Merge branch 'master' into fix-iterating-over-sharding-index

# Conflicts:
#	tests/test_codecs/test_sharding.py

Author: brokkoli71

.github/workflows/codeql-analysis.yml

@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
         numpy-version: ['1.25', '1.26', '2.0']
         dependency-set: ["minimal", "optional"]
 
@@ -43,3 +43,35 @@ jobs:
     - name: Run Tests
       run: |
         hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run
+
+  test-upstream-and-min-deps:
+    name: py=${{ matrix.python-version }}-${{ matrix.dependency-set }}
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', "3.13"]
+        dependency-set: ["upstream", "min_deps"]
+        exclude:
+          - python-version: "3.13"
+            dependency-set: min_deps
+          - python-version: "3.11"
+            dependency-set: upstream
+    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: Set Up Hatch Env
+      run: |
+        hatch env create ${{ matrix.dependency-set }}
+        hatch env run -e ${{ matrix.dependency-set }} list-env
+    - name: Run Tests
+      run: |
+        hatch env run --env ${{ matrix.dependency-set }} run

.github/workflows/test.yml

@@ -31,7 +31,6 @@ repos:
           - asciitree
           - crc32c
           - donfig
-          - fasteners
           - numcodecs
           - numpy
           - typing_extensions

.pep8speaks.yml

@@ -18,20 +18,23 @@ maintainers = [
     { name = "Juan Nunez-Iglesias", email = "[email protected]" },
     { name = "Martin Durant", email = "[email protected]" },
     { name = "Norman Rzepka" },
-    { name = "Ryan Abernathey" }
+    { name = "Ryan Abernathey" },
+    { name = "David Stansby" },
+    { name = "Tom Augspurger", email = "[email protected]" },
+    { name = "Deepak Cherian" }
 ]
 requires-python = ">=3.11"
 # If you add a new dependency here, please also add it to .pre-commit-config.yml
 dependencies = [
     'asciitree',
     'numpy>=1.25',
-    'fasteners',
-    'numcodecs>=0.10.2',
-    'fsspec>2024',
-    'crc32c',
-    'typing_extensions',
-    'donfig',
+    'numcodecs>=0.13',
+    'fsspec>=2022.10.0',
+    'crc32c>=2.3',
+    'typing_extensions>=4.6',
+    'donfig>=0.8',
 ]
+
 dynamic = [
   "version",
 ]
@@ -47,6 +50,7 @@ classifiers = [
     'Programming Language :: Python :: 3',
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: 3.13',
 ]
 license = {text = "MIT License"}
 keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"]
@@ -95,7 +99,7 @@ extra = [
 ]
 optional = [
     'lmdb',
-    'universal-pathlib',
+    'universal-pathlib>=0.0.22',
 ]
 
 [project.urls]
@@ -130,17 +134,17 @@ dependencies = [
 features = ["test", "extra"]
 
 [[tool.hatch.envs.test.matrix]]
-python = ["3.11", "3.12"]
+python = ["3.11", "3.12", "3.13"]
 numpy = ["1.25", "1.26", "2.0"]
 version = ["minimal"]
 
 [[tool.hatch.envs.test.matrix]]
-python = ["3.11", "3.12"]
+python = ["3.11", "3.12", "3.13"]
 numpy = ["1.25", "1.26", "2.0"]
 features = ["optional"]
 
 [[tool.hatch.envs.test.matrix]]
-python = ["3.11", "3.12"]
+python = ["3.11", "3.12", "3.13"]
 numpy = ["1.25", "1.26", "2.0"]
 features = ["gpu"]
 
@@ -150,7 +154,7 @@ run-coverage-gpu = "pip install cupy-cuda12x && pytest -m gpu --cov-config=pypro
 run = "run-coverage --no-cov"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/v3/test_properties.py tests/v3/test_store/test_stateful*"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
 [tool.hatch.envs.gputest]
@@ -161,7 +165,7 @@ dependencies = [
 features = ["test", "extra", "gpu"]
 
 [[tool.hatch.envs.gputest.matrix]]
-python = ["3.11", "3.12"]
+python = ["3.11", "3.12", "3.13"]
 numpy = ["1.25", "1.26", "2.0"]
 version = ["minimal"]
 
@@ -170,7 +174,7 @@ run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=pkg --cov=tests"
 run = "run-coverage --no-cov"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/v3/test_properties.py tests/v3/test_store/test_stateful*"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
 list-env = "pip list"
 
 [tool.hatch.envs.docs]
@@ -180,6 +184,65 @@ features = ['docs']
 build = "cd docs && make html"
 serve = "sphinx-autobuild docs docs/_build --host 0.0.0.0"
 
+[tool.hatch.envs.upstream]
+python = "3.13"
+dependencies = [
+    'numpy',  # from scientific-python-nightly-wheels
+    'numcodecs @ git+https://github.com/zarr-developers/numcodecs',
+    'fsspec @ git+https://github.com/fsspec/filesystem_spec',
+    's3fs @ git+https://github.com/fsspec/s3fs',
+    'universal_pathlib @ git+https://github.com/fsspec/universal_pathlib',
+    'crc32c @ git+https://github.com/ICRAR/crc32c',
+    'typing_extensions @ git+https://github.com/python/typing_extensions',
+    'donfig @ git+https://github.com/pytroll/donfig',
+    # test deps
+    'hypothesis',
+    'pytest',
+    'pytest-cov',
+    'pytest-asyncio',
+    'moto[s3]',
+]
+
+[tool.hatch.envs.upstream.env-vars]
+PIP_INDEX_URL = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple/"
+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*"
+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/
+"""
+python = "3.11"
+dependencies = [
+    'numpy==1.25.*',
+    'numcodecs==0.13.*',  # 0.13 needed for? (should be 0.11)
+    'fsspec==2022.10.0',
+    's3fs==2022.10.0',
+    'universal_pathlib==0.0.22',
+    'crc32c==2.3.*',
+    'typing_extensions==4.6.*',  # 4.5 needed for @deprecated, 4.6 for Buffer
+    'donfig==0.8.*',
+    # test deps
+    'hypothesis',
+    'pytest',
+    'pytest-cov',
+    'pytest-asyncio',
+    'moto[s3]',
+]
+
+[tool.hatch.envs.min_deps.scripts]
+run = "pytest --verbose"
+run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+list-env = "pip list"
+
+
 [tool.ruff]
 line-length = 100
 force-exclude = true
@@ -207,34 +270,34 @@ extend-exclude = [
 
 [tool.ruff.lint]
 extend-select = [
-    "ANN", # flake8-annotations
-    "B",   # flake8-bugbear
-    "C4",  # flake8-comprehensions
-    "FLY", # flynt
-    "G",   # flake8-logging-format
-    "I",   # isort
-    "ISC", # flake8-implicit-str-concat
-    "PGH", # pygrep-hooks
-    "PT",  # flake8-pytest-style
-    "PYI", # flake8-pyi
-    "RSE", # flake8-raise
-    "RET", # flake8-return
+    "ANN",  # flake8-annotations
+    "B",    # flake8-bugbear
+    "C4",   # flake8-comprehensions
+    "FLY",  # flynt
+    "FURB", # refurb
+    "G",    # flake8-logging-format
+    "I",    # isort
+    "ISC",  # flake8-implicit-str-concat
+    "PERF", # Perflint
+    "PGH",  # pygrep-hooks
+    "PT",   # flake8-pytest-style
+    "PYI",  # flake8-pyi
+    "RSE",  # flake8-raise
+    "RET",  # flake8-return
     "RUF",
-    "TCH", # flake8-type-checking
-    "TRY", # tryceratops
-    "UP",  # pyupgrade
-    "W",   # pycodestyle warnings
+    "TCH",  # flake8-type-checking
+    "TRY",  # tryceratops
+    "UP",   # pyupgrade
+    "W",    # pycodestyle warnings
 ]
 ignore = [
-    "ANN003",
-    "ANN101",
-    "ANN102",
+    "ANN101", # deprecated
+    "ANN102", # deprecated
     "ANN401",
     "PT004",  # deprecated
     "PT005",  # deprecated
     "PT011",  # TODO: apply this rule
     "PT012",  # TODO: apply this rule
-    "PYI013",
     "RET505",
     "RET506",
     "RUF005",
@@ -280,18 +343,17 @@ ignore_errors = true
 
 [[tool.mypy.overrides]]
 module = [
-    "tests.v2.*",
-    "tests.v3.package_with_entrypoint.*",
-    "tests.v3.test_codecs.test_codecs",
-    "tests.v3.test_codecs.test_transpose",
-    "tests.v3.test_metadata.*",
-    "tests.v3.test_store.*",
-    "tests.v3.test_config",
-    "tests.v3.test_group",
-    "tests.v3.test_indexing",
-    "tests.v3.test_properties",
-    "tests.v3.test_sync",
-    "tests.v3.test_v2",
+    "tests.package_with_entrypoint.*",
+    "tests.test_codecs.test_codecs",
+    "tests.test_codecs.test_transpose",
+    "tests.test_metadata.*",
+    "tests.test_store.*",
+    "tests.test_config",
+    "tests.test_group",
+    "tests.test_indexing",
+    "tests.test_properties",
+    "tests.test_sync",
+    "tests.test_v2",
 ]
 ignore_errors = true
 
@@ -328,4 +390,15 @@ ignore = [
 
 [tool.numpydoc_validation]
 # See https://numpydoc.readthedocs.io/en/latest/validation.html#built-in-validation-checks for list of checks
-checks = ["GL06", "GL07", "GL10", "PR03", "PR05", "PR06"]
+checks = [
+    "GL06",
+    "GL07",
+    "GL09",
+    "GL10",
+    "SS02",
+    "SS04",
+    "PR02",
+    "PR03",
+    "PR05",
+    "PR06",
+]