feat(toolkit): ship macro_lactone_toolkit package

Unify macrolactone detection, numbering, fragmentation, and
splicing under the installable macro_lactone_toolkit package.

- replace legacy src.* modules with the new package layout
- add analyze/number/fragment CLI entrypoints and pixi tasks
- migrate tests, README, and scripts to the new package API

pyproject.toml

@@ -1,74 +1,28 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel"]
+requires = ["setuptools>=69", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "macrolactone-fragmenter"
-version = "1.2.0"
-description = "A tool for analyzing and fragmenting macrolactone (12-20 membered ring) side chains"
+name = "macro_lactone_toolkit"
+version = "0.1.0"
+description = "Toolkit for macrolactone detection, numbering, fragmentation, and splicing."
 readme = "README.md"
-requires-python = ">=3.8"
-license = {text = "MIT"}
+requires-python = ">=3.12"
+license = { text = "MIT" }
 authors = [
-    {name = "Macro Split Team", email = "your.email@example.com"},
+  { name = "Macro Split Team" },
 ]
-keywords = ["chemistry", "cheminformatics", "macrolactone", "rdkit", "fragmentation"]
-classifiers = [
-    "Development Status :: 4 - Beta",
-    "Intended Audience :: Science/Research",
-    "Topic :: Scientific/Engineering :: Chemistry",
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-]
-
 dependencies = [
-    "pandas>=1.3.0",
-    "numpy>=1.20.0",
-    "matplotlib>=3.3.0",
-    "seaborn>=0.11.0",
-    "dataclasses-json>=0.5.0",
-    "tqdm>=4.60.0",
+  "numpy>=1.26",
+  "pandas>=2.2",
 ]
 
-[project.optional-dependencies]
-dev = [
-    "jupyter>=1.0.0",
-    "pytest>=7.0.0",
-    "black>=22.0.0",
-    "flake8>=4.0.0",
-]
-docs = [
-    "mkdocs>=1.4.0",
-    "mkdocs-material>=9.0.0",
-    "mkdocstrings[python]>=0.20.0",
-]
-
-[project.urls]
-Homepage = "https://github.com/yourusername/macro_split"
-Documentation = "https://macro-split.readthedocs.io"
-Repository = "https://github.com/yourusername/macro_split"
-Issues = "https://github.com/yourusername/macro_split/issues"
-
 [project.scripts]
-macro-fragmenter = "src.macrolactone_fragmenter:main"
+macro-lactone-toolkit = "macro_lactone_toolkit.cli:main"
 
-[tool.setuptools]
-packages = ["src"]
-
-[tool.setuptools.package-data]
-src = ["*.py"]
-
-[tool.black]
-line-length = 100
-target-version = ['py38', 'py39', 'py310', 'py311']
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["macro_lactone_toolkit*"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
-python_files = "test_*.py"
-python_classes = "Test*"
-python_functions = "test_*"
-