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fix: enable czifile workaround for 2019.7.2.1 #1246

Merged
merged 2 commits into from
Feb 20, 2025
Merged

fix: enable czifile workaround for 2019.7.2.1 #1246

merged 2 commits into from
Feb 20, 2025

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Czaki
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@Czaki Czaki commented Feb 19, 2025

Closes #1245

Summary by Sourcery

Bug Fixes:

  • Fixes a bug where the czifile workaround was not enabled for version 2019.7.2.1.

Summary by CodeRabbit

  • Bug Fixes
    • Expanded compatibility in image processing to support an additional library version, ensuring consistent decoding and functionality.
  • New Features
    • Updated project dictionary version and added czifile entry for enhanced project tracking.

@Czaki Czaki added this to the 0.16.1 milestone Feb 19, 2025
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sourcery-ai bot commented Feb 19, 2025

Reviewer's Guide by Sourcery

This pull request enables a workaround for czifile version 2019.7.2.1, in addition to the existing workaround for version 2019.7.2. It modifies the version check in package/PartSegImage/image_reader.py to include both versions, ensuring that the DECOMPRESS dictionary is updated correctly.

Updated class diagram for image_reader.py

classDiagram
    class image_reader {
        +DECOMPRESS: dict
    }
    note for image_reader "The DECOMPRESS dictionary is updated based on the czifile version."
Loading

File-Level Changes

Change Details Files
Enabled the czifile workaround for version 2019.7.2.1 in addition to 2019.7.2.
  • Modified the version check to include both 2019.7.2 and 2019.7.2.1.
  • Ensured that the DECOMPRESS dictionary is updated correctly for both versions.
package/PartSegImage/image_reader.py

Assessment against linked issues

Issue Objective Addressed Explanation
#1245 Fix the failing tests in the napari repo workflow, specifically on ubuntu-24.04 py3.10 with commit 6253b11.

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coderabbitai bot commented Feb 19, 2025

Walkthrough

The pull request modifies the conditional check in the image reader module. It expands the accepted version set for czifile from a single version (2019.7.2) to include an additional version (2019.7.2.1). This adjustment ensures that the corresponding assignments in the DECOMPRESS dictionary are applied when either version is detected. Additionally, the version number in the project dictionary is incremented from 15 to 16, and the czifile entry is added.

Changes

File Change Summary
package/PartSegImage/image_reader.py Modified the conditional check to accept an extra czifile version (2019.7.2.1) along with 2019.7.2, affecting decompression assignments.
.github/project_dict.pws Updated version from 15 to 16 and added czifile entry in the project dictionary.

Sequence Diagram(s)

sequenceDiagram
    participant IR as ImageReader
    participant CF as czifile Version

    IR->>CF: Retrieve czifile version
    IR->>IR: Parse version from czifile
    alt Version is 2019.7.2 or 2019.7.2.1
        IR->>IR: Update DECOMPRESS dictionary (keys 5 and 6)
    else Version does not match
        IR->>IR: Skip DECOMPRESS assignment
    end
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Reviewing files that changed from the base of the PR and between fd0a03d and e0215e2.

📒 Files selected for processing (1)
  • .github/project_dict.pws (2 hunks)
⏰ Context from checks skipped due to timeout of 300000ms (28)
  • GitHub Check: 4DNucleome.PartSeg (Tests_other test windows)
  • GitHub Check: 4DNucleome.PartSeg (Tests_other test macos)
  • GitHub Check: 4DNucleome.PartSeg (Tests_linux test_linux)
  • GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller windows)
  • GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos_arm)
  • GitHub Check: 4DNucleome.PartSeg (Builds sdist)
  • GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller macos)
  • GitHub Check: 4DNucleome.PartSeg (Builds pyinstaller_linux)
  • GitHub Check: Base py3.9 / ubuntu-24.04 py 3.9 latest PyQt5
  • GitHub Check: Base py3.12 / ubuntu-24.04 py 3.12 latest PyQt5
  • GitHub Check: Base py3.12 / ubuntu-22.04 py 3.12 latest PyQt6
  • GitHub Check: Base py3.11 / ubuntu-24.04 py 3.11 latest PyQt5
  • GitHub Check: Base py3.11 / windows-latest py 3.11 latest PyQt5
  • GitHub Check: Base py3.12 / macos-14 py 3.12 latest PyQt6
  • GitHub Check: Base py3.11 / macos-13 py 3.11 latest PyQt5
  • GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PySide6
  • GitHub Check: Base py3.10 / ubuntu-24.04 py 3.10 latest PyQt5
  • GitHub Check: Base py3.10 / ubuntu-20.04 py 3.10 latest PySide2
  • GitHub Check: Base py3.10 / ubuntu-22.04 py 3.10 latest PyQt5 _pydantic_1
  • GitHub Check: Test PartSeg minimal / ubuntu-24.04 py 3.9 latest PyQt5
  • GitHub Check: test_coverage / ubuntu-24.04 py 3.12 latest PyQt5
  • GitHub Check: Test PartSeg conda
  • GitHub Check: 4DNucleome.PartSeg (formatting_check check_formating)
  • GitHub Check: 4DNucleome.PartSeg (Documentation_check help)
  • GitHub Check: 4DNucleome.PartSeg (manifest_check manifest_check)
  • GitHub Check: 4DNucleome.PartSeg (GetTestData linux)
  • GitHub Check: 4DNucleome.PartSeg (Documentation_check Notebook_check)
  • GitHub Check: Codacy Static Code Analysis
🔇 Additional comments (2)
.github/project_dict.pws (2)

1-1: LGTM! Version number incremented correctly.

The version number has been properly incremented from 15 to 16 to track the addition of the new word.


17-17: LGTM! Addition of 'czifile' aligns with PR objectives.

The addition of 'czifile' to the spell checker dictionary is appropriate given the PR's focus on enabling the czifile workaround for version 2019.7.2.1.


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Hey @Czaki - I've reviewed your changes - here's some feedback:

Overall Comments:

  • Consider using packaging.version.Version instead of packaging.version.parse for direct version comparisons.
  • It might be clearer to use a tuple of strings instead of parsing the versions.
Here's what I looked at during the review
  • 🟢 General issues: all looks good
  • 🟢 Security: all looks good
  • 🟢 Testing: all looks good
  • 🟢 Complexity: all looks good
  • 🟢 Documentation: all looks good

Sourcery is free for open source - if you like our reviews please consider sharing them ✨
Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.

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codecov bot commented Feb 19, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.15%. Comparing base (6253b11) to head (e0215e2).
Report is 2 commits behind head on develop.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #1246   +/-   ##
========================================
  Coverage    93.15%   93.15%           
========================================
  Files          210      210           
  Lines        33288    33288           
========================================
  Hits         31009    31009           
  Misses        2279     2279           

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

@Czaki Czaki merged commit 409c777 into develop Feb 20, 2025
57 checks passed
@Czaki Czaki deleted the fix_czifile branch February 20, 2025 13:59
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[test-bot] napari repos test fail
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