Merge branch 'main' into pcodec-v1

Author: mwlon

.github/codecov.yml

@@ -8,7 +8,7 @@ coverage:
       default:
         target: 100
   ignore:
-    - "numcodecs/tests/**"
+    - "tests/**"
 comment:
   layout: "diff, files"
   behavior: default

.github/workflows/ci-i386.yml

@@ -45,9 +45,10 @@ jobs:
             py3-pip
             py3-pytest
 
-      - name: Install zfp
+      - name: Install zfp and numcodecs
         run: |
           uv venv
+          uv pip install --group dev
           PYTHON_INCLUDE=$(uv run python -c 'from sysconfig import get_paths; print(get_paths()["include"])');
           PYTHON_LIB=$(uv run python -c 'import sysconfig; print(sysconfig.get_config_var("LIBDIR"))');
           git clone https://github.com/LLNL/zfp
@@ -56,19 +57,9 @@ jobs:
           uv run cmake zfp -B zfp/build -DBUILD_ZFPY=ON -DBUILD_TESTING=OFF -DPYTHON_LIBRARY=$PYTHON_LIB -DPYTHON_INCLUDE_DIR=$PYTHON_INCLUDE
           uv run make -j -C zfp/build
           uv run sudo make -C zfp/build install
-          uv add "zfpy @ ./zfp"
-        shell: alpine.sh {0}
-
-      - name: Install numcodecs
-        run: |
-          export DISABLE_NUMCODECS_AVX2=""
-          uv venv
-          # TODO: Remove this conditional when pcodec supports Python 3.14
-          if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
-            uv pip install -v -e .[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]
-          else
-            uv pip install -v -e .[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]
-          fi
+          uv pip install ./zfp
+          uv pip install --no-build-isolation -v .
+          uv pip install "numcodecs[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]"
         shell: alpine.sh {0}
 
       - name: List installed packages

.github/workflows/ci.yaml

@@ -12,9 +12,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13", "3.14"]
-        # macos-13 is an intel runner, macos-14 is an arm64 runner
-        platform: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-13, macos-14]
+        python-version: ["3.12", "3.13", "3.14"]
+        # macos-15-large is an intel runner, macos-14 is an arm64 runner
+        platform: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-15-large, macos-14]
 
     defaults:
       run:
@@ -38,7 +38,7 @@ jobs:
         run: conda install -y c-compiler cxx-compiler
 
       - name: Install clang
-        if: matrix.platform == 'macos-13'
+        if: matrix.platform == 'macos-15-large'
         run: conda install -y 'clang>=12.0.1,<17'
 
       - name: Show conda environment info
@@ -49,12 +49,11 @@ jobs:
 
       - name: Install numcodecs
         run: |
-          export DISABLE_NUMCODECS_AVX2=""
           # TODO: Remove this conditional when pcodec supports Python 3.14
           if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
-            python -m pip install -v -e .[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]
+            python -m pip install -v ".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]"
           else
-            python -m pip install -v -e .[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]
+            python -m pip install -v ".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]"
           fi
 
       - name: List installed packages
@@ -70,12 +69,72 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true
 
+  test-crc32c:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: google-crc32c
+            extras: "google_crc32c"
+          - name: crc32c
+            extras: "crc32c"
+          - name: no-crc32c
+            extras: ""
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3.2.0
+        with:
+          channels: conda-forge
+          miniforge-version: latest
+          python-version: "3.13"
+
+      - name: Install compilers
+        run: conda install -y c-compiler cxx-compiler
+
+      - name: Install numcodecs
+        run: |
+          if [[ -n "${{ matrix.extras }}" ]]; then
+            python -m pip install -v ".[${{ matrix.extras }},test]"
+          else
+            python -m pip install -v ".[test]"
+          fi
+
+      - name: List installed packages
+        run: python -m pip list
+
+      - name: Run checksum tests
+        run: pytest -v tests/test_checksum32.py
+
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+
   test-zarr:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        zarr-version: ["312", "313", "main"]
+        include:
+          - zarr-version: "308"
+            zarr-pkg: "zarr==3.0.8"
+          - zarr-version: "316"
+            zarr-pkg: "zarr==3.1.6"
+          - zarr-version: "main"
+            zarr-pkg: "zarr @ git+https://github.com/zarr-developers/zarr-python.git@main"
 
     defaults:
       run:
@@ -88,19 +147,24 @@ jobs:
           submodules: recursive
           fetch-depth: 0 # required for version resolution
 
-      - name: Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.9.0
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3.2.0
         with:
-          pixi-version: v0.49.0
-          cache: false
+          channels: conda-forge
+          miniforge-version: latest
+          python-version: "3.13"
+
+      - name: Install compilers
+        run: conda install -y c-compiler cxx-compiler
 
+      - name: Install numcodecs and Zarr
+        run: |
+          python -m pip install -v ".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
       - name: List installed packages
-        shell: "bash -l {0}"
-        run: pixi run ls-deps-${{matrix.zarr-version}}
+        run: python -m pip list
 
-      - name: Run tests with Zarr ${{ matrix.zarr-version }}
-        shell: "bash -l {0}"
-        run: pixi run test-zarr-${{ matrix.zarr-version }}
+      - name: Run Zarr integration tests
+        run: pytest tests/test_zarr3.py tests/test_zarr3_import.py
 
       - uses: codecov/codecov-action@v5
         with:

.github/workflows/wheel.yaml

@@ -19,13 +19,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-14 is an arm64 runner
-        os: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-13, macos-14]
+        # macos-15-large is an intel runner, macos-14 is an arm64 runner
+        os: [ubuntu-latest, ubuntu-22.04-arm, windows-latest, macos-15-large, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
-      CIBW_BUILD: "cp311-* cp312-* cp313-* cp314-*"
+      CIBW_BUILD: "cp312-* cp313-* cp314-*"
       CIBW_SKIP: "*-musllinux_* *win32 *_i686 *_s390x"
-      # note: CIBW_ENVIRONMENT is now set in pyproject.toml
+      # note: cibuildwheel config-settings are set in pyproject.toml
 
     steps:
       - uses: actions/checkout@v5
@@ -52,7 +52,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Build sdist
         run: pipx run build --sdist

.gitignore

@@ -3,9 +3,7 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
-numcodecs/**/*.c
-numcodecs/**/*.h
+# Shared libraries (legacy, meson builds out-of-source)
 *.so
 
 # editor
@@ -50,8 +48,6 @@ coverage.xml
 .hypothesis/
 cover/
 
-# Cython annotation files
-numcodecs/*.html
 
 # Translations
 *.mo
@@ -99,12 +95,8 @@ ENV/
 # PyCharm
 .idea
 
-# setuptools-scm
-numcodecs/version.py
-
-# Cython generated
-numcodecs/*.c
 # pixi environments
 .pixi/*
 *.egg-info
-pixi.lock
+pixi.lock
+uv.lock

.readthedocs.yaml

@@ -4,7 +4,7 @@ submodules:
   include: all
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
   jobs:

MANIFEST.in

@@ -0,0 +1,9 @@
+# Numcodecs
+
+Numcodecs is a Python package providing buffer compression and transformation
+codecs for use in data storage and communication applications.
+
+[![Docs](https://readthedocs.org/projects/numcodecs/badge/?version=latest)](https://numcodecs.readthedocs.io/en/latest/?badge=latest)
+[![Tests](https://github.com/zarr-developers/numcodecs/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/zarr-developers/numcodecs/actions/workflows/ci.yaml)
+[![Wheels](https://github.com/zarr-developers/numcodecs/actions/workflows/wheel.yaml/badge.svg?branch=main)](https://github.com/zarr-developers/numcodecs/actions/workflows/wheel.yaml)
+[![Codecov](https://codecov.io/gh/zarr-developers/numcodecs/branch/main/graph/badge.svg)](https://codecov.io/gh/zarr-developers/numcodecs)

README.md

@@ -1,9 +1,10 @@
 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])):

adhoc/blosc_memleak_check.py

@@ -1,5 +1,6 @@
-Codec API
-=========
+# Codec API
+
+```{eval-rst}
 .. automodule:: numcodecs.abc
 
 .. autoclass:: Codec
@@ -9,3 +10,4 @@ Codec API
     .. automethod:: decode
     .. automethod:: get_config
     .. automethod:: from_config
+```