Modernize packaging with uv support and upgrade to NumPy 2.0 #2
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- 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.
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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/