chore/update hatch + use dependency groups (#3728)

Author: d-v-b

.github/workflows/codspeed.yml

@@ -31,9 +31,9 @@ jobs:
       with:
         python-version: "3.11"
     - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Run the benchmarks
       uses: CodSpeedHQ/action@v4
       with:

.github/workflows/gpu_test.yml

@@ -19,13 +19,12 @@ concurrency:
 
 jobs:
   test:
-    name: py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }}
+    name: py=${{ matrix.python-version }}
 
     runs-on: gpu-runner
     strategy:
       matrix:
         python-version: ['3.11']
-        dependency-set: ["minimal"]
 
     steps:
     - uses: actions/checkout@v6
@@ -54,17 +53,17 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
-    - name: Install Hatch and CuPy
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+    - name: Install Hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Set Up Hatch Env
       run: |
-        hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
-        hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env
+        hatch env create gputest.py${{ matrix.python-version }}
+        hatch env run -e gputest.py${{ matrix.python-version }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage-gpu
+        hatch env run --env gputest.py${{ matrix.python-version }} run-coverage
 
     - name: Upload coverage
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1

.github/workflows/hypothesis.yaml

@@ -41,9 +41,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Set Up Hatch Env
       run: |
         hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}

.github/workflows/nightly_wheels.yml

@@ -22,10 +22,10 @@ jobs:
         with:
           python-version: '3.13'
 
-      - name: Install build dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install hatch
+      - name: Install Hatch
+        uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+        with:
+          version: '1.16.5'
 
       - name: Build wheel and sdist
         run: hatch build

.github/workflows/releases.yml

@@ -21,10 +21,10 @@ jobs:
         with:
           python-version: '3.11'
 
-      - name: Install PyBuild
-        run: |
-          python -m pip install --upgrade pip
-          pip install hatch
+      - name: Install Hatch
+        uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+        with:
+          version: '1.16.5'
       - name: Build wheel and sdist
         run: hatch build
       - uses: actions/upload-artifact@v6

.github/workflows/test.yml

@@ -51,9 +51,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Set Up Hatch Env
       run: |
         hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
@@ -93,9 +93,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Set Up Hatch Env
       run: |
         hatch env create ${{ matrix.dependency-set }}
@@ -122,9 +122,9 @@ jobs:
         python-version: '3.13'
         cache: 'pip'
     - name: Install Hatch
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
     - name: Set Up Hatch Env
       run: |
         hatch run doctest:pip list

.readthedocs.yaml

@@ -5,6 +5,9 @@ build:
   tools:
     python: "3.12"
   jobs:
+    install:
+      - pip install --upgrade pip
+      - pip install .[remote] --group docs
     pre_build:
       - |
         if [ "$READTHEDOCS_VERSION_TYPE" != "tag" ];
@@ -16,11 +19,3 @@ build:
           - mkdocs build --strict --site-dir $READTHEDOCS_OUTPUT/html
 mkdocs:
   configuration: mkdocs.yml
-
-python:
-   install:
-   - method: pip
-     path: .
-     extra_requirements:
-        - docs
-        - remote

changes/3728.misc.md

@@ -0,0 +1 @@
+Move development dependencies (`test`, `remote_tests`, `docs`, `dev`) from optional dependencies to [dependency groups](https://packaging.python.org/en/latest/specifications/dependency-groups/). This may cause breakage for anyone who used e.g. `pip install zarr[test]` to get access to test dependencies. To install these dependency groups from a local checkout, use `pip install --group <name>` (pip 25.1+) or `uv run --group <name>`.

docs/contributing.md

@@ -64,7 +64,7 @@ hatch env show  # list all available environments
 To verify that your development environment is working, you can run the unit tests for one of the test environments, e.g.:
 
 ```bash
-hatch env run --env test.py3.12-2.2-optional run-pytest
+hatch env run --env test.py3.12-optional run
 ```
 
 ### Creating a branch
@@ -102,7 +102,7 @@ Again, any conflicts need to be resolved before submitting a pull request.
 Zarr includes a suite of unit tests. The simplest way to run the unit tests is to activate your development environment (see [creating a development environment](#creating-a-development-environment) above) and invoke:
 
 ```bash
-hatch env run --env test.py3.12-2.2-optional run-pytest
+hatch env run --env test.py3.12-optional run
 ```
 
 All tests are automatically run via GitHub Actions for every pull request and must pass before code can be accepted. Test coverage is also collected automatically via the Codecov service.
@@ -164,15 +164,15 @@ If you would like to skip the failing checks and push the code for further discu
 Zarr strives to maintain 100% test coverage under the latest Python stable release. Both unit tests and docstring doctests are included when computing coverage. Running:
 
 ```bash
-hatch env run --env test.py3.12-2.2-optional run-coverage
+hatch env run --env test.py3.12-optional run-coverage
 ```
 
 will automatically run the test suite with coverage and produce an XML coverage report. This should be 100% before code can be accepted into the main code base.
 
 You can also generate an HTML coverage report by running:
 
 ```bash
-hatch env run --env test.py3.12-2.2-optional run-coverage-html
+hatch env run --env test.py3.12-optional run-coverage-html
 ```
 
 When submitting a pull request, coverage will also be collected across all supported Python versions via the Codecov service, and will be reported back within the pull request. Codecov coverage must also be 100% before code can be accepted.