Make numba dependency optional

[mschwoer]

This would be the required changes to have the numba dependency optional. Let me know what you think.

Note that in the first two commits, I removed numba decorators. According to Claude Code, they should not have given any benefit in the first place.

Called the extra "full", as next steps could be to make rdkit optional. But maybe more fine-granular choice of dependencies is desired here?

[Copilot]

Pull request overview

This PR makes the numba dependency optional to support environments where numba is unavailable or undesired, introducing a new alphabase[full] installation option.

Changes:

• Introduced a numba_wrapper module that provides fallback implementations when numba is not installed
• Moved numba from core requirements to optional full dependencies
• Added test markers to skip numba-dependent tests when the package is not available

Reviewed changes

Copilot reviewed 28 out of 28 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
alphabase/numba_wrapper.py	New compatibility module providing fallback decorators and types when numba is unavailable
alphabase/constants/atom.py	Replaced direct numba imports with wrapper imports
alphabase/constants/isotope.py	Replaced direct numba imports with wrapper imports
alphabase/constants/modification.py	Replaced direct numba imports with wrapper imports
alphabase/peptide/fragment.py	Replaced direct numba imports with wrapper imports
alphabase/peptide/precursor.py	Replaced direct numba imports with wrapper imports
alphabase/protein/fasta.py	Replaced direct numba imports with wrapper imports
alphabase/protein/lcp_digest.py	Replaced direct numba imports with wrapper imports
alphabase/psm_reader/alphapept_reader.py	Removed numba decorators that provided no benefit
alphabase/psm_reader/maxquant_reader.py	Removed numba decorators that provided no benefit
alphabase/spectral_library/annotate.py	Replaced direct numba imports with wrapper imports
alphabase/spectral_library/translate.py	Replaced direct numba imports with wrapper imports
requirements/requirements.txt	Removed numba from core dependencies with clarifying comments
requirements/requirements_loose.txt	Removed numba and contextlib2 from loose requirements
requirements/requirements_full.txt	New file pinning numba version for full installation
requirements/requirements_full_loose.txt	New file for unpinned numba requirement
pyproject.toml	Added full and full-stable optional dependencies
tests/integration/conftest.py	Added pytest marker for skipping tests requiring numba
tests/unit/constants/test_isotope.py	Added requires_numba marker
tests/unit/constants/test_modification_functions.py	Added requires_numba marker
tests/unit/protein/test_fasta.py	Added requires_numba marker
tests/unit/spectral_library/test_annotate.py	Added requires_numba marker
tests/test_fragment.py	Added requires_numba marker
nbs_tests/conftest.py	New conftest to skip notebook tests when numba unavailable
nbs_tests/test_thread.ipynb	Removed test notebook that directly used numba
README.md	Updated installation instructions for optional numba dependency
.github/workflows/pip_installation.yml	Added test jobs for both with and without numba installation
.github/workflows/branch-checks.yaml	Updated to test both full and not-full installations

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[Copilot]

The @numba.njit decorator was removed from truncate_isotope, but this function is still called from numba-compiled code in reset_elements. When numba is installed, numba cannot compile calls to undecorated functions. This will cause compilation errors in reset_elements when numba is available.

[mschwoer]

yikes.. fixed this using a conditional decorator