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Prepare v0.5.0 release#42

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braniii merged 5 commits intomainfrom
copilot/prepare-release-v0-5-0
Nov 24, 2025
Merged

Prepare v0.5.0 release#42
braniii merged 5 commits intomainfrom
copilot/prepare-release-v0-5-0

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Copilot AI commented Nov 11, 2025

Release v0.5.0 with kmedoids deprecation, TUI support, Python version updates, and numpy 2.x migration.

Version Updates

  • Bumped to 0.5.0 in __init__.py, setup.py, CITATION.cff
  • Updated copyright to 2021-2025

CHANGELOG

  • Moved unreleased changes to v0.5.0 (2025-11-11)
  • Added comprehensive API changes:
    • Deprecated and removed kmedoids clustering mode
    • Dropped Python 3.8 support
    • Removed scikit-learn-extra dependency (was used for k-medoids)
    • Switched to numpy 2.x (minimum version numpy>=2.0.0)
  • Added features and improvements:
    • Added trogon terminal user interface for easier usage of CI
    • Added support for Python 3.12, 3.13, and 3.14
  • Added bugfix for matplotlib plotting error (matplotlib artist error in CI plotting #28) - fixed typo: vimvmin
  • Updated version comparison links

Documentation

  • Added FAQ entry explaining kmedoids deprecation with alternatives
  • Removed kmedoids from module docstring
  • Fixed clustering mode examples to list all available modes

Users of mode='kmedoids' should migrate to 'CPM', 'modularity', or 'linkage':

clust = mosaic.Clustering(
    mode='CPM',  # or 'modularity', 'linkage'
)
Original prompt

Prepare the release of v0.5.0

  • bump version
  • update CHANGELOG.md
  • Add a note in the FAQ and README regarding deprecated kmedoids feature
  • Update the README where needed
  • Please check if anything else should be adjusted

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

Copilot AI and others added 2 commits November 11, 2025 11:33
- Updated version to 0.5.0 in __init__.py, setup.py, and CITATION.cff
- Updated CHANGELOG.md with v0.5.0 release notes and kmedoids deprecation
- Added FAQ entry about deprecated kmedoids feature
- Updated README with new version and copyright year
- Fixed clustering mode comment in README to include all modes

Co-authored-by: braniii <28560129+braniii@users.noreply.github.com>
Co-authored-by: braniii <28560129+braniii@users.noreply.github.com>
Copilot AI changed the title [WIP] Prepare release of version 0.5.0 Prepare v0.5.0 release Nov 11, 2025
Copilot AI requested a review from braniii November 11, 2025 11:37
@braniii braniii marked this pull request as ready for review November 11, 2025 12:19
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braniii commented Nov 11, 2025

@copilot Please add more details to the changelog. Check all changes since last version:
v0.4.1...main

You are missing for sure the dropped py3.8 support, added py3.12-3.14 support, switch to numpy2, the fixed open issue #28 and probably even more.

- Added dropped Python 3.8 support to API changes
- Added support for Python 3.12-3.14 to improvements
- Added numpy 2.x migration to API changes
- Added removal of scikit-learn-extra dependency
- Added bugfix for matplotlib plotting error (#28)
- Added copyright year update to other changes

Co-authored-by: braniii <28560129+braniii@users.noreply.github.com>
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Copilot AI commented Nov 11, 2025

@copilot Please add more details to the changelog. Check all changes since last version:
v0.4.1...main
...

I've expanded the CHANGELOG with comprehensive details from all changes since v0.4.1:

Added to API changes:

  • Dropped Python 3.8 support
  • Removed scikit-learn-extra dependency
  • Switched to numpy 2.x (minimum numpy>=2.0.0)

Added to improvements:

  • Added support for Python 3.12, 3.13, and 3.14

Added bugfix section:

Added to other changes:

  • Updated copyright year to 2024

Commit: 8432405

@braniii braniii merged commit ac7c5d0 into main Nov 24, 2025
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@braniii braniii deleted the copilot/prepare-release-v0-5-0 branch November 24, 2025 16:39
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2 participants