Merge branch 'main' into mypy

Author: d-v-b

.github/workflows/ci.yaml

@@ -27,25 +27,11 @@ jobs:
           submodules: recursive
           fetch-depth: 0 # required for version resolution
 
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3.2.0
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
-          channels: conda-forge
-          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
-
-      - name: Install compilers
-        run: conda install -y c-compiler cxx-compiler
-
-      - name: Install clang
-        if: matrix.platform == 'macos-15-large'
-        run: conda install -y 'clang>=12.0.1,<17'
-
-      - name: Show conda environment info
-        run: |
-          conda info
-          conda config --show-sources
-          conda list --show-channel-urls
+          cache: 'pip'
 
       - name: Install numcodecs
         run: |
@@ -93,15 +79,11 @@ jobs:
           submodules: recursive
           fetch-depth: 0
 
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3.2.0
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
-          channels: conda-forge
-          miniforge-version: latest
-          python-version: "3.13"
-
-      - name: Install compilers
-        run: conda install -y c-compiler cxx-compiler
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
       - name: Install numcodecs
         run: |
@@ -147,15 +129,11 @@ jobs:
           submodules: recursive
           fetch-depth: 0 # required for version resolution
 
-      - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3.2.0
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
-          channels: conda-forge
-          miniforge-version: latest
-          python-version: "3.13"
-
-      - name: Install compilers
-        run: conda install -y c-compiler cxx-compiler
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
 
       - name: Install numcodecs and Zarr
         run: |

docs/design/meson-python-migration.md

@@ -43,7 +43,7 @@ build-backend = "setuptools.build_meta"
 
 ### Shared Cython declarations
 
-- `compat_ext.pxd` — `PyBytes_RESIZE`, `ensure_continguous_memoryview` (used by blosc, zstd, lz4, vlen)
+- `compat_ext.pxd` — `PyBytes_RESIZE`, `ensure_contiguous_memoryview` (used by blosc, zstd, lz4, vlen)
 - `_utils.pxd` — `store_le32`, `load_le32` (used by lz4, fletcher32, vlen)
 
 ### Vendored C sources (c-blosc git submodule)

src/numcodecs/__init__.py

@@ -126,7 +126,7 @@
 
 register_codec(Fletcher32)
 
-# Optional depenedencies
+# Optional dependencies
 with suppress(ImportError):
     from numcodecs.zfpy import ZFPY
 

src/numcodecs/abc.py

@@ -65,7 +65,7 @@ def decode(self, buf, out=None):  # pragma: no cover
             Encoded data. May be any object supporting the new-style buffer
             protocol.
         out : buffer-like, optional
-            Writeable buffer to store decoded data. N.B. if provided, this buffer must
+            Writable buffer to store decoded data. N.B. if provided, this buffer must
             be exactly the right size to store the decoded data.
 
         Returns

src/numcodecs/blosc.pyx

@@ -11,7 +11,7 @@ import os
 from cpython.bytes cimport PyBytes_AS_STRING, PyBytes_FromStringAndSize
 from cpython.memoryview cimport PyMemoryView_GET_BUFFER
 
-from .compat_ext cimport PyBytes_RESIZE, ensure_continguous_memoryview
+from .compat_ext cimport PyBytes_RESIZE, ensure_contiguous_memoryview
 
 from .compat import ensure_contiguous_ndarray
 from .abc import Codec
@@ -140,7 +140,7 @@ def _cbuffer_sizes(source):
         size_t nbytes, cbytes, blocksize
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # determine buffer size
@@ -156,7 +156,7 @@ def cbuffer_complib(source):
         const Py_buffer* source_pb
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # determine buffer size
@@ -186,7 +186,7 @@ def _cbuffer_metainfo(source):
         int flags
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # determine buffer size
@@ -251,7 +251,7 @@ def compress(source, char* cname, int clevel, int shuffle=SHUFFLE,
         _err_bad_cname(cname_str)
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # extract metadata
@@ -353,7 +353,7 @@ def decompress(source, dest=None):
         size_t nbytes, cbytes, blocksize
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # get source pointer

src/numcodecs/compat_ext.pxd

@@ -10,4 +10,4 @@ cdef extern from *:
     int PyBytes_RESIZE(object b, Py_ssize_t n) except -1
 
 
-cpdef memoryview ensure_continguous_memoryview(obj)
+cpdef memoryview ensure_contiguous_memoryview(obj)

src/numcodecs/compat_ext.pyx

@@ -8,7 +8,7 @@ from cpython.buffer cimport PyBuffer_IsContiguous
 from cpython.memoryview cimport PyMemoryView_GET_BUFFER
 
 
-cpdef memoryview ensure_continguous_memoryview(obj):
+cpdef memoryview ensure_contiguous_memoryview(obj):
     cdef memoryview mv
     if type(obj) is memoryview:
         mv = <memoryview>obj

src/numcodecs/lz4.pyx

@@ -10,7 +10,7 @@ from libc.stdint cimport uint8_t, uint32_t
 from cpython.bytes cimport PyBytes_AS_STRING, PyBytes_FromStringAndSize
 from cpython.memoryview cimport PyMemoryView_GET_BUFFER
 
-from .compat_ext cimport PyBytes_RESIZE, ensure_continguous_memoryview
+from .compat_ext cimport PyBytes_RESIZE, ensure_contiguous_memoryview
 from ._utils cimport store_le32, load_le32
 
 from .compat import ensure_contiguous_ndarray
@@ -79,7 +79,7 @@ def compress(source, int acceleration=DEFAULT_ACCELERATION):
         acceleration = DEFAULT_ACCELERATION
 
     # setup source buffer
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # extract metadata
@@ -141,7 +141,7 @@ def decompress(source, dest=None):
         int source_size, dest_size, decompressed_size
 
     # setup source buffer
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # extract source metadata

src/numcodecs/vlen.pyx

@@ -17,7 +17,7 @@ from cpython.unicode cimport PyUnicode_FromStringAndSize
 
 from numpy cimport ndarray
 
-from .compat_ext cimport ensure_continguous_memoryview
+from .compat_ext cimport ensure_contiguous_memoryview
 from ._utils cimport store_le32, load_le32
 
 import numpy as np
@@ -139,7 +139,7 @@ class VLenUTF8(Codec):
 
         # obtain memoryview
         buf = ensure_contiguous_ndarray(buf)
-        buf_mv = ensure_continguous_memoryview(buf)
+        buf_mv = ensure_contiguous_memoryview(buf)
         buf_pb = PyMemoryView_GET_BUFFER(buf_mv)
 
         # sanity checks
@@ -268,7 +268,7 @@ class VLenBytes(Codec):
 
         # obtain memoryview
         buf = ensure_contiguous_ndarray(buf)
-        buf_mv = ensure_continguous_memoryview(buf)
+        buf_mv = ensure_contiguous_memoryview(buf)
         buf_pb = PyMemoryView_GET_BUFFER(buf_mv)
 
         # sanity checks
@@ -375,7 +375,7 @@ class VLenArray(Codec):
         for i in range(n_items):
             o = values[i]
             # replace missing value and coerce to typed data
-            value_mv = ensure_continguous_memoryview(
+            value_mv = ensure_contiguous_memoryview(
                 np.array([], dtype=self.dtype) if o is None
                 else np.ascontiguousarray(o, self.dtype)
             )
@@ -424,7 +424,7 @@ class VLenArray(Codec):
 
         # obtain memoryview
         buf = ensure_contiguous_ndarray(buf)
-        buf_mv = ensure_continguous_memoryview(buf)
+        buf_mv = ensure_contiguous_memoryview(buf)
         buf_pb = PyMemoryView_GET_BUFFER(buf_mv)
 
         # sanity checks

src/numcodecs/zstd.pyx

@@ -8,7 +8,7 @@
 from cpython.bytes cimport PyBytes_AS_STRING, PyBytes_FromStringAndSize
 from cpython.memoryview cimport PyMemoryView_GET_BUFFER
 
-from .compat_ext cimport PyBytes_RESIZE, ensure_continguous_memoryview
+from .compat_ext cimport PyBytes_RESIZE, ensure_contiguous_memoryview
 
 from .compat import ensure_contiguous_ndarray
 from .abc import Codec
@@ -134,7 +134,7 @@ def compress(source, int level=DEFAULT_CLEVEL, bint checksum=False):
         level = MAX_CLEVEL
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # setup source buffer
@@ -211,7 +211,7 @@ def decompress(source, dest=None):
         unsigned long long content_size
 
     # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
+    source_mv = ensure_contiguous_memoryview(source)
     source_pb = PyMemoryView_GET_BUFFER(source_mv)
 
     # get source pointer