ci: repair CI on the v0.15.x maintenance branch

.github/codecov.yml

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

.github/workflows/ci.yaml

@@ -13,8 +13,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
-        # macos-13 is an intel runner, macos-14 is a arm64 runner
-        platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-15-large is an intel runner, macos-14 is a arm64 runner
+        platform: [ubuntu-latest, windows-latest, macos-15-large, macos-14]
 
     defaults:
       run:
@@ -37,9 +37,11 @@ jobs:
       - name: Install compilers
         run: conda install -y c-compiler cxx-compiler
 
-      - name: Install clang
-        if: matrix.platform == 'macos-13'
-        run: conda install -y 'clang>=12.0.1,<17'
+      - name: Install GCC 14
+        # GCC 15 defaults to C23, where `bool` is a keyword, and the c-blosc
+        # version bundled on this branch still defines `bool` with a typedef.
+        if: runner.os == 'Linux'
+        run: conda install -y 'gcc<15' 'gxx<15'
 
       - name: Show conda environment info
         run: |
@@ -49,15 +51,36 @@ jobs:
 
       - name: Install numcodecs
         run: |
-          export DISABLE_NUMCODECS_AVX2=""
+          # On this branch setup.py adds -mno-avx2 whenever this variable is set, and
+          # recent clang rejects that flag on arm64, so only set it on x86_64.
+          if [[ "$(uname -m)" == "x86_64" ]]; then
+            export DISABLE_NUMCODECS_AVX2=""
+          fi
           python -m pip install -v -e .[test,test_extras,msgpack,crc32c,pcodec,zfpy]
 
+      - name: Deduplicate LC_RPATH entries
+        # The conda-forge compilers inject -Wl,-rpath,$PREFIX/lib multiple
+        # times, producing duplicate LC_RPATH load commands. macOS 15's dyld
+        # rejects duplicate LC_RPATH at load time, so strip the extras.
+        if: runner.os == 'macOS'
+        run: |
+          rpaths() { otool -l "$1" | awk '/ LC_RPATH$/{getline; getline; print $2}'; }
+          for so in numcodecs/*.so; do
+            for rp in $(rpaths "$so" | sort | uniq -d); do
+              while [ "$(rpaths "$so" | grep -cx "$rp")" -gt 1 ]; do
+                echo "Removing duplicate LC_RPATH '$rp' from $so"
+                install_name_tool -delete_rpath "$rp" "$so"
+              done
+            done
+          done
+
       - name: Install zarr-python
         # Since zarr v3 requires numpy >= 1.25, on Python 3.11 leave it out
         # so we can have some tests of our minimum version of numpy (1.24)
         if: matrix.python-version != '3.11'
-        # TODO: remove --pre option when zarr v3 is out
-        run: python -m pip install --pre zarr>=3.0.0b2
+        # numcodecs.zarr3 in this branch targets the zarr 3.0.x API; zarr 3.1+
+        # moved these codecs into zarr itself and changed internal APIs.
+        run: python -m pip install "zarr>=3.0,<3.1"
 
       - name: List installed packages
         run: python -m pip list

.github/workflows/wheel.yaml

@@ -13,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-14 is a arm64 runner
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        # macos-15-large is an intel runner, macos-14 is an arm64 runner
+        os: [ubuntu-latest, windows-latest, macos-15-large, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
       CIBW_BUILD: "cp311-* cp312-* cp313-*"

.pre-commit-config.yaml

@@ -30,4 +30,4 @@ repos:
       hooks:
       -   id: mypy
           args: [--config-file, pyproject.toml]
-          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0rc1']
+          additional_dependencies: [numpy, pytest, crc32c, zfpy, 'zarr>=3.0.0rc1,<3.1']

.readthedocs.yaml

@@ -4,12 +4,12 @@ submodules:
   include: all
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
   jobs:
     post_install:
-      - python -m pip install --pre 'zarr>=3.0.0b2'
+      - python -m pip install --pre 'zarr~=3.0.0'
 
 sphinx:
   configuration: docs/conf.py

numcodecs/tests/test_checksum32.py

@@ -54,12 +54,12 @@
     )
 
 
-@pytest.mark.parametrize(("codec", "arr"), itertools.product(codecs, arrays))
+@pytest.mark.parametrize(("codec", "arr"), tuple(itertools.product(codecs, arrays)))
 def test_encode_decode(codec, arr):
     check_encode_decode(arr, codec)
 
 
-@pytest.mark.parametrize(("codec", "arr"), itertools.product(codecs, arrays))
+@pytest.mark.parametrize(("codec", "arr"), tuple(itertools.product(codecs, arrays)))
 def test_errors(codec, arr):
     enc = codec.encode(arr)
     with pytest.raises(RuntimeError):

numcodecs/tests/test_zarr3.py

@@ -92,12 +92,14 @@ def test_generic_compressor(
         (numcodecs.zarr3.FixedScaleOffset, {"offset": 0, "scale": 25.5}),
         (numcodecs.zarr3.FixedScaleOffset, {"offset": 0, "scale": 51, "astype": "uint16"}),
         (numcodecs.zarr3.AsType, {"encode_dtype": "float32", "decode_dtype": "float32"}),
+        (numcodecs.zarr3.AsType, {"encode_dtype": "float32"}),
     ],
     ids=[
         "delta",
         "fixedscaleoffset",
         "fixedscaleoffset2",
         "astype",
+        "astype_no_decode_dtype",
     ],
 )
 def test_generic_filter(

numcodecs/zarr3.py

@@ -286,7 +286,7 @@ def __init__(self, **codec_config: dict[str, JSON]) -> None:
 
     def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec:
         if astype := self.codec_config.get("astype"):
-            return replace(chunk_spec, dtype=np.dtype(astype))  # type: ignore[arg-type]
+            return replace(chunk_spec, dtype=np.dtype(astype))  # type: ignore[call-overload]
         return chunk_spec
 
 
@@ -304,7 +304,7 @@ def __init__(self, **codec_config: JSON) -> None:
 
     def resolve_metadata(self, chunk_spec: ArraySpec) -> ArraySpec:
         if astype := self.codec_config.get("astype"):
-            return replace(chunk_spec, dtype=np.dtype(astype))  # type: ignore[arg-type]
+            return replace(chunk_spec, dtype=np.dtype(astype))  # type: ignore[call-overload]
         return chunk_spec
 
     def evolve_from_array_spec(self, array_spec: ArraySpec) -> FixedScaleOffset:

pyproject.toml

@@ -117,6 +117,9 @@ write_to = "numcodecs/version.py"
 skip = "./.git,fixture"
 ignore-words-list = "ba, compiletime, hist, nd, unparseable"
 
+[tool.coverage.run]
+omit = ["numcodecs/tests/*"]
+
 [tool.coverage.report]
 exclude_lines = [
     "pragma: no cover",
@@ -156,6 +159,10 @@ filterwarnings = [
 
 [tool.cibuildwheel]
 environment = { DISABLE_NUMCODECS_AVX2=1 }
+[tool.cibuildwheel.linux]
+# Only install NumPy from wheels when building. Recent NumPy releases have no manylinux2014
+# wheels, and building them from source fails with the GCC in the manylinux2014 image.
+environment = { DISABLE_NUMCODECS_AVX2=1, PIP_ONLY_BINARY="numpy" }
 [tool.cibuildwheel.macos]
 environment = { MACOSX_DEPLOYMENT_TARGET=10.9, DISABLE_NUMCODECS_AVX2=1, CFLAGS="$CFLAGS -Wno-implicit-function-declaration" }
 [[tool.cibuildwheel.overrides]]