Remove deprecated blosc code (#712)

* Remove deprecated blosc code

* mypy fixes

Author: dstansby

.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']

docs/release.rst

@@ -20,10 +20,30 @@ Unreleased
 Enhancements
 ~~~~~~~~~~~~
 
-* Add support for the Linux AArch64 architecture, and bump the minimum
+* Add support for the Linux aarch64 architecture, and bump the minimum
 macOS deployment target for x86_64 to 10.13.
   By :user:`Agriya Khetarpal <agriyakhetarpal>`, :issue:`288`.
 
+Removals
+~~~~~~~~
+
+The following ``blosc`` funcitons are removed, with no replacement.
+This is because they were not intended to be public API.
+
+- ``numcodecs.blosc.init``
+- ``numcodecs.blosc.destroy``
+- ``numcodecs.blosc.compname_to_compcode``
+- ``numcodecs.blosc.cbuffer_sizes``
+- ``numcodecs.blosc.cbuffer_metainfo``
+
+In addition, ``numcodecs.blosc.decompress_partial`` is removed as
+has always been experimental and there is no equivalent in the official
+blsoc Python package.
+By :user:`David Stansby <dstansby>`, :issue:`712`
+
+0.15.1
+------
+
 Improvements
 ~~~~~~~~~~~~
 * Raise a custom `UnknownCodecError` when trying to retrieve an unavailable codec.
@@ -70,7 +90,7 @@ This is because they are not intended to be public API.
 In addition, ``numcodecs.blosc.decompress_partial`` is deprecated as
 has always been experimental and there is no equivalent in the official
 blsoc Python package.
-By :user:`David Stansby <dstansby>`, :issue`619`
+By :user:`David Stansby <dstansby>`, :issue:`619`
 
 Fixes
 ~~~~~

numcodecs/__init__.py

@@ -51,7 +51,7 @@
     ncores = 1
 blosc._init()
 blosc.set_nthreads(min(8, ncores))
-atexit.register(blosc.destroy)
+atexit.register(blosc._destroy)
 
 from numcodecs import zstd as zstd
 from numcodecs.zstd import Zstd

numcodecs/blosc.pyx

@@ -6,7 +6,6 @@
 import threading
 import multiprocessing
 import os
-from deprecated import deprecated
 
 
 from cpython.bytes cimport PyBytes_AS_STRING, PyBytes_FromStringAndSize
@@ -44,7 +43,6 @@ cdef extern from "blosc.h":
                        void* src, void* dest, size_t destsize) nogil
     int blosc_decompress(void *src, void *dest, size_t destsize) nogil
     int blosc_getitem(void* src, int start, int nitems, void* dest)
-    int blosc_compname_to_compcode(const char* compname)
     int blosc_compress_ctx(int clevel, int doshuffle, size_t typesize, size_t nbytes,
                            const void* src, void* dest, size_t destsize,
                            const char* compressor, size_t blocksize,
@@ -99,28 +97,12 @@ def _init():
     """Initialize the Blosc library environment."""
     blosc_init()
 
-init = deprecated(_init)
-
 
 def _destroy():
     """Destroy the Blosc library environment."""
     blosc_destroy()
 
 
-destroy = deprecated(_destroy)
-
-
-def _compname_to_compcode(cname):
-    """Return the compressor code associated with the compressor name. If the compressor
-    name is not recognized, or there is not support for it in this build, -1 is returned
-    instead."""
-    if isinstance(cname, str):
-        cname = cname.encode('ascii')
-    return blosc_compname_to_compcode(cname)
-
-compname_to_compcode = deprecated(_compname_to_compcode)
-
-
 def list_compressors():
     """Get a list of compressors supported in the current build."""
     s = blosc_list_compressors()
@@ -166,7 +148,6 @@ def _cbuffer_sizes(source):
 
     return nbytes, cbytes, blocksize
 
-cbuffer_sizes = deprecated(_cbuffer_sizes)
 
 def cbuffer_complib(source):
     """Return the name of the compression library used to compress `source`."""
@@ -222,13 +203,10 @@ def _cbuffer_metainfo(source):
 
     return typesize, shuffle, memcpyed
 
-cbuffer_metainfo = deprecated(_cbuffer_metainfo)
-
 def _err_bad_cname(cname):
     raise ValueError('bad compressor or compressor not supported: %r; expected one of '
                      '%s' % (cname, list_compressors()))
 
-err_bad_cname = deprecated(_err_bad_cname)
 
 def compress(source, char* cname, int clevel, int shuffle=SHUFFLE,
              int blocksize=AUTOBLOCKS, typesize=None):
@@ -423,86 +401,6 @@ def decompress(source, dest=None):
     return dest
 
 
-def _decompress_partial(source, start, nitems, dest=None):
-    """**Experimental**
-    Decompress data of only a part of a buffer.
-
-    Parameters
-    ----------
-    source : bytes-like
-        Compressed data, including blosc header. Can be any object supporting the buffer
-        protocol.
-    start: int,
-        Offset in item where we want to start decoding
-    nitems: int
-        Number of items we want to decode
-    dest : array-like, optional
-        Object to decompress into.
-
-
-    Returns
-    -------
-    dest : bytes
-        Object containing decompressed data.
-
-    """
-    cdef:
-        int ret
-        int encoding_size
-        int nitems_bytes
-        int start_bytes
-        memoryview source_mv
-        const Py_buffer* source_pb
-        const char* source_ptr
-        memoryview dest_mv
-        Py_buffer* dest_pb
-        char* dest_ptr
-        size_t dest_nbytes
-
-    # obtain source memoryview
-    source_mv = ensure_continguous_memoryview(source)
-    source_pb = PyMemoryView_GET_BUFFER(source_mv)
-
-    # setup source pointer
-    source_ptr = <const char*>source_pb.buf
-
-    # get encoding size from source buffer header
-    encoding_size = source[3]
-
-    # convert variables to handle type and encoding sizes
-    nitems_bytes = nitems * encoding_size
-    start_bytes = (start * encoding_size)
-
-    # setup destination buffer
-    if dest is None:
-        # allocate memory
-        dest_1d = dest = PyBytes_FromStringAndSize(NULL, nitems_bytes)
-    else:
-        dest_1d = ensure_contiguous_ndarray(dest)
-
-    # obtain dest memoryview
-    dest_mv = memoryview(dest_1d)
-    dest_pb = PyMemoryView_GET_BUFFER(dest_mv)
-    dest_ptr = <char*>dest_pb.buf
-    dest_nbytes = dest_pb.len
-
-    # try decompression
-    try:
-        if dest_nbytes < nitems_bytes:
-            raise ValueError('destination buffer too small; expected at least %s, '
-                             'got %s' % (nitems_bytes, dest_nbytes))
-        ret = blosc_getitem(source_ptr, start, nitems, dest_ptr)
-    finally:
-        pass
-
-    # ret refers to the number of bytes returned from blosc_getitem.
-    if ret <= 0:
-        raise RuntimeError('error during blosc partial decompression: %d', ret)
-
-    return dest
-
-decompress_partial = deprecated(_decompress_partial)
-
 # set the value of this variable to True or False to override the
 # default adaptive behaviour
 use_threads = None
@@ -601,11 +499,6 @@ class Blosc(Codec):
         buf = ensure_contiguous_ndarray(buf, self.max_buffer_size)
         return decompress(buf, out)
 
-    def decode_partial(self, buf, int start, int nitems, out=None):
-        '''**Experimental**'''
-        buf = ensure_contiguous_ndarray(buf, self.max_buffer_size)
-        return _decompress_partial(buf, start, nitems, dest=out)
-
     def __repr__(self):
         r = '%s(cname=%r, clevel=%r, shuffle=%s, blocksize=%s)' % \
             (type(self).__name__,

numcodecs/tests/common.py

@@ -115,74 +115,6 @@ def check_encode_decode(arr, codec, precision=None):
     compare_arrays(arr, out, precision=precision)
 
 
-def check_encode_decode_partial(arr, codec, precision=None):
-    # N.B., watch out here with blosc compressor, if the itemsize of
-    # the source buffer is different then the results of encoding
-    # (i.e., compression) may be different. Hence we *do not* require that
-    # the results of encoding be identical for all possible inputs, rather
-    # we just require that the results of the encode/decode round-trip can
-    # be compared to the original array.
-
-    itemsize = arr.itemsize
-    start, nitems = 5, 10
-    compare_arr = arr[start : start + nitems]
-    # test encoding of numpy array
-    enc = codec.encode(arr)
-    dec = codec.decode_partial(enc, start, nitems)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # out = np.empty_like(compare_arr)
-    out = np.empty_like(compare_arr)
-    print(len(out))
-
-    # test partial decode of encoded bytes
-    buf = arr.tobytes(order='A')
-    enc = codec.encode(buf)
-    dec = codec.decode_partial(enc, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test partial decode of encoded bytearray
-    buf = bytearray(arr.tobytes(order='A'))
-    enc = codec.encode(buf)
-    dec = codec.decode_partial(enc, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test partial decode of encoded array.array
-    buf = array.array('b', arr.tobytes(order='A'))
-    enc = codec.encode(buf)
-    dec = codec.decode_partial(enc, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # # decoding should support any object exporting the buffer protocol,
-
-    # # setup
-    enc_bytes = ensure_bytes(enc)
-
-    # test decoding of raw bytes into numpy array
-    dec = codec.decode_partial(enc_bytes, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test partial decoding of bytearray
-    dec = codec.decode_partial(bytearray(enc_bytes), start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test partial decoding of array.array
-    buf = array.array('b', enc_bytes)
-    dec = codec.decode_partial(buf, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test decoding of numpy array into numpy array
-    buf = np.frombuffer(enc_bytes, dtype='u1')
-    dec = codec.decode_partial(buf, start * itemsize, nitems * itemsize, out=out)
-    compare_arrays(compare_arr, dec, precision=precision)
-
-    # test decoding directly into bytearray
-    out = bytearray(compare_arr.nbytes)
-    codec.decode_partial(enc_bytes, start * itemsize, nitems * itemsize, out=out)
-    # noinspection PyTypeChecker
-    compare_arrays(compare_arr, out, precision=precision)
-
-
 def assert_array_items_equal(res, arr):
     assert isinstance(res, np.ndarray)
     res = res.reshape(-1, order='A')

numcodecs/tests/test_blosc.py

@@ -15,7 +15,6 @@
     check_backwards_compatibility,
     check_config,
     check_encode_decode,
-    check_encode_decode_partial,
     check_err_decode_object_buffer,
     check_err_encode_object_buffer,
     check_max_buffer_size,
@@ -75,19 +74,6 @@ def test_encode_decode(array, codec):
     check_encode_decode(array, codec)
 
 
-@pytest.mark.parametrize('codec', codecs)
-@pytest.mark.parametrize(
-    'array',
-    [
-        pytest.param(x) if len(x.shape) == 1 else pytest.param(x, marks=[pytest.mark.xfail])
-        for x in arrays
-    ],
-)
-def test_partial_decode(codec, array):
-    _skip_null(codec)
-    check_encode_decode_partial(array, codec)
-
-
 def test_config():
     codec = Blosc(cname='zstd', clevel=3, shuffle=1)
     check_config(codec)

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

@@ -14,7 +14,7 @@ description = """
 A Python package providing buffer compression and transformation codecs \
 for use in data storage and communication applications."""
 readme = "README.rst"
-dependencies = ["numpy>=1.24", "deprecated", "typing_extensions"]
+dependencies = ["numpy>=1.24", "typing_extensions"]
 requires-python = ">=3.11"
 dynamic = [
   "version",