chore: cleanup Python dependencies and use [dependency-groups] (#101)

and update `contributing.md`

Author: LDeakin

.github/workflows/ci.yml

@@ -41,17 +41,17 @@ jobs:
           python-version: "3.x"
 
       - name: Install UV
-        uses: astral-sh/setup-uv@v3
+        uses: astral-sh/setup-uv@v6
         with:
-          version: "0.5.0"
+          version: "0.7.19"
           enable-cache: true
           cache-dependency-glob:  |
             pyproject.toml
             Cargo.toml
 
       - name: Install python deps + Build
         run: |
-          uv pip install --system -e ".[test,dev]" --verbose
+          uv pip install --system -e . --group dev --verbose
 
       - name: Python Tests
         run: pytest -n auto

docs/contributing.md

@@ -2,38 +2,54 @@
 
 ## Rust
 
-You will need `rust` and `cargo` installed on your local system.  For more info, see [the rust docs](https://doc.rust-lang.org/cargo/getting-started/installation.html).
+You will need `Rust` and `cargo` installed on your local system.
+For more info, see [the Rust docs](https://doc.rust-lang.org/cargo/getting-started/installation.html).
 
 ## Environment management
 
-We encourage the use of [uv](https://docs.astral.sh/uv/) for environment management.  To install the package for development, run
+We encourage the use of [`uv`](https://docs.astral.sh/uv/) for environment management.
+To create a virtual environment for development with all `dev` dependencies, run
 
 ```shell
-uv pip install -e ".[test,dev,doc]"
+uv sync
 ```
 
-However, take note that while this does build the rust package, the rust package will not be rebuilt upon edits despite the `-e` flag.  You will need to manually rebuild it using either `uv pip install -e .` or `maturin develop`.  Take note that for benchmarking/speed testing, it is advisable to build a release version of the rust package by passing the `-r` flag to `maturin`.  For more information on the `rust`-`python` bridge, see the [`PyO3` docs](https://pyo3.rs/v0.22.6/).
+If you prefer not to use `uv`, simply create and activate a virtual environment, then run:
+```shell
+pip install --group dev -e .
+```
 
-## Testing
+> [!NOTE]
+> The rest of this document assumes you are using `uv`.
+> If you are not using `uv`, just remove the `uv run` preceeding commands.
 
-To install test dependencies, simply run
+> [!WARNING]
+> The above commands initially build the `Rust` package, but it will not be rebuilt upon edits.
+> You will need to manually rebuild it using `uv run maturin develop`.
 
-```shell
-pytest
-```
+For more information on the `Rust`-`Python` bridge, see the [`PyO3` docs](https://pyo3.rs/v0.22.6/).
 
-or
+## Testing
+
+To run tests
 
 ```shell
-pytest -n auto
+uv run maturin develop
+uv run pytest -n auto
 ```
 
-for parallelized tests.  Most tests have been copied from the `zarr-python` repository with the exception of `test_pipeline.py` which we have written.
+Most tests have been copied from the `zarr-python` repository with the exception of `test_pipeline.py` which we have written.
+
+For benchmarking/speed testing, it is advisable to build a release version of the `Rust` package by passing the `-r` flag to `maturin`.
 
 ## Type hints
 
 Thanks to [`pyo3-stub-gen`][], we can generate type stubs for the `zarrs._internal` module.
-If the “Check formatting” CI step fails, run `cargo run --bin stub_gen`, then `pre-commit run --all-files`, and commit the changes.
+If the “Check formatting” CI step fails, run the following and commit the changes:
+```shell
+cargo run --bin stub_gen
+uv run pre-commit run --all-files
+```
 
 Once `maturin` can be run as a `hatchling` plugin, this can be made automatic.
 

pyproject.toml

@@ -19,39 +19,27 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-    'asciitree',
-    'numpy>=1.24',
-    'fasteners',
-    'numcodecs[msgpack]>=0.10.0',
-    'fsspec>2024',
-    'crc32c',
-    'zstandard',
-    'typing_extensions',
-    'donfig',
-    'pytest',
-    'universal_pathlib>=0.2.0',
+    "numpy>=1.24",
     "zarr>=3.0.3,<3.1",
 ]
 
-[project.optional-dependencies]
+[dependency-groups]
 test = [
-    "coverage",
+    "aiohttp",
+    "fsspec>2024",
+    "numcodecs>=0.16.1",
     "pytest",
-    "pytest-cov",
-    "msgpack",
-    "lmdb",
-    "s3fs",
     "pytest-asyncio",
-    "moto[s3]",
-    "flask-cors",
-    "flask",
-    "requests",
-    "mypy",
-    "hypothesis",
     "pytest-xdist",
 ]
-dev = ["maturin", "pip", "pre-commit"]
 doc = ["sphinx>=7.4.6", "myst-parser"]
+dev = [
+    "maturin",
+    "pip",
+    "pre-commit",
+    {include-group = "test"},
+    {include-group = "doc"},
+]
 
 [tool.maturin]
 python-source = "python"