Merge branch 'support/v2' into recursive-getsize

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -27,7 +27,7 @@ body:
     attributes:
       label: Python Version
       description: Version of Python interpreter
-      placeholder: 3.10, 3.11, 3.12 etc.
+      placeholder: 3.11, 3.12, 3.13 etc.
     validations:
       required: true
   - type: input

.github/workflows/minimal.yml

@@ -4,9 +4,9 @@ name: Minimal installation
 
 on:
   push:
-    branches: [ main ]
+    branches: [ support/v2 ]
   pull_request:
-    branches: [ main ]
+    branches: [ support/v2 ]
 
 jobs:
   minimum_build:

.github/workflows/python-package.yml

@@ -5,21 +5,23 @@ name: Linux Testing
 
 on:
   push:
-    branches: [ main ]
+    branches: [ support/v2]
   pull_request:
-    branches: [ main ]
+    branches: [ support/v2]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
         numpy_version: ['>=2.1', '==1.24.*']
         exclude:
           - python-version: '3.12'
             numpy_version: '==1.24.*'
+          - python-version: '3.13'
+            numpy_version: '==1.24.*'
     services:
       redis:
         image: redis
@@ -50,7 +52,7 @@ jobs:
     - name: Create Conda environment with the rights deps
       shell: "bash -l {0}"
       run: |
-        conda create -n zarr-env python==${{matrix.python-version}} bsddb3 pip nodejs
+        conda create -n zarr-env python==${{matrix.python-version}} pip nodejs
         conda activate zarr-env
         npm install -g azurite
     - name: Install dependencies

.github/workflows/releases.yml

@@ -64,7 +64,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/[email protected].1
+      - uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/windows-testing.yml

@@ -5,9 +5,9 @@ name: Python package
 
 on:
   push:
-    branches: [ main ]
+    branches: [ support/v2 ]
   pull_request:
-    branches: [ main ]
+    branches: [ support/v2 ]
 
 jobs:
   windows:
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: True
       matrix:
-        python-version: ['3.10', '3.11']
+        python-version: ['3.11', '3.12']
     steps:
       - uses: actions/checkout@v4
         with:

TEAM.md

@@ -8,6 +8,8 @@
 - @martindurant (Martin Durant)
 - @normanrz (Norman Rzepka)
 - @dstansby (David Stansby)
+- @dcherian (Deepak Cherian)
+- @TomAugspurger (Tom Augspurger)
 
 ## Emeritus core-developers
 - @alimanfoo (Alistair Miles)

docs/_static/custom.css

@@ -74,7 +74,6 @@ Nat Methods 8, 441 (2011). https://doi.org/10.1038/nmeth.1618
 .sd-card .sd-card-header {
   border: none;
   background-color: white;
-  color: #150458 !important;
   font-size: var(--pst-font-size-h5);
   font-weight: bold;
   padding: 2.5rem 0rem 0.5rem 0rem;
@@ -107,7 +106,6 @@ html[data-theme=dark] .sd-shadow-sm {
 
 html[data-theme=dark] .sd-card .sd-card-header {
   background-color:var(--pst-color-background);
-  color: #150458 !important;
 }
 
 html[data-theme=dark] .sd-card .sd-card-footer {

docs/release.rst

@@ -25,11 +25,19 @@ Release notes
 
 Enhancements
 ~~~~~~~~~~~~
+* Added testing on Python 3.13.
 
 Maintenance
 ~~~~~~~~~~~
-* ``getsize`` now returns the total size of all nested arrays. 
+* ``getsize`` now returns the total size of all nested arrays.
   By :user:`Ben Jeffery <benjeffery>` :issue:`253`.
+* Dropped support for Python 3.10.
+  By :user:`David Stansby <dstansby>` (:issue:`2344`).
+* Removed testing for compatibility with the ``bsddb3`` package.
+  ``bsddb3`` was last released four years ago, and should still work with
+  ``zarr-python`` if you can install it, but to reduce our maintenance
+  burden we will no longer run our compatibility tests for it.
+  By :user:`David Stansby <dstansby>` (:issue:`2344`).
 
 Deprecations
 ~~~~~~~~~~~~
@@ -43,7 +51,7 @@ Enhancements
 ~~~~~~~~~~~~
 * Added support for creating a copy of data when converting a `zarr.Array`
   to a numpy array.
-  By :user:`David Stansby <dstansby>` (:issue:`2106`) and 
+  By :user:`David Stansby <dstansby>` (:issue:`2106`) and
   :user:`Joe Hamman <jhamman>` (:issue:`2123`).
 
 Maintenance

docs/tutorial.rst

@@ -811,6 +811,8 @@ storing an array or group. Here is an example using a Berkeley DB B-tree
 database for storage (requires `bsddb3
 <https://www.jcea.es/programacion/pybsddb.htm>`_ to be installed)::
 
+.. doctest-requires:: bsddb3
+
     >>> import bsddb3
     >>> store = zarr.DBMStore('data/example.bdb', open=bsddb3.btopen)
     >>> root = zarr.group(store=store, overwrite=True)
@@ -1009,12 +1011,12 @@ class from ``fsspec``. The following example demonstrates how to access
 a ZIP-archived Zarr group on s3 using `s3fs <https://s3fs.readthedocs.io/en/latest/>`_ and ``ZipFileSystem``:
 
     >>> s3_path = "s3://path/to/my.zarr.zip"
-    >>> 
+    >>>
     >>> s3 = s3fs.S3FileSystem()
     >>> f = s3.open(s3_path)
     >>> fs = ZipFileSystem(f, mode="r")
     >>> store = FSMap("", fs, check=False)
-    >>> 
+    >>>
     >>> # caching may improve performance when repeatedly reading the same data
     >>> cache = zarr.storage.LRUStoreCache(store, max_size=2**28)
     >>> z = zarr.group(store=cache)

pyproject.toml

@@ -7,19 +7,15 @@ build-backend = "setuptools.build_meta"
 name = "zarr"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 readme = { file = "README.md", content-type = "text/markdown" }
-maintainers = [
-    { name = "Alistair Miles", email = "[email protected]" }
-]
-requires-python = ">=3.10"
+maintainers = [{ name = "Alistair Miles", email = "[email protected]" }]
+requires-python = ">=3.11"
 dependencies = [
     'asciitree',
     'numpy>=1.24',
     'fasteners; sys_platform != "emscripten"',
     'numcodecs>=0.10.0',
 ]
-dynamic = [
-  "version",
-]
+dynamic = ["version"]
 classifiers = [
     'Development Status :: 6 - Mature',
     'Intended Audience :: Developers',
@@ -30,18 +26,14 @@ classifiers = [
     'Topic :: Software Development :: Libraries :: Python Modules',
     'Operating System :: Unix',
     'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
+    'Programming Language :: Python :: 3.13',
 ]
 license = { text = "MIT" }
 
 [project.optional-dependencies]
-jupyter = [
-    'notebook',
-    'ipytree>=0.2.2',
-    'ipywidgets>=8.0.0',
-]
+jupyter = ['notebook', 'ipytree>=0.2.2', 'ipywidgets>=8.0.0']
 docs = [
     'sphinx',
     'sphinx-automodapi',
@@ -64,14 +56,11 @@ Homepage = "https://github.com/zarr-developers/zarr-python"
 exclude_lines = [
     "pragma: no cover",
     "pragma: ${PY_MAJOR_VERSION} no cover",
-    '.*\.\.\.' # Ignore "..." lines
+    '.*\.\.\.',                             # Ignore "..." lines
 ]
 
 [tool.coverage.run]
-omit = [
-    "zarr/meta_v1.py",
-    "bench/compress_normal.py",
-]
+omit = ["zarr/meta_v1.py", "bench/compress_normal.py"]
 
 [tool.setuptools]
 packages = ["zarr", "zarr._storage", "zarr.tests"]
@@ -100,14 +89,12 @@ exclude = [
     "build",
     "dist",
     "venv",
-    "docs"
+    "docs",
 ]
 
 [tool.ruff.lint]
-extend-select = [
-    "B"
-]
-ignore = ["B905"] # zip-without-explicit-strict
+extend-select = ["B"]
+ignore = ["B905"]     # zip-without-explicit-strict
 
 [tool.black]
 line-length = 100
@@ -136,19 +123,17 @@ doctest_optionflags = [
     "ELLIPSIS",
     "IGNORE_EXCEPTION_DETAIL",
 ]
-addopts = [
-    "--durations=10",
-]
+addopts = ["--durations=10"]
 filterwarnings = [
     "error:::zarr.*",
     "ignore:PY_SSIZE_T_CLEAN will be required.*:DeprecationWarning",
     "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
     "ignore:The .* is deprecated and will be removed in a Zarr-Python version 3*:FutureWarning",
     "ignore:The experimental Zarr V3 implementation in this version .*:FutureWarning",
 ]
-doctest_subpackage_requires =[
+doctest_subpackage_requires = [
     "zarr/core.py = numpy>=2",
-    "zarr/creation.py = numpy>=2"
+    "zarr/creation.py = numpy>=2",
 ]
 
 

requirements_dev_minimal.txt

@@ -1,7 +1,7 @@
 # library requirements
 asciitree==0.3.3
 fasteners==0.19
-numcodecs==0.13.0
+numcodecs==0.13.1
 msgpack-python==0.5.6
 setuptools-scm==8.1.0
 # test requirements

requirements_dev_numpy.txt

@@ -1,4 +1,4 @@
 # Break this out into a separate file to allow testing against
 # different versions of numpy. This file should pin to the latest
 # numpy version.
-numpy==2.1.1
+numpy==2.1.2

requirements_dev_optional.txt

@@ -8,16 +8,16 @@ ipywidgets==8.1.5
 # don't let pyup change pinning for azure-storage-blob, need to pin to older
 # version to get compatibility with azure storage emulator on appveyor (FIXME)
 azure-storage-blob==12.21.0 # pyup: ignore
-redis==5.0.8
+redis==5.1.1
 types-redis
 types-setuptools
-pymongo==4.8.0
+pymongo==4.10.1
 # optional test requirements
 coverage
 pytest-cov==5.0.0
 pytest-doctestplus==1.2.1
 pytest-timeout==2.3.1
-h5py==3.11.0
+h5py==3.12.1
 fsspec==2023.12.2
 s3fs==2023.12.2
 moto[server]>=5.0.1

zarr/storage.py

@@ -1699,7 +1699,6 @@ class NestedDirectoryStore(DirectoryStore):
     def __init__(
         self, path, normalize_keys=False, dimension_separator: Optional[DIMENSION_SEPARATOR] = "/"
     ):
-
         warnings.warn(
             V3_DEPRECATION_MESSAGE.format(store=self.__class__.__name__),
             FutureWarning,
@@ -2073,6 +2072,8 @@ class DBMStore(Store):
     <https://www.jcea.es/programacion/pybsddb.htm>`_ package is installed, a
     Berkeley DB database can be used::
 
+    .. doctest-requires:: bsddb3
+
         >>> import bsddb3
         >>> store = zarr.DBMStore('data/array.bdb', open=bsddb3.btopen)
         >>> z = zarr.zeros((10, 10), chunks=(5, 5), store=store, overwrite=True)