Make: NumBa is now optional

Author: ashvardanian

CONTRIBUTING.md

@@ -10,10 +10,10 @@ pytest test.py -s -x
 Alternatively, consider using `uv`:
 
 ```sh
-uv venv --python 3.12                       # Or your preferred Python version
-source .venv/bin/activate                   # To activate the virtual environment
-uv pip install ".[dev]"                     # To install the package and development dependencies
-uv run pytest -ra -q test.py                # To run the tests
+uv venv --python 3.12           # Or your preferred Python version
+source .venv/bin/activate       # To activate the virtual environment
+uv pip install ".[dev]"         # To install the package and development dependencies
+uv run pytest -ra -q test.py    # To run the tests
 ```
 
 ### Symmetry Test for Needleman-Wunsch

README.md

@@ -30,17 +30,18 @@ During my exploration of exiting implementations, I've noticed several bugs:
 
 ## Installation
 
-Even without installing Python, you can just use `uv` to get the latest version of the library:
+Numba is optional.
+Installing without it gives a pure-Python baseline; installing with the `numba` extra enables JIT acceleration when a compatible Numba is available.
 
-```bash
-$ uv tool install git+https://github.com/ashvardanian/affine-gaps.git
-$ affine-gaps --help
+```sh
+uv pip install affine-gaps          # minimal
+uv pip install 'affine-gaps[numba]' # with JIT
 ```
 
-Alternatively, you can install it using `pip`:
+Even without installing Python or touching PyPi, you can just use `uv` to get the latest version of the library:
 
 ```bash
-$ pip install git+https://github.com/ashvardanian/affine-gaps.git
+$ uv tool install git+https://github.com/ashvardanian/affine-gaps.git
 $ affine-gaps --help
 ```
 

affine_gaps.py

@@ -1,7 +1,20 @@
 from typing import Tuple, Optional, Callable
 
 import numpy as np
-import numba as nb
+
+# Numba is optional: provide a no-op fallback for the decorator
+try:
+    import numba as nb  # type: ignore
+except Exception:  # pragma: no cover - fallback when Numba isn't available
+    class _NoNumba:
+        def jit(self, *args, **kwargs):
+            def _decorator(fn):
+                return fn
+
+            return _decorator
+
+    nb = _NoNumba()  # type: ignore
+    
 from colorama import Fore, Style
 from colorama import init as _colorama_init
 

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
     { name = "Ash Vardanian", email = "1983160+ashvardanian@users.noreply.github.com" },
 ]
 requires-python = ">=3.6"
-dependencies = ["numba", "numpy", "colorama"]
+dependencies = ["numpy", "colorama"]
 keywords = ["bioinformatics", "sequence alignment", "numba", "affine gaps"]
 classifiers = [
     "Programming Language :: Python :: 3",
@@ -21,6 +21,7 @@ classifiers = [
 
 [project.optional-dependencies]
 dev = ["biopython", "stringzilla", "pytest", "pytest-repeat"]
+numba = ["numba"]
 
 [tool.pytest.ini_options]
 addopts = "-s -x"

setup.py

@@ -10,14 +10,17 @@
     long_description_content_type="text/markdown",
     url="https://github.com/ashvardanian/affine-gaps",
     py_modules=["affine_gaps"],
-    install_requires=["numba", "numpy", "colorama"],
+    install_requires=["numpy", "colorama"],
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: OS Independent",
     ],
     python_requires=">=3.6",
-    extras_require={"dev": ["biopython", "stringzilla", "pytest", "pytest-repeat"]},
+    extras_require={
+        "dev": ["biopython", "stringzilla", "pytest", "pytest-repeat"],
+        "numba": ["numba"],
+    },
     entry_points={
         "console_scripts": [
             "affine-gaps=affine_gaps:main",