Modernize packaging with uv support and upgrade to NumPy 2.0#2
Open
Modernize packaging with uv support and upgrade to NumPy 2.0#2
Conversation
- Replace setup.cfg/setup.py with PEP 621 compliant pyproject.toml - Organize dependencies into optional groups (plot, segmentation, jf, burst, dev, all) - Update installation instructions in README - Rename Readme.md to README.md - Remove legacy requirements.txt and minimum_requirements.txt
- Replace deprecated numpy type aliases (np.float -> np.float64, np.int -> np.intp, np.bool -> np.bool_) - Update dependencies: numpy>=2.0.0, scipy>=1.14.0 - Update dev dependencies: pytest>=7.0.0, tqdm>=4.64.0 - Require Python 3.10+ (numpy 2.0 requirement) - Update .gitignore to exclude .venv and .egg-info
Extract first element from seqmap_file when it's returned as a list.
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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:
Summary
setup.cfg/setup.pyto modern PEP 621 compliantpyproject.tomluvChanges
Packaging Modernization
setup.cfg,setup.py,requirements.txt, andminimum_requirements.txtwith a singlepyproject.tomlplot,segmentation,jf,burst,dev,allReadme.mdtoREADME.mduvandpipNumPy 2.0 Migration
np.float→np.float64np.int→np.intpnp.bool→np.bool_numpy>=2.0.0,scipy>=1.14.0pytest>=7.0.0,tqdm>=4.64.0Other
.gitignoreto exclude.venv/and*.egg-info/