chore: Migrate dev setup from hatch to uv (#46)

Author: manzt

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: Release
+name: CI
 
 on:
   push:
@@ -14,34 +14,33 @@ jobs:
   Lint:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      # this could be replaced with pre-commit.ci
-      - run: pipx run pre-commit run --all-files
+      - uses: actions/checkout@v3
+      - uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.4.x"
+      - run: |
+          uv run ruff check
+          uv run ruff format
 
   Test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-
+        python-version:
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v3
+      - run: echo "${{ matrix.python-version }}" > .python-version
+      - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .[test,dev]
-
-      - name: Run tests
-        run: pytest --color=yes
+          python-version-file: ".python-version"
+      - uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.4.x"
+      - run: uv run pytest --color=yes
 
   Release:
     if: startsWith(github.ref, 'refs/tags/')
@@ -50,24 +49,17 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Setup Python
-        uses: actions/setup-python@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 twine
+          version: "0.4.x"
 
-      - name: Build
-        run: |
-          python -m build
-          twine check dist/*
+      - run: |
+          uv build
+          uvx twine check dist/*
           ls -lh dist
 
       - name: Publish to PyPI
-        run: twine upload dist/*
+        run: uvx twine upload dist/*
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}

.pre-commit-config.yaml

@@ -73,60 +73,24 @@ umap_vs_ozette
 <img width="1269" alt="User interface of cev's comparison widget" src="https://github.com/OzetteTech/comparative-embedding-visualization/assets/84813279/db28944b-fa36-475c-b3b9-efd07272e1b9">
 
 
-
 See [notebooks/getting-started.ipynb](notebooks/getting-started.ipynb) for the complete example.
 
 ## Development
 
-First, create a virtual environment with all the required dependencies. We highly recommend to use [`hatch`](https://github.com/pypa/hatch), which installs and sync all dependencies from `pyproject.toml` automatically.
-
-```sh
-hatch shell
-```
-
-Alternatively, you can also use [`conda`](https://docs.conda.io/en/latest/).
+We use [`uv`](https://astral.sh/uv) for development.
 
 ```sh
-conda env create -n cev python=3.11
-conda activate cev
-```
-
-Next, install `cev` with all development assets.
-
-```sh
-pip install -e ".[notebooks,dev]"
-```
-
-Finally, you can now run the notebooks with:
-
-```sh
-jupyterlab
+uv run jupyterlab
 ```
 
 ### Commands Cheatsheet
 
-If using `hatch` CLI, the following commands are available in the default environment:
-
 | Command                | Action                                                              |
 | :--------------------- | :------------------------------------------------------------------ |
-| `hatch run fix`        | Format project with `black .` and apply linting with `ruff --fix .` |
-| `hatch run fmt`        | Format project with `black .` and apply linting with `ruff --fix .` |
-| `hatch run check`      | Check formatting and linting with `black --check .` and `ruff .`.   |
-| `hatch run test`       | Run unittests with `pytest` in base environment.                    |
-| `hatch run test:test`  | Run unittests with `pytest` in all supported environments.          |
-
-Alternatively, you can devlop **cev** by manually creating a virtual environment and managing
-dependencies with `pip`.
-
-Our CI linting/formatting checks are configured with [`pre-commit`](https://pre-commit.com/).
-We recommend installing the git hook scripts to allow `pre-commit` to run automatically on `git commit`.
-
-```sh
-pre-commit install # run this once to install the git hooks
-```
+| `uv run ruff format`   | Format the source code.                                             |
+| `uv run ruff check`    | Check the source code for formatting issues.                        |
+| `uv run pytest`        | Run unit tests with `pytest` in base environment.                   |
 
-This will ensure that code pushed to CI meets our linting and formatting criteria. Code that does
-not comply will fail in CI.
 
 ## Release
 

README.md

@@ -33,9 +33,10 @@
    "outputs": [],
    "source": [
     "import pathlib\n",
-    "import sys\n",
+    "\n",
     "import pandas as pd\n",
-    "from cev.widgets import Embedding, EmbeddingComparisonWidget, compare\n",
+    "\n",
+    "from cev.widgets import Embedding, EmbeddingComparisonWidget\n",
     "\n",
     "\n",
     "def get_embedding(folder: str, sample: str):\n",

notebooks/abundance-analysis.ipynb

@@ -22,6 +22,7 @@
    "outputs": [],
    "source": [
     "import pandas as pd\n",
+    "\n",
     "from cev.widgets import Embedding, EmbeddingComparisonWidget"
    ]
   },

notebooks/getting-started.ipynb

@@ -31,9 +31,10 @@
    "outputs": [],
    "source": [
     "import pathlib\n",
-    "import sys\n",
+    "\n",
     "import pandas as pd\n",
-    "from cev.widgets import Embedding, EmbeddingComparisonWidget, compare"
+    "\n",
+    "from cev.widgets import Embedding, EmbeddingComparisonWidget"
    ]
   },
   {
@@ -126,18 +127,18 @@
     "for column in marker_annotations:\n",
     "    marker_annotations[column] = marker_annotations[column].str.slice(-1)\n",
     "\n",
-    "df_ozette_umap_ozette_labels[\n",
-    "    [f\"{m}_faust_annotation\" for m in markers]\n",
-    "] = marker_annotations\n",
-    "df_ozette_umap_symphony_labels[\n",
-    "    [f\"{m}_faust_annotation\" for m in markers]\n",
-    "] = marker_annotations\n",
-    "df_symphony_umap_ozette_labels[\n",
-    "    [f\"{m}_faust_annotation\" for m in markers]\n",
-    "] = marker_annotations\n",
-    "df_symphony_umap_symphony_labels[\n",
-    "    [f\"{m}_faust_annotation\" for m in markers]\n",
-    "] = marker_annotations"
+    "df_ozette_umap_ozette_labels[[f\"{m}_faust_annotation\" for m in markers]] = (\n",
+    "    marker_annotations\n",
+    ")\n",
+    "df_ozette_umap_symphony_labels[[f\"{m}_faust_annotation\" for m in markers]] = (\n",
+    "    marker_annotations\n",
+    ")\n",
+    "df_symphony_umap_ozette_labels[[f\"{m}_faust_annotation\" for m in markers]] = (\n",
+    "    marker_annotations\n",
+    ")\n",
+    "df_symphony_umap_symphony_labels[[f\"{m}_faust_annotation\" for m in markers]] = (\n",
+    "    marker_annotations\n",
+    ")"
    ]
   },
   {

notebooks/lui-2021.ipynb

@@ -33,14 +33,7 @@ dependencies = [
 ]
 dynamic = ["version"]
 
-# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
-dev = [
-    "black[jupyter]==23.1.0",
-    "jupyterlab",
-    "pytest",
-    "ruff==0.0.246",
-]
 notebooks = [
     "pyarrow",
     "fastparquet",
@@ -59,31 +52,15 @@ sources = ["src"]
 [tool.hatch.version]
 source = "vcs"
 
-[tool.hatch.envs.default]
-python = "3.10"
-features = ["dev", "notebooks"]
-
-[tool.hatch.envs.default.scripts]
-fmt = [
-    "black .",
-    "ruff --fix .",
-]
-check = [
-    "black --check --diff .",
-    "ruff .",
-]
-test = "pytest --color=yes"
-
-[[tool.hatch.envs.test.matrix]]
-python = ["38", "39", "310", "311"]
-
 [tool.ruff]
 line-length = 88
 target-version = "py38"
+
+[tool.ruff.lint]
 extend-select = [
     "E",    # style errors
     "F",    # flake
-    # "D",    # pydocstyle
+    # "D",  # pydocstyle
     "I001", # isort
     "UP",   # pyupgrade
     "RUF",  # ruff-specific rules
@@ -98,3 +75,10 @@ filterwarnings = [
     "ignore:Jupyter is migrating its paths:DeprecationWarning",
     "ignore:Deprecated in traitlets 4.1, use the instance .metadata:DeprecationWarning",
 ]
+
+[tool.uv]
+dev-dependencies = [
+    "jupyterlab>=4.2.5",
+    "pytest>=8.3.3",
+    "ruff>=0.7.0",
+]

pyproject.toml

@@ -24,7 +24,7 @@
 
 
 def _create_titles(
-    titles: tuple[str, str]
+    titles: tuple[str, str],
 ) -> tuple[ipywidgets.Widget, ipywidgets.Widget]:
     left_title, right_title = titles
     spacer = ipywidgets.HTML(

src/cev/_embedding_comparison_widget.py

@@ -399,15 +399,13 @@ def robust_labels(labels: npt.ArrayLike, robust: npt.NDArray[np.bool_] | None =
 
 
 @typing.overload
-def create_colormaps(cats: typing.Iterable[str]) -> dict:
-    ...
+def create_colormaps(cats: typing.Iterable[str]) -> dict: ...
 
 
 @typing.overload
 def create_colormaps(
     cats: typing.Iterable[str], *other: typing.Iterable[str]
-) -> tuple[dict, ...]:
-    ...
+) -> tuple[dict, ...]: ...
 
 
 def create_colormaps(

src/cev/_widget_utils.py

@@ -1,4 +1,5 @@
 import pandas as pd
+
 from cev._widget_utils import trim_label_series