refactor: Reorganize project to use uv and uv_build

.github/workflows/ci.yml

@@ -17,14 +17,14 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     steps:
       - uses: actions/checkout@v6
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - run: |
-          python -m pip install --upgrade pip hatch
-          pip install -e .[dev]
-          hatch run test
+          python -m pip install --upgrade pip
+          pip install --group test -e .
+          pytest

.readthedocs.yaml

@@ -2,29 +2,13 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
-version: 2
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: docs/conf.py
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
-
-# Optionally set the version of Python and requirements required to build your docs
-# setup_py_install: true
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - dev
-        - docs
+    python: "3.13"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --group dev
+    - uv run python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html

CONTRIBUTING.md

@@ -20,81 +20,62 @@ This project has a number of requirements for all code contributed.
 
 ## Setting up Your Development Environment
 
-This project uses the [hatch](https://hatch.pypa.io/latest/) project manager and build system. We recommend you install `hatch` as a global isolated application using [pipx](https://pipx.pypa.io/stable/). See other installation options [here](https://hatch.pypa.io/latest/install/).
+This project uses the [uv](https://docs.astral.sh/uv/) project manager and [uv_build](https://docs.astral.sh/uv/concepts/build-backend/) build backend.
 
-```sh
-pipx install hatch
-```
-
-> [!NOTE]
-> Many custom command shortcuts are accessible through hatch (and shown below). See `tool.hatch.envs.default.scripts` in our project's `pyproject.toml` configuration file.
-
-After forking and cloning the repository, you can create an isolated Python development environment and install the package in "editable" (i.e. development) mode as follows:
+To set up your dev environment, run:
 
 ```sh
-git clone https://github.com/open2c/bioframe.git
-cd bioframe
-hatch shell
+uv sync
 ```
 
-The first time you run `hatch shell` the environment will be created and activated, and the package will be installed. In future sessions, running `hatch shell` will reactivate your development environment.
-
-> [!TIP]
-> If you prefer to store your virtual environments in your working directory (like classic virtualenvs) rather than in a centralized location (similar to conda), configure hatch as follows:
->
-> ```sh
-> hatch config set dirs.env.virtual .venv
-> ```
->
-> This will make hatch set up its environments within the current working directory under `.venv`.
+This command will include the requirements from the `dev` [dependency group](https://peps.python.org/pep-0735/) by default, which includes dependencies for development, testing, and documentation.
 
 Alternatively, if you prefer to manage your virtual environments yourself, you can install the package for development using, for example:
 
 ```sh
 python -m venv .venv
 source .venv/bin/activate
-pip install -e '.[dev,test,docs]'
+pip install --group dev -e .
 ```
 
 For all pull requests, linting and unit tests are automatically run using the [GitHub Actions](https://docs.github.com/en/actions) Continuous Integration service. However, you are still encouraged to run these checks locally before pushing code to a PR.
 
 ## Linting and Formatting
 
-We use [ruff](https://docs.astral.sh/ruff/) for style checking. Run `ruff check .` or:
+We use [ruff](https://docs.astral.sh/ruff/) for style checking.
 
 ```sh
-hatch run lint
+uv run ruff check
 ```
 
-Ruff can fix a lot of errors itself. Run `ruff check --fix .` or:
+Ruff can fix a lot of errors itself.
 
 ```sh
-hatch run fix
+uv run ruff check --fix
 ```
 
 Ruff includes a formatter that mimics [black](https://black.readthedocs.io/en/stable/). To automatically reformat your code, you can use `ruff format {source_file}`.
 
 We use [pre-commit](https://github.com/pre-commit/pre-commit) to make sure the coding style is enforced. You first need to install pre-commit and the corresponding git commit hooks:
 
 ```sh
-pip install pre-commit
-pre-commit install
+uv run pre-commit install
 ```
 
 The last command installs the hooks listed in `.pre-commit-config.yaml` locally into your git repo. If you do this, the checks will run automatically before every commit. You can also manually make sure your code satisfies the coding style:
 
 ```sh
-pre-commit run --all-files
+uv run pre-commit run --all-files
 ```
 
 ## Testing
 
 It is best if all new functionality and/or bug fixes have unit tests added with each use-case.
 
-We use [pytest](https://docs.pytest.org/en/latest) as our unit testing framework. Once you've configured your environment, you can just `cd` to the root of your repository and run `pytest` or:
+We use [pytest](https://docs.pytest.org/en/latest) as our unit testing framework. Once you've configured your environment, you can just `cd` to the root of your repository and run:
 
 ```sh
-hatch run test
+uv run pytest
 ```
 
 ## Documentation
@@ -108,7 +89,7 @@ We use the [Sphinx Autosummary extension](http://www.sphinx-doc.org/en/stable/ex
 To build the documentation, run `sphinx-autobuild` using:
 
 ```sh
-hatch run docs
+uv run sphinx-autobuild docs docs/_build/html
 ```
 
 This will build the documentation and serve it on a local http server which listens for changes and automatically rebuilds.

docs/conf.py

@@ -9,14 +9,11 @@
 from datetime import datetime
 from importlib.metadata import metadata
 
-# autodoc_mock_imports = ["numpy", "pandas", "matplotlib", "requests"]
-
-
 # -- Project information -----------------------------------------------------
 # NOTE: If you installed your project in editable mode, this might be stale.
 #       If this is the case, reinstall it to refresh the metadata
 info = metadata("bioframe")
-project_name = info["Name"]
+project = info["Name"]
 author = "Open2C"
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
@@ -31,25 +28,35 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    # "sphinx.ext.autodoc",
-    # 'sphinx.ext.doctest',
-    # 'sphinx.ext.todo',
-    # 'sphinx.ext.coverage',
-    # 'sphinx.ext.mathjax',
-    # 'sphinx.ext.ifconfig',
     "autodocsumm",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.autosummary",
-    "sphinx.ext.napoleon",  # 'numpydoc'
+    # "myst_parser",
     "myst_nb",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_autodoc_typehints",
+    "sphinx_copybutton",
 ]
+
+source_suffix = [".rst", ".md"]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+exclude_patterns = [
+    "_build",
+    "**.ipynb_checkpoints",
+    "Thumbs.db",
+    ".DS_Store",
+    ".env",
+    ".venv",
+]
 
 # nbsphinx_custom_formats = {
 #     '.md': ['jupytext.reads', {'fmt': 'MyST'}],
@@ -75,5 +82,9 @@
 add_module_names = False
 
 # Cache MyST (.md or .ipynb) notebook outputs if unmodified
-jupyter_execute_notebooks = "cache"
-execution_excludepatterns = ["guide-performance.ipynb"]
+nb_execution_mode = "cache"
+nb_execution_excludepatterns = ["guide-performance.ipynb"]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
-requires = ["hatchling", "hatch-vcs"]
-build-backend = "hatchling.build"
+requires = ["uv_build>=0.7.19"]
+build-backend = "uv_build"
 
 [project]
 name = "bioframe"
@@ -33,6 +33,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 readme = "README.md"
 requires-python = ">=3.8"
@@ -47,35 +48,38 @@ dependencies = [
     "importlib-resources ; python_version<'3.9'",
 ]
 
-[project.optional-dependencies]
-dev = [
+[dependency-groups]
+test = [
+    "pytest>=6.0",
     "biopython",
-    "pre-commit",
     "pysam",
     "pybbi",
-    "pytest",
-    "ruff",
-]
-test = [
-    "pytest",
 ]
 docs = [
     "autodocsumm",
     "myst_nb",
-    "jinja2",
-    "Sphinx",
+    "myst_parser",
+    "sphinx >=4.0",
     "sphinx-autobuild",
     "sphinx_rtd_theme",
+    "sphinx-copybutton",
+    "sphinx-autodoc-typehints",
+]
+dev = [
+    { include-group = "test" },
+    { include-group = "docs" },
+    "pre-commit",
+    "ruff",
 ]
 
 [project.urls]
 homepage = "https://github.com/open2c/bioframe"
-documentation = "https://bioframe.readthedocs.io/en/latest"
-repository = "https://github.com/open2c/bioframe"
+documentation = "https://bioframe.readthedocs.io"
+source = "https://github.com/open2c/bioframe"
+issues = "https://github.com/open2c/bioframe/issues"
 changelog = "https://github.com/open2c/bioframe/blob/main/CHANGES.md"
 
 [tool.ruff]
-target-version = "py37"
 exclude = [
     ".venv",
 ]
@@ -100,30 +104,11 @@ known-first-party = ["bioframe"]
 convention = "numpy"
 
 [tool.pytest.ini_options]
-minversion = "7"
-log_cli_level = "info"
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
 xfail_strict = true
-addopts = [
-    "-ra",
-    "--showlocals",
-    "--strict-config",
-    "--strict-markers",
+filterwarnings = ["error"]
+log_level = "INFO"
+testpaths = [
+  "tests",
 ]
-filterwarnings = ["ignore::PendingDeprecationWarning"]
-testpaths = ["tests"]
-
-[tool.hatch.envs.default]
-features = ["dev", "test", "docs"]
-
-[tool.hatch.envs.default.scripts]
-fix = "ruff check --fix ."
-lint = "ruff check bioframe tests"
-format = "ruff format bioframe tests"
-test = "pytest ."
-docs = "sphinx-autobuild docs docs/_build/html"
-
-[tool.hatch.envs.test]
-features = ["dev", "test"]
-
-[[tool.hatch.envs.test.matrix]]
-python = ["3.9", "3.10", "3.11", "3.12"]