chore: Migrate dev from hatch to uv (#151)

higlass · Oct 18, 2024 · 4491d73 · 4491d73
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diff --git 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
@@ -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
@@ -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
@@ -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
diff --git 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
@@ -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
diff --git a/docs/environment.yml b/docs/environment.yml
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/serve.sh b/docs/serve.sh
diff --git 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"