pyproject.toml and CONTRIBUTING.md

Author: katosh

CHANGELOG.md

@@ -1,11 +1,9 @@
-# 1.6.1
-
- - forward randome state to k-means to compute landmarks
-
 # v1.6.0
 
  - use [PyNNDescent](https://github.com/lmcinnes/pynndescent) for faster nearest neighbor distance computation
  - update deprecated `tol` argument of `jax.numpy.linalg.matrix_rank` to `rtol`
+ - forward random state to k-means to compute landmarks
+ - modernize build system using pyproject.toml instead of setup.py
 
 # v1.5.0
 

CONTRIBUTING.md

@@ -0,0 +1,86 @@
+# Contributing to Mellon
+
+Thank you for your interest in contributing to Mellon!
+
+## Development Environment
+
+### Setting up with micromamba or conda
+
+We recommend using micromamba or conda for your development environment:
+
+```bash
+# Create development environment
+micromamba create -n mellon_dev python=3.9 -y
+micromamba activate mellon_dev
+
+# Install in development mode with dev dependencies
+pip install -e ".[dev]"
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run tests with coverage report
+pytest --cov=mellon
+```
+
+### Code Formatting
+
+We use Black and isort for code formatting:
+
+```bash
+# Format code with Black
+black mellon tests
+
+# Sort imports with isort
+isort mellon tests
+```
+
+### Type Checking
+
+```bash
+# Run static type checking with mypy
+mypy mellon
+```
+
+### Linting
+
+```bash
+# Run flake8 for linting
+flake8 mellon tests
+```
+
+## Building the Package
+
+```bash
+# Build wheel
+python -m build --wheel
+
+# Build source distribution
+python -m build --sdist
+```
+
+## Documentation
+
+To build the documentation:
+
+```bash
+# Install docs dependencies
+pip install -e ".[docs]"
+
+# Build documentation
+cd docs
+make html
+```
+
+## Pull Request Process
+
+1. Ensure your code passes all tests
+2. Update documentation where necessary
+3. Add an entry to CHANGELOG.md
+4. Submit a pull request
+
+Thank you for helping improve Mellon!

MANIFEST.in

@@ -0,0 +1,9 @@
+include LICENSE
+include README.rst
+include CHANGELOG.md
+include CITATION.cff
+include pyproject.toml
+include pytest.ini
+
+recursive-include tests *.py
+recursive-include docs *.py *.rst *.txt *.ico

pyproject.toml

@@ -0,0 +1,76 @@
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mellon"
+version = "1.6.0"
+description = "Non-parametric density estimator."
+authors = [
+    {name = "Setty Lab", email = "dominik.otto@gmail.com"}
+]
+readme = "README.rst"
+license = {text = "GNU General Public License v3.0"}
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+]
+requires-python = ">=3.6"
+dependencies = [
+    "jax",
+    "jaxopt",
+    "scikit-learn",
+    "pynndescent",
+]
+
+[project.urls]
+Homepage = "https://github.com/settylab/mellon"
+
+[tool.setuptools]
+packages = ["mellon"]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "flake8",
+    "isort",
+    "mypy",
+    "pytest",
+    "pytest-cov",
+    "typing-extensions",
+]
+docs = [
+    "sphinxcontrib-autoprogram",
+    "sphinxcontrib-napoleon",
+    "sphinx-autodocgen",
+    "sphinx-github-style>=1.2.2",
+    "sphinx-mdinclude",
+    "m2r2",
+    "nbsphinx",
+    "furo",
+    "typing-extensions",
+    "IPython",
+]
+
+[project.scripts]
+mellon-test = "pytest:main"
+
+[tool.pytest]
+testpaths = ["tests"]
+
+[tool.black]
+line-length = 88
+target-version = ["py36", "py37", "py38", "py39"]
+include = '\.pyi?$'
+
+[tool.isort]
+profile = "black"
+line_length = 88
+multi_line_output = 3
+
+[tool.mypy]
+python_version = "3.9"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = false
+disallow_incomplete_defs = false

readthedocs.yaml

@@ -12,4 +12,6 @@ python:
    install:
    - requirements: docs/requirements.txt
    - method: pip
-     path: .
+     path: .
+     extra_requirements:
+       - docs

requirements.txt

@@ -1 +1 @@
-.
+-e .

setup.py

@@ -1,47 +1,8 @@
-from setuptools import setup
-
-# read the contents of your README file
-from pathlib import Path
-
-this_directory = Path(__file__).parent
-
-
-def get_version(rel_path):
-    for line in (this_directory / rel_path).read_text().splitlines():
-        if line.startswith("__version__"):
-            delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
-    else:
-        raise RuntimeError("Unable to find version string.")
+"""
+This setup.py file is only for backward compatibility.
+The actual configuration is in pyproject.toml.
+"""
 
+from setuptools import setup
 
-setup(
-    name="mellon",
-    version=get_version("mellon/__init__.py"),
-    description="Non-parametric density estimator.",
-    url="https://github.com/settylab/mellon",
-    author="Setty Lab",
-    author_email="dominik.otto@gmail.com",
-    license="GNU General Public License v3.0",
-    packages=["mellon"],
-    install_requires=[
-        "jax",
-        "jaxopt",
-        "scikit-learn",
-        "pynndescent",
-    ],
-    extras_require={
-        'dev': [
-            'flake8',
-            'pytest',
-            'coverage',
-            'typing-extensions'
-        ]
-    },
-    classifiers=[
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-    ],
-    long_description=(this_directory / "README.rst").read_text(),
-    long_description_content_type="text/x-rst",
-)
+setup()