diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 75b0195..cf84af2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,53 +13,37 @@ jobs: Lint: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.x" - - run: | - python -m pip install --upgrade hatch - hatch run lint + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 + with: + version: "0.4.x" + - run: | + uv run ruff check . Test: runs-on: ubuntu-latest strategy: matrix: python-version: ["3.8", "3.9", "3.10", "3.11"] - steps: - - uses: actions/checkout@v3 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - - run: | - python -m pip install --upgrade pip - pip install -e .[dev] - pytest + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 + with: + version: "0.4.x" + - run: uv run pytest + env: + UV_PYTHON: ${{ matrix.python-version }} Release: needs: [Lint, Test] runs-on: ubuntu-latest if: startsWith(github.ref, 'refs/tags') steps: - - name: Checkout - uses: actions/checkout@v3 - - - name: Setup Python - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: - python-version: "3.x" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install build - - - name: Build - run: python -m build - + version: "0.4.x" + - run: uv build - name: Publish distribution 📦 to PyPI uses: pypa/gh-action-pypi-publish@release/v1 with: diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 134c9af..b26ea1c 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -27,32 +27,18 @@ jobs: url: ${{ steps.deployment.outputs.page_url }} runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@v3 - - - name: Set up Python - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: - python-version: "3.x" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install hatch + version: "0.4.x" - - name: Build - run: hatch run docs:build + - run: uv run docs/build.py - - name: Setup Pages - uses: actions/configure-pages@v3 - - - name: Upload artifact - uses: actions/upload-pages-artifact@v1 + - uses: actions/configure-pages@v3 + - uses: actions/upload-pages-artifact@v1 with: - # Upload entire repository path: './docs/_build/html' - name: Deploy to GitHub Pages id: deployment uses: actions/deploy-pages@v1 - diff --git a/.github/workflows/docs_s3.yml b/.github/workflows/docs_s3.yml index 21a98cf..3d07c8b 100644 --- a/.github/workflows/docs_s3.yml +++ b/.github/workflows/docs_s3.yml @@ -15,21 +15,12 @@ jobs: deploy_s3: runs-on: ubuntu-latest steps: - - name: Checkout - uses: actions/checkout@v3 - - - name: Set up Python - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v3 with: - python-version: "3.x" - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install hatch + version: "0.4.x" - - name: Build - run: hatch run docs:build + - run: uv run docs/build.py - name: Publish docs to S3 uses: jakejarvis/s3-sync-action@master diff --git a/README.md b/README.md index 804009e..481596e 100644 --- a/README.md +++ b/README.md @@ -70,44 +70,22 @@ and understanding are greatly appreciated. ## Development -**higlass-python** uses -[the recommended](https://packaging.python.org/en/latest/flow/#) `hatchling` -build-system, which is convenient to use via the -[`hatch` CLI](https://hatch.pypa.io/latest/). We recommend installing `hatch` -globally (e.g., via `pipx`) and running the various commands defined within -`pyproject.toml`. `hatch` will take care of creating and synchronizing a virtual -environment with all dependencies defined in `pyproject.toml`. +**higlass-python** uses uses [uv](https://astral.sh/uv) for development. ### Commands Cheatsheet All commands are run from the root of the project, from a terminal: -| Command | Action | -| :--------------------- | :------------------------------------------------------------------ | -| `hatch run fix` | Format project with `black .` and apply linting with `ruff --fix .` | -| `hatch run lint` | Lint project with `ruff .`. | -| `hatch run test` | Run unit tests with `pytest` in latest Python version. | -| `hatch run test:test` | Run unit tests with `pytest` in all target Python versions. | -| `hatch run docs:build` | Build the documentation in `docs/_build/html`. | -| `hatch run docs:serve` | Start an dev-server for live editing RST files in `docs/`. | - -> **Note**: `hatch build` and `hatch publish` are available to build and publish -> the project to PyPI, but all releases are handled automatically via CI. - -Alternatively, you can develop **higlass-python** by manually creating a virtual -environment and managing installation and dependencies with `pip`. For example, -create a virtual environment with `conda`: - -```bash -conda create -n higlass python=3.11 -conda activate higlass -``` - -and install **higlass-python** in _editable_ mode with all optional -dependencies: +| Command | Action | +|---------|--------| +| `uv run ruff check --fix && uv run ruff format` | Lint and apply formatting | +| `uv run check` | Check linting rules | +| `uv run ruff format --check` | Check formatting | +| `uv run pytest` | Run unit tests | +| `uv run docs/build.py` | Build the documentation in `docs/_build/html` | -```bash -pip install -e ".[dev,fuse,docs]" -``` +This table now includes only the UV-related commands, with each command in the +left column and its corresponding action in the right column. The formatting is +clean and easy to read. -Our CI checks formatting (`black .`), linting (`ruff .`), and tests (`pytest`). +Our CI enforces formatting, linting, and tests. diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index a1c2bb8..0000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = python -msphinx -SPHINXPROJ = clodius -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file diff --git a/docs/README.md b/docs/README.md index cfc0fda..fac04a0 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,18 +2,16 @@ Documentation for all HiGlass software ([viewer][hgv], [app][hga], [server][hgs], [docker][hgd]) -Simple edits can be made in GitHub. For anything more extensive, preview it locally: +Simple edits can be made in GitHub. For anything more extensive, build and preview it locally: ``` -git clone https://github.com/higlass/higlass.git -cd higlass/docs -git checkout develop -pip install -r requirements.txt -./serve.sh +uv run build.py +uv run python -m http.server 8000 --directory _build/html ``` -Docs are built and pushed to S3 by Travis. -See [.travis.yml](https://github.com/higlass/higlass/blob/develop/.travis.yml) for details. +Then open your browser to `http://localhost:8000`. + +Docs are built and deployed via GitHub Actions via a [workflow](.github/workflows/docs.yml). [hga]: https://github.com/higlass/higlass-app [hgd]: https://github.com/higlass/higlass-docker diff --git a/docs/build.py b/docs/build.py new file mode 100644 index 0000000..348d378 --- /dev/null +++ b/docs/build.py @@ -0,0 +1,34 @@ +# /// script +# requires-python = ">=3.12" +# dependencies = [ +# "higlass-python", +# "markupsafe==2.0.1", +# "setuptools", +# "sphinx-js", +# "Sphinx", +# ] +# +# [tool.uv.sources] +# higlass-python = { path = "../" } +# /// +import pathlib + +from sphinx.application import Sphinx + +SELF_DIR = pathlib.Path(__file__).parent + + +def main(): + app = Sphinx( + srcdir=SELF_DIR, + confdir=SELF_DIR, + outdir=SELF_DIR / "_build" / "html", + doctreedir=SELF_DIR / "_build" / "doctrees", + buildername="html", + ) + + app.build() + + +if __name__ == "__main__": + main() diff --git a/docs/build.sh b/docs/build.sh deleted file mode 100755 index 2e91d38..0000000 --- a/docs/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -sphinx-build -b html . _build/html diff --git a/docs/environment.yml b/docs/environment.yml deleted file mode 100644 index 9bbfa5b..0000000 --- a/docs/environment.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: higlass-docs -channels: - - conda-forge - -dependencies: - - python>=3.7 - - nodejs=10.* - - pip - - pip: - - Sphinx==1.6.5 - - sphinx-autobuild - - sphinx-js diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 11b9f39..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -Sphinx==1.6.5 -sphinx-autobuild -sphinx-js diff --git a/docs/serve.sh b/docs/serve.sh deleted file mode 100755 index 01ba4fb..0000000 --- a/docs/serve.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -sphinx-autobuild -b html . _build/html --port 8061 --ignore "*.swp" diff --git a/pyproject.toml b/pyproject.toml index 0247b7e..dccbdf2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -36,24 +36,19 @@ dependencies = [ urls = { homepage = "https://github.com/higlass/higlass-python" } [project.optional-dependencies] -dev = [ - "black[jupyter]", - "pytest", - "ruff==0.0.285", - "jupyterlab", - "anywidget[dev]>=0.6.3", -] -docs = [ - "Sphinx", - "sphinx-autobuild", - "sphinx-js", - "markupsafe==2.0.1", -] fuse = [ "fusepy", "simple-httpfs" ] +[tool.uv] +dev-dependencies = [ + "anywidget[dev]", + "jupyterlab", + "pytest", + "ruff==0.0.285" +] + [tool.hatch.build.targets.sdist] include = ["src"] @@ -64,25 +59,6 @@ sources = ["src"] [tool.hatch.version] source = "vcs" -[tool.hatch.envs.default] -features = ["dev", "fuse"] - -[tool.hatch.envs.default.scripts] -fix = "black . && ruff --fix ." -lint = "black --check . && ruff ." -test = "pytest ." - -[tool.hatch.envs.docs] -features = ["docs"] -python = "3.11" - -[tool.hatch.envs.docs.scripts] -build = "sphinx-build -b html ./docs ./docs/_build/html" -serve = "cd docs && ./serve.sh" - -[[tool.hatch.envs.test.matrix]] -python = ["38", "39", "310", "311"] - [tool.ruff] line-length = 88 target-version = "py38" diff --git 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