Merge branch 'main' into maxrjones-patch-1

Author: maxrjones

.github/codecov.yml

@@ -7,6 +7,8 @@ coverage:
     patch:
       default:
         target: 100
+  ignore:
+    - "tests/**"
 comment:
   layout: "diff, files"
   behavior: default

.github/workflows/ci-i386.yml

@@ -63,7 +63,12 @@ jobs:
         run: |
           export DISABLE_NUMCODECS_AVX2=""
           uv venv
-          uv pip install -v -e .[test,test_extras,msgpack,crc32c,pcodec,zfpy]
+          # 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
         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"]
-        # 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: ["3.11", "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
@@ -50,7 +50,12 @@ jobs:
       - name: Install numcodecs
         run: |
           export DISABLE_NUMCODECS_AVX2=""
-          python -m pip install -v -e .[test,test_extras,msgpack,crc32c,pcodec,zfpy]
+          # 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]
+          else
+            python -m pip install -v -e .[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]
+          fi
 
       - name: List installed packages
         run: python -m pip list
@@ -70,7 +75,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        zarr-version: ["312", "313"]
+        zarr-version: ["312", "313", "main"]
 
     defaults:
       run:
@@ -95,4 +100,10 @@ jobs:
 
       - name: Run tests with Zarr ${{ matrix.zarr-version }}
         shell: "bash -l {0}"
-        run: pixi run test-zarr-${{ matrix.zarr-version }}
+        run: pixi run test-zarr-${{ matrix.zarr-version }}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.github/workflows/wheel.yaml

@@ -19,8 +19,8 @@ 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-*"

.pre-commit-config.yaml

@@ -14,9 +14,9 @@ repos:
     - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.14.6
     hooks:
-    - id: ruff
+    - id: ruff-check
       args: ["--fix", "--show-fixes"]
     - id: ruff-format
 

MANIFEST.in

@@ -1,4 +1,3 @@
 recursive-include c-blosc *
 recursive-include numcodecs *.pyx
 recursive-include numcodecs *.pxd
-include numcodecs/tests/package_with_entrypoint-0.1.dist-info/entry_points.txt

README.md

@@ -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)

docs/abc.rst docs/abc.mddocs/abc.rst renamed to docs/abc.md

@@ -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
+```

docs/api.md

@@ -0,0 +1,13 @@
+# API reference
+
+```{toctree}
+:maxdepth: 2
+
+compression/index
+filter/index
+other/index
+checksum32
+abc
+registry
+zarr3
+```