov · 2024-07-05T14:33:00Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.93%. Comparing base (2e64542) to head (cdb9c71).
Report is 78 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1124   +/-   ##
========================================
  Coverage    92.93%   92.93%           
========================================
  Files          205      205           
  Lines        32519    32519           
========================================
  Hits         30220    30220           
  Misses        2299     2299

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 4bab6f6 and 89f8b9d.

Files selected for processing (1)

package/PartSeg/common_gui/napari_image_view.py (3 hunks)

Files skipped from review as they are similar to previous changes (1)

package/PartSeg/common_gui/napari_image_view.py

sonarcloud · 2024-07-05T16:09:39Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

coderabbitai

Actionable comments posted: 0

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 89f8b9d and cdb9c71.

Files selected for processing (1)

package/PartSeg/common_gui/napari_image_view.py (3 hunks)

Files skipped from review as they are similar to previous changes (1)

package/PartSeg/common_gui/napari_image_view.py

Czaki added 4 commits July 5, 2024 15:48

Auto stash before checking out "HEAD"

e77b3d6

move creation of menu bar to separate function

fix all extras

6062ff1

try to get working on macos-arm

6cfb077

move menu bar creation in roi mask to separate function

4bab6f6

Czaki added this to the 0.15.3 milestone Jul 5, 2024

sourcery-ai bot reviewed Jul 5, 2024

View reviewed changes

coderabbitai bot reviewed Jul 5, 2024

View reviewed changes

Exclude hard to test lines from coverage

89f8b9d

coderabbitai bot reviewed Jul 5, 2024

View reviewed changes

no cover second branch of if

cdb9c71

coderabbitai bot reviewed Jul 5, 2024

View reviewed changes

Czaki merged commit af44d19 into develop Jul 5, 2024
58 checks passed

Czaki deleted the simplify_code branch July 5, 2024 16:56

Czaki mentioned this pull request Aug 11, 2024

Calculate status in a separate thread napari/napari#7146

Merged

coderabbitai bot mentioned this pull request Oct 21, 2024

chore: Update CI configuration to use more modern OS and python versions #1207

Merged

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chore: refactor and simplify menu bar creation, add workaround for macOS numpy problem #1124

chore: refactor and simplify menu bar creation, add workaround for macOS numpy problem #1124

Czaki commented Jul 5, 2024 •

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chore: refactor and simplify menu bar creation, add workaround for macOS numpy problem #1124

chore: refactor and simplify menu bar creation, add workaround for macOS numpy problem #1124

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Czaki commented Jul 5, 2024 • edited by coderabbitai bot Loading

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coderabbitai bot commented Jul 5, 2024 • edited Loading

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Quality Gate passed

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Czaki commented Jul 5, 2024 •

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