Merge branch 'main' into unsigned-buffer

Author: jakirkham

.github/ISSUE_TEMPLATE/config.yml

@@ -5,7 +5,7 @@ contact_links:
     about: A new major feature should be discussed in the Zarr specifications repository.
   - name: Discuss something on ZulipChat
     url: https://ossci.zulipchat.com/
-    about: For questions like "How do I do X with Zarr?", you can move to our ZulipChat.
+    about: For questions like "How do I do X with Zarr?", consider posting your question to our developer chat.
   - name: Discuss something on GitHub Discussions
     url: https://github.com/zarr-developers/zarr-python/discussions
     about: For questions like "How do I do X with Zarr?", you can move to GitHub Discussions.

.github/labeler.yml

@@ -1,4 +1,4 @@
 needs release notes:
   - all:
     - changed-files:
-      - any-glob-to-any-file: '!changes/*.rst'
+      - all-globs-to-all-files: '!changes/*.rst'

.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:
@@ -98,6 +102,11 @@ jobs:
     - name: Run Tests
       run: |
         hatch env run --env ${{ matrix.dependency-set }} run
+    - name: Upload coverage
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        verbose: true # optional (default = false)
 
   doctests:
     name: doctests

.pre-commit-config.yaml

@@ -6,23 +6,23 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.1
+    rev: v0.9.9
     hooks:
-    - id: ruff
-      args: ["--fix", "--show-fixes"]
-    - id: ruff-format
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
-    - id: check-yaml
-    - id: trailing-whitespace
+      - id: check-yaml
+      - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         files: src|tests
@@ -31,13 +31,14 @@ repos:
           - packaging
           - donfig
           - numcodecs[crc32c]
-          - numpy==2.1  # until https://github.com/numpy/numpy/issues/28034 is resolved
+          - numpy==2.1 # until https://github.com/numpy/numpy/issues/28034 is resolved
           - typing_extensions
           - universal-pathlib
+          - obstore>=0.5.1
           # Tests
           - pytest
   - repo: https://github.com/scientific-python/cookie
-    rev: 2024.08.19
+    rev: 2025.01.22
     hooks:
       - id: sp-repo-review
   - repo: https://github.com/pre-commit/pygrep-hooks
@@ -50,6 +51,6 @@ repos:
     hooks:
       - id: numpydoc-validation
   - repo: https://github.com/twisted/towncrier
-    rev: 23.11.0
+    rev: 24.8.0
     hooks:
       - id: towncrier-check

README.md

@@ -70,7 +70,7 @@
   </td>
 </tr>
 <tr>
-	<td>Zulip</td>
+	<td>Developer Chat</td>
 	<td>
 		<a href="https://ossci.zulipchat.com/">
 		<img src="https://img.shields.io/badge/zulip-join_chat-brightgreen.svg" />
@@ -101,13 +101,13 @@ Zarr is a Python package providing an implementation of compressed, chunked, N-d
 
 ## Main Features
 
-- [**Create**](https://zarr.readthedocs.io/en/stable/tutorial.html#creating-an-array) N-dimensional arrays with any NumPy `dtype`.
-- [**Chunk arrays**](https://zarr.readthedocs.io/en/stable/tutorial.html#chunk-optimizations) along any dimension.
-- [**Compress**](https://zarr.readthedocs.io/en/stable/tutorial.html#compressors) and/or filter chunks using any NumCodecs codec.
-- [**Store arrays**](https://zarr.readthedocs.io/en/stable/tutorial.html#tutorial-storage) in memory, on disk, inside a zip file, on S3, etc...
-- [**Read**](https://zarr.readthedocs.io/en/stable/tutorial.html#reading-and-writing-data) an array [**concurrently**](https://zarr.readthedocs.io/en/stable/tutorial.html#parallel-computing-and-synchronization) from multiple threads or processes.
-- Write to an array concurrently from multiple threads or processes.
-- Organize arrays into hierarchies via [**groups**](https://zarr.readthedocs.io/en/stable/tutorial.html#groups).
+- [**Create**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#creating-an-array) N-dimensional arrays with any NumPy `dtype`.
+- [**Chunk arrays**](https://zarr.readthedocs.io/en/stable/user-guide/performance.html#chunk-optimizations) along any dimension.
+- [**Compress**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#compressors) and/or filter chunks using any NumCodecs codec.
+- [**Store arrays**](https://zarr.readthedocs.io/en/stable/user-guide/storage.html) in memory, on disk, inside a zip file, on S3, etc...
+- [**Read**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#reading-and-writing-data) an array [**concurrently**](https://zarr.readthedocs.io/en/stable/user-guide/performance.html#parallel-computing-and-synchronization) from multiple threads or processes.
+- [**Write**](https://zarr.readthedocs.io/en/stable/user-guide/arrays.html#reading-and-writing-data) to an array concurrently from multiple threads or processes.
+- Organize arrays into hierarchies via [**groups**](https://zarr.readthedocs.io/en/stable/quickstart.html#hierarchical-groups).
 
 ## Where to get it
 

changes/1661.feature.rst

@@ -0,0 +1 @@
+Add experimental ObjectStore storage class based on obstore.

changes/2533.bigfix.rst

@@ -0,0 +1 @@
+Add ``zarr.from_array`` using concurrent streaming of source data