Merge pull request #43 from zarr-developers/chore/dump-poetry

refactor the entire build system to use hatch instead of poetry.

.github/dependabot.yml

@@ -0,0 +1,11 @@
+---
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    groups:
+      actions:
+        patterns:
+          - '*'

.github/workflows/cd.yml

@@ -6,7 +6,7 @@ jobs:
     build-n-publish:
       name: Build and publish Python 🐍 distributions 📦 to PyPI
       runs-on: ubuntu-latest
-      if: 
+      if:
         startsWith(github.ref, 'refs/tags')
       steps:
         - uses: actions/checkout@v3
@@ -23,4 +23,4 @@ jobs:
         - name: Publish distribution 📦 to PyPI
           uses: pypa/gh-action-pypi-publish@release/v1
           with:
-            password: ${{ secrets.PYPI_API_TOKEN }}          
+            password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: ci 
+name: ci
 on:
   push:
     branches:
@@ -13,14 +13,13 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: 3.x
-      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - uses: actions/cache@v3
         with:
           key: mkdocs-material-${{ env.cache_id }}
           path: .cache
           restore-keys: |
             mkdocs-material-
       - run: |
-            pip install poetry
-            poetry install --with docs
-            poetry run mkdocs gh-deploy --force
+            pip install hatch
+            hatch run docs:deploy --force

.github/workflows/test.yml

@@ -1,24 +1,84 @@
-name: Linux Testing
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test
 
 on:
   push:
     branches: [ main ]
   pull_request:
     branches: [ main ]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  build:
-    runs-on: ubuntu-latest
+  test:
+    name: os=${{ matrix.os }}, py=${{ matrix.python-version }}, np=${{ matrix.numpy-version }}, deps=${{ matrix.dependency-set }}
+
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
+        numpy-version: ['1.25', '2.1']
+        dependency-set: ["minimal", "optional"]
+        os: ["ubuntu-latest"]
+        include:
+          - python-version: '3.11'
+            numpy-version: '1.25'
+            dependency-set: 'optional'
+            os: 'macos-latest'
+          - python-version: '3.13'
+            numpy-version: '2.1'
+            dependency-set: 'optional'
+            os: 'macos-latest'
+          - python-version: '3.11'
+            numpy-version: '1.25'
+            dependency-set: 'optional'
+            os: 'windows-latest'
+          - python-version: '3.13'
+            numpy-version: '2.1'
+            dependency-set: 'optional'
+            os: 'windows-latest'
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Run Tests
+      run: |
+        hatch run test.py${{ matrix.python-version }}:test-cov
+    - name: Upload coverage
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true # optional (default = false)
+
+  doctests:
+    name: doctests
+    runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - name: Install dependencies
-      shell: "bash -l {0}"
+      with:
+        fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+    - name: Install Hatch
       run: |
-        pip install poetry
-        poetry install
-    - name: Test
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Run Tests
       run: |
-        poetry run pytest
+        hatch run docs:test

.gitignore

@@ -161,3 +161,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# VCS versioning
+src/pydantic_zarr/_version.py

.pre-commit-config.yaml

@@ -1,19 +1,44 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autoupdate_schedule: "monthly"
   autofix_commit_msg: "style: pre-commit fixes"
-default_stages: [commit, push]
-default_language_version:
-  python: python3
+  autofix_prs: false
+default_stages: [pre-commit, pre-push]
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
+    hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
-      - id: check-yaml
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.1.4
+    - id: check-yaml
+    - id: trailing-whitespace
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.14.1
+    hooks:
+      - id: mypy
+        files: src|tests
+        additional_dependencies:
+          - pytest
+          - pydantic
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.08.19
+    hooks:
+      - id: sp-repo-review
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
     hooks:
-      # Run the linter.
-      - id: ruff
-      # Run the formatter.
-      - id: ruff-format
+      - id: numpydoc-validation

README.md

@@ -14,7 +14,7 @@ This project is under flux -- I want to add [zarr version 3](https://zarr-specs.
 ## Getting help
 
 - Docs: see the [documentation](https://zarr.dev/pydantic-zarr/) for detailed information about this project.
-- Chat: We use [Zulip](https://ossci.zulipchat.com/#narrow/channel/423692-Zarr) for project-related chat. 
+- Chat: We use [Zulip](https://ossci.zulipchat.com/#narrow/channel/423692-Zarr) for project-related chat.
 
 ## Example
 

docs/index.md

@@ -2,7 +2,7 @@
 
 [![PyPI](https://img.shields.io/pypi/v/pydantic-zarr)](https://pypi.python.org/pypi/pydantic-zarr)
 
-Static typing and runtime validation for Zarr hierachies.
+Static typing and runtime validation for Zarr hierarchies.
 
 ## Overview
 

docs/usage_zarr_v2.md

@@ -107,7 +107,7 @@ instances, then providing those objects as `members` to the constructor of anoth
 other words, with this approach we create "child nodes" and give those nodes to the "parent node",
 recursively.
 
-Constructing deeply nested hierarchies this way can be tedious. 
+Constructing deeply nested hierarchies this way can be tedious.
 For this reason, `pydantic-zarr` supports an alternative representation of the Zarr
 hierarchy in the form of a dictionary with `str` keys and `ArraySpec` / `GroupSpec` values, and
 methods to convert to / from these dictionaries.
@@ -118,11 +118,11 @@ This example demonstrates how to create a `GroupSpec` from a `dict` representati
 
 ```python
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-# other than the key representing the root path "", 
+# other than the key representing the root path "",
 # the keys must be valid paths in the Zarr storage hierarchy
 # note that the `members` attribute is `None` for the `GroupSpec` instances in this `dict`.
 tree = {
-    "": GroupSpec(members=None, attributes={"root": True}), 
+    "": GroupSpec(members=None, attributes={"root": True}),
     "/a": GroupSpec(members=None, attributes={"root": False}),
     "/a/b": ArraySpec(shape=(10,10), dtype="uint8", chunks=(1,1))
     }
@@ -158,12 +158,12 @@ print(GroupSpec.from_flat(tree).model_dump())
 
 #### flattening `GroupSpec` objects
 
-This is similar to the example above, except that we are working in reverse -- we are making the 
+This is similar to the example above, except that we are working in reverse -- we are making the
 flat `dict` from the `GroupSpec` object.
 
 ```python
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-# other than the key representing the root path "", 
+# other than the key representing the root path "",
 # the keys must be valid paths in the Zarr storage hierarchy
 # note that the `members` attribute is `None` for the `GroupSpec` instances in this `dict`.
 
@@ -193,9 +193,9 @@ print(root.to_flat())
 ```
 
 #### Implicit groups
-`zarr-python` supports creating Zarr arrays or groups deep in the 
-hierarchy without explicitly creating the intermediate groups first. 
-`from_flat` models this behavior. For example, `{'/a/b/c': ArraySpec(...)}` implicitly defines the existence of a groups named `a` and `b` (which is contained in `a`). `from_flat` will create the expected `GroupSpec` object from such `dict` instances. 
+`zarr-python` supports creating Zarr arrays or groups deep in the
+hierarchy without explicitly creating the intermediate groups first.
+`from_flat` models this behavior. For example, `{'/a/b/c': ArraySpec(...)}` implicitly defines the existence of a groups named `a` and `b` (which is contained in `a`). `from_flat` will create the expected `GroupSpec` object from such `dict` instances.
 
 ```python
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
@@ -237,7 +237,7 @@ print(GroupSpec.from_flat(tree).model_dump())
 
 ## Comparing `GroupSpec` and `ArraySpec` models
 
-`GroupSpec` and `ArraySpec` both have `like` methods that take another `GroupSpec` or `ArraySpec` as an argument and return `True` (the models are like each other) or `False` (the models are not like each other). 
+`GroupSpec` and `ArraySpec` both have `like` methods that take another `GroupSpec` or `ArraySpec` as an argument and return `True` (the models are like each other) or `False` (the models are not like each other).
 
 The `like` method works by converting both input models to `dict` via `pydantic.BaseModel.model_dump`, and comparing the `dict` representation of the models. This means that instances of two different subclasses of `GroupSpec`, which would not be considered equal according to the `==` operator, will be considered `like` if and only if they serialize to identical `dict` instances.
 
@@ -251,7 +251,7 @@ arr_a = ArraySpec(shape=(1,), dtype='uint8', chunks=(1,))
 arr_b = ArraySpec(shape=(2,), dtype='uint8', chunks=(1,))
 
 # Returns False, because of mismatched shape
-print(arr_a.like(arr_b)) 
+print(arr_a.like(arr_b))
 #> False
 
 # Returns True, because we exclude shape.
@@ -264,11 +264,11 @@ store = zarr.MemoryStore()
 arr_a_stored = arr_a.to_zarr(store, path='arr_a')
 
 # arr_a is like the zarr.Array version of itself
-print(arr_a.like(arr_a_stored)) 
+print(arr_a.like(arr_a_stored))
 #> True
 
 # Returns False, because of mismatched shape
-print(arr_b.like(arr_a_stored)) 
+print(arr_b.like(arr_a_stored))
 #> False
 
 # Returns True, because we exclude shape.
@@ -284,7 +284,7 @@ print(g_a.like(g_a))
 #> True
 
 # Returns False, because of mismatched attributes
-print(g_a.like(g_b)) 
+print(g_a.like(g_b))
 #> False
 
 # Returns True, because we ignore attributes
@@ -335,7 +335,7 @@ print(SpecificAttrsGroup(attributes={'a': 100, 'b': 100}))
 #> zarr_version=2 attributes={'a': 100, 'b': 100} members={}
 
 # a Zarr group that only contains arrays -- no subgroups!
-# we re-use the TAttr type variable defined in pydantic_zarr.core
+# we reuse the TAttr type variable defined in pydantic_zarr.core
 ArraysOnlyGroup = GroupSpec[TAttr, ArraySpec]
 
 try:

docs/usage_zarr_v3.md

@@ -2,8 +2,8 @@
 
 ## Disclaimer
 
-At the moment, [Zarr version 3](https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html) is only *barely* support by this project. That will likely 
-change when the Zarr storage backend used here ([`zarr-python`](https://zarr.readthedocs.io/en/stable/)) 
+At the moment, [Zarr version 3](https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html) is only *barely* support by this project. That will likely
+change when the Zarr storage backend used here ([`zarr-python`](https://zarr.readthedocs.io/en/stable/))
 fully implements version 3. Until then, the only Zarr v3 stuff you can do with this repo
 is create abstract hierarchies. You cannot use the `to_zarr` or `from_zarr` methods, because
 the backend for that doesn't exist.

mkdocs.yaml

@@ -13,11 +13,11 @@ copyright: Copyright © 2016 - 2024 HHMI / Janelia
 
 theme:
   name: material
-  palette: 
+  palette:
   # Palette toggle for light mode
   - scheme: default
     toggle:
-      icon: material/brightness-7 
+      icon: material/brightness-7
       name: Switch to dark mode
 
   # Palette toggle for dark mode