Merge branch 'main' of https://github.com/zarr-developers/zarr-python into perf/codec-chain

Author: d-v-b

.github/workflows/gpu_test.yml

@@ -72,4 +72,5 @@ jobs:
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: gpu
         verbose: true # optional (default = false)

.github/workflows/hypothesis.yaml

@@ -81,6 +81,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
     - name: Generate and publish the report

.github/workflows/test.yml

@@ -71,6 +71,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
   test-upstream-and-min-deps:
@@ -110,6 +111,7 @@ jobs:
       uses: codecov/codecov-action@v5
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
+        flags: tests
         verbose: true # optional (default = false)
 
   doctests:

changes/2720.doc.md

@@ -0,0 +1 @@
+Document removal of `zarr.storage.init_group` in v3 migration guide, with replacement using `zarr.open_group`/`zarr.create_group`.

changes/3845.doc.md

@@ -0,0 +1 @@
+Remove result="ansi" from code blocks in the user guide that were causing empty output cells in the rendered documentation.

codecov.yml

@@ -8,9 +8,21 @@ coverage:
       default:
         target: auto
         threshold: 0.1
+        flags:
+          - tests
+flags:
+  tests:
+    paths:
+      - src/
+    carryforward: true
+  gpu:
+    paths:
+      - src/
+    carryforward: true
 codecov:
   notify:
-    after_n_builds: 10 # Wait for all 10 reports before updating the status
+    # 6 = test.yml: 3 (optional+ubuntu) + 2 (upstream + min_deps), hypothesis: 1
+    after_n_builds: 6
     wait_for_ci: yes
 comment:
   layout: "diff, files"

docs/user-guide/experimental.md

@@ -55,7 +55,7 @@ such as a remote store for source data and a local store for persistent caching.
 
 The CacheStore provides significant performance improvements for repeated data access:
 
-```python exec="true" session="experimental" source="above" result="ansi"
+```python exec="true" session="experimental" source="above"
 import time
 
 # Benchmark reading with cache
@@ -121,7 +121,7 @@ cache = CacheStore(
 
 **cache_set_data**: Controls whether written data is cached
 
-```python exec="true" session="experimental" source="above" result="ansi"
+```python exec="true" session="experimental" source="above"
 # Cache data when writing (default)
 cache = CacheStore(
     store=source_store,
@@ -141,7 +141,7 @@ cache = CacheStore(
 
 The CacheStore provides statistics to monitor cache performance and state:
 
-```python exec="true" session="experimental" source="above" result="ansi"
+```python exec="true" session="experimental" source="above"
 # Access some data to generate cache activity
 data = zarr_array[0:50, 0:50]  # First access - cache miss
 data = zarr_array[0:50, 0:50]  # Second access - cache hit
@@ -232,7 +232,7 @@ of source and cache stores for your specific use case.
 
 Here's a complete example demonstrating cache effectiveness:
 
-```python exec="true" session="experimental-final" source="above" result="ansi"
+```python exec="true" session="experimental-final" source="above"
 import numpy as np
 import time
 from tempfile import mkdtemp

docs/user-guide/v3_migration.md

@@ -114,6 +114,15 @@ The following sections provide details on breaking changes in Zarr-Python 3.
    - Use [`zarr.Group.require_array`][] in place of `zarr.Group.require_dataset`
 3. Disallow "." syntax for getting group members. To get a member of a group named `foo`,
    use `group["foo"]` in place of `group.foo`.
+4. The `zarr.storage.init_group` low-level helper function has been removed. Use
+   [`zarr.open_group`][] or [`zarr.create_group`][] instead:
+
+   ```diff
+   - from zarr.storage import init_group
+   - init_group(store, overwrite=True, path="my/path")
+   + import zarr
+   + zarr.open_group(store, mode="w", path="my/path")
+   ```
 
 ### The Store class
 

pyproject.toml

@@ -155,10 +155,6 @@ hooks.vcs.version-file = "src/zarr/_version.py"
 dependency-groups = ["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 = ["3.12", "3.13", "3.14"]
@@ -175,13 +171,23 @@ matrix.deps.dependency-groups = [
 ]
 
 [tool.hatch.envs.test.scripts]
-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 = "run-coverage --no-cov --ignore tests/benchmarks"
+run-coverage = [
+    "coverage run --source=src -m pytest --junitxml=junit.xml -o junit_family=legacy {args:}",
+    "coverage xml",
+]
+run-coverage-html = [
+    "coverage run --source=src -m pytest {args:}",
+    "coverage html",
+]
+run = "pytest --ignore tests/benchmarks"
 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*"
+run-hypothesis = [
+    "coverage run --source=src -m pytest -nauto --run-slow-hypothesis tests/test_properties.py tests/test_store/test_stateful* {args:}",
+    "coverage xml",
+]
 run-benchmark = "pytest --benchmark-enable tests/benchmarks"
+serve-coverage-html = "python -m http.server -d htmlcov 8000"
 list-env = "pip list"
 
 [tool.hatch.envs.gputest]
@@ -195,8 +201,11 @@ features = ["gpu"]
 python = ["3.12", "3.13"]
 
 [tool.hatch.envs.gputest.scripts]
-run-coverage = "pytest -m gpu --cov-config=pyproject.toml --cov=src --cov-report xml --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks"
-run = "run-coverage --no-cov"
+run-coverage = [
+    "coverage run --source=src -m pytest -m gpu --junitxml=junit.xml -o junit_family=legacy --ignore tests/benchmarks {args:}",
+    "coverage xml",
+]
+run = "pytest -m gpu --ignore tests/benchmarks"
 
 [tool.hatch.envs.upstream]
 template = 'test'