Merge main

Author: agriyakhetarpal

.github/workflows/ci.yaml

@@ -72,10 +72,13 @@ jobs:
 
       - name: Install zarr-python
         shell: "bash -l {0}"
+        # Since zarr v3 requires numpy >= 1.25, on Python 3.11 leave it out
+        # so we can have some tests of our minimum version of numpy (1.24)
+        if: matrix.python-version != '3.11'
         run: |
           conda activate env
           # TODO: remove --pre option when zarr v3 is out
-          python -m pip install --pre zarr
+          python -m pip install --pre zarr>=3.0.0b2
 
       # This is used to test with zfpy, which does not yet support numpy 2.0
       - name: Install older numpy and zfpy
@@ -97,7 +100,8 @@ jobs:
           conda activate env
           pytest -v
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
+          fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true

.github/workflows/wheel.yaml

@@ -26,7 +26,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: pypa/cibuildwheel@v2.21.3
+      - uses: pypa/cibuildwheel@v2.22.0
 
       - uses: actions/upload-artifact@v4
         with:

.pre-commit-config.yaml

@@ -1,11 +1,10 @@
 exclude: ^fixture/  # files with trailing whitespaces on purpose
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autoupdate_schedule: "monthly"
   autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
 default_stages: [pre-commit, pre-push]
-default_language_version:
-  python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
@@ -15,7 +14,7 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.8.4
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
@@ -25,3 +24,10 @@ repos:
     rev: 2024.08.19
     hooks:
     - id: sp-repo-review
+
+  -   repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.14.0
+      hooks:
+      -   id: mypy
+          args: [--config-file, pyproject.toml]
+          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0b2']

.readthedocs.yaml

@@ -9,7 +9,7 @@ build:
     python: "3.12"
   jobs:
     post_install:
-      - python -m pip install --pre 'zarr'
+      - python -m pip install --pre 'zarr>=3.0.0b2'
 
 sphinx:
   configuration: docs/conf.py

adhoc/blosc_memleak_check.py

@@ -1,10 +1,9 @@
 import sys
 
+import numcodecs
 import numpy as np
 from numpy.testing import assert_array_equal
 
-import numcodecs
-
 codec = numcodecs.Blosc()
 data = np.arange(int(sys.argv[1]))
 for _ in range(int(sys.argv[2])):

docs/conf.py

@@ -12,7 +12,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-
 import os
 import sys
 from unittest.mock import Mock as MagicMock
@@ -232,7 +231,7 @@ def __getattr__(cls, name):
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #'papersize': 'letterpaper',
     # The font size ('10pt', '11pt' or '12pt').

docs/contributing.rst

@@ -0,0 +1,9 @@
+{
+    "delta_encoding_order": 2,
+    "delta_spec": "auto",
+    "equal_pages_up_to": 262144,
+    "id": "pcodec",
+    "level": 8,
+    "mode_spec": "auto",
+    "paging_spec": "equal_pages_up_to"
+}