Merge branch 'main' of github.com:K-Meech/zarr-python into km/v2-v3-conversion

Author: K-Meech

.github/workflows/gpu_test.yml

@@ -65,7 +65,7 @@ jobs:
         hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage
+        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu
 
     - name: Upload coverage
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.12.7
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -22,7 +22,7 @@ repos:
       - id: check-yaml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v1.17.1
     hooks:
       - id: mypy
         files: src|tests

changes/3098.misc.rst

@@ -0,0 +1,3 @@
+Define Zarr-specific warning classes that subclass the Python built-in warnings.
+These classes makes it easier to control the visibility of warnings emitted by Zarr Python.
+See `zarr.errors` for these warning classes.

changes/3144.bugfix.rst

@@ -0,0 +1 @@
+Ensure that -0.0 is not considered equal to 0.0 when checking if all the values in a chunk are equal to an array's fill value.```

codecov.yml

@@ -3,6 +3,7 @@ coverage:
     patch:
       default:
         target: auto
+        informational: true
     project:
       default:
         target: auto

docs/developers/contributing.rst

@@ -98,7 +98,7 @@ you can do something like the following::
 To verify that your development environment is working, you can run the unit tests
 for one of the test environments, e.g.::
 
-    $ hatch env run --env test.py3.12-2.1-optional run-pytest
+    $ hatch env run --env test.py3.12-2.2-optional run-pytest
 
 Creating a branch
 ~~~~~~~~~~~~~~~~~
@@ -140,7 +140,7 @@ 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`_ above) and invoke::
 
-    $ hatch env run --env test.py3.12-2.1-optional run-pytest
+    $ hatch env run --env test.py3.12-2.2-optional run-pytest
 
 All tests are automatically run via GitHub Actions for every pull
 request and must pass before code can be accepted. Test coverage is
@@ -188,14 +188,14 @@ Test coverage
 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::
 
-    $ hatch env run --env test.py3.12-2.1-optional run-coverage
+    $ hatch env run --env test.py3.12-2.2-optional run-coverage
 
 will automatically run the test suite with coverage and produce a 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::
 
-     $ hatch env run --env test.py3.12-2.1-optional run-coverage-html
+     $ hatch env run --env test.py3.12-2.2-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

docs/user-guide/arrays.rst

@@ -238,6 +238,8 @@ built-in delta filter::
 
    >>> import lzma
    >>> from numcodecs.zarr3 import LZMA
+   >>> import warnings
+   >>> warnings.filterwarnings("ignore", category=UserWarning)
    >>>
    >>> lzma_filters = [dict(id=lzma.FILTER_DELTA, dist=4), dict(id=lzma.FILTER_LZMA2, preset=1)]
    >>> compressors = LZMA(filters=lzma_filters)

docs/user-guide/consolidated_metadata.rst

@@ -27,6 +27,8 @@ In Python, the consolidated metadata is available on the ``.consolidated_metadat
 attribute of the ``GroupMetadata`` object.
 
    >>> import zarr
+   >>> import warnings
+   >>> warnings.filterwarnings("ignore", category=UserWarning)
    >>>
    >>> store = zarr.storage.MemoryStore()
    >>> group = zarr.create_group(store=store)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling>=1.27.0", "hatch-vcs"]
+requires = ["hatchling>=1.27.0", "hatch-vcs", "setuptools-scm!=9.0.0"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.sdist]
@@ -154,6 +154,12 @@ dependencies = [
 ]
 features = ["test"]
 
+[tool.hatch.envs.test.env-vars]
+# Required to test with a pytest plugin; see https://pytest-cov.readthedocs.io/en/latest/plugins.html
+COV_CORE_SOURCE = "src"
+COV_CORE_CONFIG = ".coveragerc"
+COV_CORE_DATAFILE = ".coverage.eager"
+
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
 numpy = ["1.26", "2.2"]
@@ -165,25 +171,18 @@ matrix.deps.dependencies = [
 ]
 
 [tool.hatch.envs.test.scripts]
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
+run-coverage = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
+run-coverage-html = "pytest --cov-config=pyproject.toml --cov=src --cov-append --cov-report html"
+run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-append --cov-report xml --junitxml=junit.xml -o junit_family=legacy"
 run = "run-coverage --no-cov"
 run-pytest = "run"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
 run-hypothesis = "run-coverage -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
-[tool.hatch.envs.doctest]
-features = ["test", "optional", "remote", "remote_tests"]
-description = "Test environment for doctests"
-
-[tool.hatch.envs.doctest.scripts]
-run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'"
-fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept"
-list-env = "pip list"
-
 [tool.hatch.envs.gputest]
+template = "test"
 dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
@@ -195,22 +194,8 @@ python = ["3.11", "3.12", "3.13"]
 numpy = ["1.26", "2.2"]
 version = ["minimal"]
 
-[tool.hatch.envs.gputest.scripts]
-run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run = "run-coverage --no-cov"
-run-verbose = "run-coverage --verbose"
-run-mypy = "mypy src"
-run-hypothesis = "run-coverage --hypothesis-profile ci --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful*"
-list-env = "pip list"
-
-[tool.hatch.envs.docs]
-features = ['docs']
-
-[tool.hatch.envs.docs.scripts]
-build = "cd docs && make html"
-serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
-
 [tool.hatch.envs.upstream]
+template = 'test'
 python = "3.13"
 dependencies = [
     'packaging @ git+https://github.com/pypa/packaging',
@@ -230,20 +215,12 @@ PIP_INDEX_URL = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simp
 PIP_EXTRA_INDEX_URL = "https://pypi.org/simple/"
 PIP_PRE = "1"
 
-[tool.hatch.envs.upstream.scripts]
-run = "pytest --verbose"
-run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
-list-env = "pip list"
-
 [tool.hatch.envs.min_deps]
 description = """Test environment for minimum supported dependencies
 
 See Spec 0000 for details and drop schedule: https://scientific-python.org/specs/spec-0000/
 """
+template = "test"
 python = "3.11"
 dependencies = [
     'zarr[remote]',
@@ -261,13 +238,22 @@ dependencies = [
     'zarr[remote_tests]',
 ]
 
-[tool.hatch.envs.min_deps.scripts]
-run = "pytest --verbose"
-run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+
+[tool.hatch.envs.doctest]
+features = ["test", "optional", "remote", "remote_tests"]
+description = "Test environment for doctests"
+
+[tool.hatch.envs.doctest.scripts]
+run = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst'"
+fix = "rm -r data/; pytest docs/user-guide --doctest-glob='*.rst' --accept"
 list-env = "pip list"
-run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov-report xml --cov=src --junitxml=junit.xml -o junit_family=legacy"
-run-coverage-html = "pytest --cov-config=pyproject.toml --cov=pkg --cov-report html --cov=src"
+
+[tool.hatch.envs.docs]
+features = ['docs']
+
+[tool.hatch.envs.docs.scripts]
+build = "cd docs && make html"
+serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
 
 [tool.ruff]
 line-length = 100
@@ -407,16 +393,6 @@ addopts = [
 ]
 filterwarnings = [
     "error",
-    # TODO: explicitly filter or catch the warnings below where we expect them to be emitted in the tests
-    "ignore:Consolidated metadata is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:Creating a zarr.buffer.gpu.Buffer with an array that does not support the __cuda_array_interface__.*:UserWarning",
-    "ignore:Automatic shard shape inference is experimental and may change without notice.*:UserWarning",
-    "ignore:The codec .* is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:The dtype .* is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:Use zarr.create_array instead.:DeprecationWarning",
-    "ignore:Duplicate name.*:UserWarning",
-    "ignore:The `compressor` argument is deprecated. Use `compressors` instead.:UserWarning",
-    "ignore:Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations.:UserWarning",
     "ignore:Unclosed client session <aiohttp.client.ClientSession.*:ResourceWarning"
 ]
 markers = [

src/zarr/_compat.py

@@ -4,6 +4,8 @@
 from inspect import Parameter, signature
 from typing import Any, TypeVar
 
+from zarr.errors import ZarrFutureWarning
+
 T = TypeVar("T")
 
 # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63
@@ -54,7 +56,7 @@ def inner_f(*args: Any, **kwargs: Any) -> T:
                     f"{version} passing these as positional arguments "
                     "will result in an error"
                 ),
-                FutureWarning,
+                ZarrFutureWarning,
                 stacklevel=2,
             )
             kwargs.update(zip(sig.parameters, args, strict=False))