Merge branch 'main' into support-FSMap

Author: maxrjones

.github/workflows/hypothesis.yaml

@@ -69,6 +69,12 @@ jobs:
         path: .hypothesis/
         key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
 
+    - name: Upload coverage
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true # optional (default = false)
+
     - name: Generate and publish the report
       if: |
         failure()

.github/workflows/test.yml

@@ -45,6 +45,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # grab all branches and tags
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -82,6 +84,8 @@ jobs:
             dependency-set: upstream
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v5
       with:

changes/2755.bugfix.rst

@@ -0,0 +1,3 @@
+The array returned by ``zarr.empty`` and an empty ``zarr.core.buffer.cpu.NDBuffer`` will now be filled with the
+specified fill value, or with zeros if no fill value is provided.
+This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes.

changes/2758.bugfix.rst

@@ -0,0 +1 @@
+Fix zip-store path checking for stores with directories listed as files.

changes/2784.feature.rst

@@ -0,0 +1 @@
+Avoid reading chunks during writes where possible. :issue:`757`

changes/2799.bugfix.rst

@@ -0,0 +1 @@
+Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types

changes/2804.feature.rst

@@ -0,0 +1 @@
+:py:class:`LocalStore` learned to ``delete_dir``. This makes array and group deletes more efficient.

changes/2807.bugfix.rst

@@ -0,0 +1 @@
+Fix pickling for ZipStore

changes/2811.bugfix.rst

@@ -0,0 +1 @@
+Update numcodecs to not overwrite codec configuration ever. Closes :issue:`2800`.

pyproject.toml

@@ -161,7 +161,7 @@ run = "run-coverage --no-cov"
 run-pytest = "run"
 run-verbose = "run-coverage --verbose"
 run-mypy = "mypy src"
-run-hypothesis = "pytest --hypothesis-profile ci tests/test_properties.py tests/test_store/test_stateful*"
+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.doctest]
@@ -398,7 +398,8 @@ filterwarnings = [
     "ignore:.*is currently not part in the Zarr format 3 specification.*:UserWarning",
 ]
 markers = [
-    "gpu: mark a test as requiring CuPy and GPU"
+    "gpu: mark a test as requiring CuPy and GPU",
+    "slow_hypothesis: slow hypothesis tests",
 ]
 
 [tool.repo-review]