Add Pyodide support and CI jobs for Zarr

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -27,7 +27,7 @@ body:
     attributes:
       label: Python Version
       description: Version of Python interpreter
-      placeholder: 3.8.5, 3.9, 3.10, etc.
+      placeholder: 3.9, 3.10, 3.11, etc.
     validations:
       required: true
   - type: input

.github/ISSUE_TEMPLATE/config.yml

@@ -3,9 +3,9 @@ contact_links:
   - name: ✨ Propose a new major feature
     url: https://github.com/zarr-developers/zarr-specs
     about: A new major feature should be discussed in the Zarr specifications repository.
-  - name: ❓ Discuss something on gitter
-    url: https://gitter.im/zarr-developers/community
-    about: For questions like "How do I do X with Zarr?", you can move to our Gitter channel.
+  - name: ❓ Discuss something on Zulip
+    url: https://ossci.zulipchat.com/
+    about: For questions like "How do I do X with Zarr?", you can move to our Zulip 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/dependabot.yml

@@ -5,6 +5,10 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
+    groups:
+      requirements:
+        patterns:
+          - "*"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/minimal.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2.3.0
+      uses: conda-incubator/setup-miniconda@v3.0.4
       with:
           channels: conda-forge
           environment-file: environment.yml

.github/workflows/python-package.yml

@@ -15,13 +15,15 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        numpy_version: ['>=1.22.0', '==1.20.*']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        numpy_version: ['>=1.24.0', '==1.23.*']
         exclude:
           - python-version: '3.10'
-            numpy_version: '==1.20.*'
+            numpy_version: '==1.23.*'
           - python-version: '3.11'
-            numpy_version: '==1.20.*'
+            numpy_version: '==1.23.*'
+          - python-version: '3.12'
+            numpy_version: '==1.23.*'
     services:
       redis:
         image: redis
@@ -42,7 +44,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2.3.0
+      uses: conda-incubator/setup-miniconda@v3.0.4
       with:
           channels: conda-forge
           python-version: ${{ matrix.python-version }}
@@ -62,7 +64,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install -U pip setuptools wheel line_profiler
         python -m pip install -rrequirements_dev_minimal.txt numpy${{matrix.numpy_version}} -rrequirements_dev_optional.txt pymongo redis
-        python -m pip install .
+        python -m pip install -e .
         python -m pip freeze
     - name: Tests
       shell: "bash -l {0}"
@@ -78,11 +80,8 @@ jobs:
         mkdir ~/blob_emulator
         azurite -l ~/blob_emulator --debug debug.log 2>&1 > stdouterr.log &
         pytest --cov=zarr --cov-config=pyproject.toml --doctest-plus --cov-report xml --cov=./ --timeout=300
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
-        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          #files: ./coverage1.xml,./coverage2.xml # optional
-          #flags: unittests # optional
-          #name: codecov-umbrella # optional
-          #fail_ci_if_error: true # optional (default = false)
         verbose: true # optional (default = false)

.github/workflows/releases.yml

@@ -16,10 +16,10 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4.7.1
+      - uses: actions/setup-python@v5.1.0
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install PyBuild
         run: |
@@ -36,7 +36,7 @@ jobs:
           else
             echo "All seem good"
           fi
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -45,7 +45,7 @@ jobs:
     needs: [build_artifacts]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
@@ -60,11 +60,11 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.8.10
+      - uses: pypa/gh-action-pypi-publish@v1.8.14
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/windows-testing.yml

@@ -16,12 +16,12 @@ jobs:
     strategy:
       fail-fast: True
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11']
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2.3.0
+      - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

.pre-commit-config.yaml

@@ -6,28 +6,25 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.224'
+    rev: 'v0.4.4'
     hooks:
     - id: ruff
-      # Respect `exclude` and `extend-exclude` settings.
-      args: ["--force-exclude"]
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 24.4.2
     hooks:
     - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
-        args: ["-L", "ba,ihs,kake,nd,noe,nwo,te,fo,zar", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: zarr

.readthedocs.yaml

@@ -16,4 +16,6 @@ python:
       extra_requirements:
         - docs
 
-formats: all
+formats:
+  - htmlzip
+  - pdf

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2023 Zarr Developers <https://github.com/zarr-developers>
+Copyright (c) 2015-2024 Zarr Developers <https://github.com/zarr-developers>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -70,10 +70,10 @@
   </td>
 </tr>
 <tr>
-	<td>Gitter</td>
+	<td>Zulip</td>
 	<td>
-		<a href="https://gitter.im/zarr-developers/community">
-		<img src="https://badges.gitter.im/zarr-developers/community.svg" />
+		<a href="https://ossci.zulipchat.com/">
+		<img src="https://img.shields.io/badge/zulip-join_chat-brightgreen.svg" />
 		</a>
 	</td>
 </tr>

TEAM.md

@@ -0,0 +1,26 @@
+## Active core-developers
+- @joshmoore (Josh Moore)
+- @jni (Juan Nunez-Iglesias)
+- @rabernat (Ryan Abernathey)
+- @jhamman (Joe Hamman)
+- @d-v-b (Davis Bennett)
+- @jakirkham (jakirkham)
+- @martindurant (Martin Durant)
+- @normanrz (Norman Rzepka)
+
+## Emeritus core-developers
+- @alimanfoo (Alistair Miles)
+- @shoyer (Stephan Hoyer)
+- @ryan-williams (Ryan Williams)
+- @jrbourbeau (James Bourbeau)
+- @mzjp2 (Zain Patel)
+- @grlee77 (Gregory Lee)
+
+## Former core-developers
+- @jeromekelleher (Jerome Kelleher)
+- @tjcrone (Tim Crone)
+- @funkey (Jan Funke)
+- @shikharsg
+- @Carreau (Matthias Bussonnier)
+- @dazzag24
+- @WardF (Ward Fisher)

bench/compress_normal.py

@@ -8,7 +8,6 @@
 from zarr import blosc
 
 if __name__ == "__main__":
-
     sys.path.insert(0, "..")
 
     # setup

docs/api/v3.rst

@@ -1,13 +1,12 @@
 V3 Specification Implementation(``zarr._storage.v3``)
 =====================================================
 
-This module contains the implementation of the `Zarr V3 Specification <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html>`_.
+This module contains an experimental implementation of the `Zarr V3 Specification <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html>`_.
 
 .. warning::
-    Since Zarr Python 2.12 release, this module provides experimental infrastructure for reading and
-    writing the upcoming V3 spec of the Zarr format. Users wishing to prepare for the migration can set
-    the environment variable ``ZARR_V3_EXPERIMENTAL_API=1`` to begin experimenting, however data
-    written with this API should be expected to become stale, as the implementation will still change.
+    The experimental v3 implementation included in Zarr Python >2.12,<3 is not aligned with the final
+    V3 specification. This version is deprecated and will be removed in Zarr Python 3.0 in favor of a
+    spec compliant version.
 
 The new ``zarr._store.v3`` package has the necessary classes and functions for evaluating Zarr V3.
 Since the design is not finalised, the classes and functions are not automatically imported into

docs/conf.py

@@ -72,7 +72,7 @@
 
 # General information about the project.
 project = "zarr"
-copyright = "2023, Zarr Developers"
+copyright = "2024, Zarr Developers"
 author = "Zarr Developers"
 
 version = zarr.__version__

docs/index.rst

@@ -19,13 +19,13 @@ Zarr-Python
 
 **Version**: |version|
 
-**Download documentation**: `PDF/Zipped HTML/EPUB <https://readthedocs.org/projects/zarr/downloads/>`_
+**Download documentation**: `PDF/Zipped HTML <https://readthedocs.org/projects/zarr/downloads/>`_
 
 **Useful links**:
 `Installation <installation.html>`_ |
 `Source Repository <https://github.com/zarr-developers/zarr-python>`_ |
 `Issue Tracker <https://github.com/zarr-developers/zarr-python/issues>`_ |
-`Gitter <https://gitter.im/zarr-developers/community>`_
+`Zulip Chat <https://ossci.zulipchat.com/>`_
 
 Zarr is a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.
 

docs/installation.rst

@@ -6,6 +6,11 @@ Zarr depends on NumPy. It is generally best to `install NumPy
 appropriate for your operating system and Python distribution. Other dependencies should be
 installed automatically if using one of the installation methods below.
 
+Note: Zarr has endorsed `Scientific-Python SPEC 0 <https://scientific-python.org/specs/spec-0000/>`_ and now follows the version support window as outlined below: 
+
+- Python: 36 months after initial release
+- Core package dependencies (e.g. NumPy): 24 months after initial release
+
 Install Zarr from PyPI::
 
     $ pip install zarr