chore: modernize to new algorithm parameters API

[Czaki]

Use new API to stop following warning:

/home/czaki/Projekty/PartSeg-smfish/src/PartSeg_smfish/segmentation.py:236: FutureWarning: Access to attribute by [] is deprecated. Use . instead
  self.new_parameters["nucleus_threshold"]["values"],

Summary by CodeRabbit

• Style
  • Improved type hinting for better clarity.
  • Updated import statements for consistency.
  • Renamed some internal variables for clarity.
  • Switched to attribute-style access for certain values.

No changes to app functionality or user experience.

[coderabbitai]

Walkthrough

This update makes minor refinements to type hints, imports, and variable naming within the segmentation module. Type hints are modernized, imports are adjusted for consistency, and some local variables are renamed to clarify their unused status. No logic, control flow, or public interface changes occur.

Changes

File(s)	Change Summary
src/PartSeg_smfish/segmentation.py	Updated type hints to use Sequence[float], moved Callable import to collections.abc, removed unused Union import, and renamed unused local variables with underscore prefix. Changed dictionary-style access to attribute-style for threshold values.

Poem

In fields of code where segments dwell,
A rabbit hops, and all is well.
Type hints pruned, imports neat,
Unused names admit defeat.
No logic changed, just tidied ground—
In burrows, clean code does abound! 🐇✨

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9dbf84d and 7bdf62d.

📒 Files selected for processing (1)

• src/PartSeg_smfish/segmentation.py (5 hunks)

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

• src/PartSeg_smfish/segmentation.py

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (9)

• GitHub Check: macos-latest py3.10
• GitHub Check: macos-latest py3.11
• GitHub Check: ubuntu-latest py3.12
• GitHub Check: windows-latest py3.10
• GitHub Check: macos-latest py3.12
• GitHub Check: windows-latest py3.12
• GitHub Check: ubuntu-latest py3.11
• GitHub Check: windows-latest py3.11
• GitHub Check: ubuntu-latest py3.10

✨ Finishing Touches

• 📝 Generate Docstrings

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Explain this complex logic.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai explain this code block.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and explain its main purpose.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Support

Need help? Create a ticket on our support page for assistance with any issues or questions.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai generate docstrings to generate docstrings for this PR.
• @coderabbitai generate sequence diagram to generate a sequence diagram of the changes in this PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[coderabbitai]

Actionable comments posted: 1

♻️ Duplicate comments (1)

src/PartSeg_smfish/segmentation.py (1)

442-445: Same Python-version concern as above

Please harmonise this signature with the previous suggestion to avoid divergent hints and potential 3.9 breakage.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 3af09e8 and 9dbf84d.

📒 Files selected for processing (1)

• src/PartSeg_smfish/segmentation.py (5 hunks)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (9)

• GitHub Check: windows-latest py3.11
• GitHub Check: windows-latest py3.12
• GitHub Check: macos-latest py3.12
• GitHub Check: macos-latest py3.11
• GitHub Check: macos-latest py3.10
• GitHub Check: ubuntu-latest py3.12
• GitHub Check: ubuntu-latest py3.10
• GitHub Check: windows-latest py3.10
• GitHub Check: ubuntu-latest py3.11

🔇 Additional comments (3)

src/PartSeg_smfish/segmentation.py (3)

3-3: Import source modernised correctly

Using Callable from collections.abc is preferred since typing.Callable is deprecated in 3.12+. No issues spotted.

---

233-238: Good: unused-value made explicit

Renaming the second return value to _nucleus_thr_val quiets linters while still leaving a breadcrumb for future debugging—sensible choice.

---

276-281: Mirrors nucleus-mask change – looks fine

Same pattern applied for molecule mask; change is consistent and correct.