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Merged
merged 3 commits into from
Apr 7, 2025
Merged

In vlen, define and use const HEADER_LENGTH #723

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0a99c43
In `vlen`, define and use `const` `HEADER_LENGTH`
jakirkham Apr 7, 2025
a2c3ee9
Add news on `const` `HEADER_LENGTH` in `vlen`
jakirkham Apr 7, 2025
e46d36e
Merge zarr-developers/main into jakirkham/def_const_header_vlen
jakirkham Apr 7, 2025
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19 changes: 19 additions & 0 deletions docs/release.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,25 @@ Release notes

.. _unreleased:

Unreleased
----------

Enhancements
~~~~~~~~~~~~

Improvements
~~~~~~~~~~~~

* In ``vlen``, define and use ``const`` ``HEADER_LENGTH``.
By :user:`John Kirkham <jakirkham>`, :issue:`723`

Fixes
~~~~~

Maintenance
~~~~~~~~~~~


0.16.0
------

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34 changes: 19 additions & 15 deletions numcodecs/vlen.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

cimport cython

from libc.stdint cimport uint8_t
from libc.stdint cimport uint8_t, uint32_t
from libc.string cimport memcpy

from cpython.buffer cimport PyBuffer_IsContiguous
Expand Down Expand Up @@ -39,8 +39,12 @@ from .abc import Codec
from .compat import ensure_contiguous_ndarray


# 4 bytes to store number of items
cdef Py_ssize_t HEADER_LENGTH = 4
# Define header size used to store number of items that follow.
cdef extern from *:
"""
const Py_ssize_t HEADER_LENGTH = sizeof(uint32_t);
"""
const Py_ssize_t HEADER_LENGTH


def check_out_param(out, n_items):
Expand Down Expand Up @@ -116,7 +120,7 @@ class VLenUTF8(Codec):
b = PyUnicode_AsUTF8String(u)
l = PyBytes_GET_SIZE(b)
encoded_values[i] = b
data_length += l + 4 # 4 bytes to store item length
data_length += l + HEADER_LENGTH
encoded_lengths[i] = l

# setup output
Expand All @@ -132,7 +136,7 @@ class VLenUTF8(Codec):
for i in range(n_items):
l = encoded_lengths[i]
store_le32(<uint8_t*>data, l)
data += 4
data += HEADER_LENGTH
encv = PyBytes_AS_STRING(encoded_values[i])
memcpy(data, encv, l)
data += l
Expand Down Expand Up @@ -178,10 +182,10 @@ class VLenUTF8(Codec):
# https://github.com/cython/cython/issues/1608
data += HEADER_LENGTH
for i in range(n_items):
if data + 4 > data_end:
if data + HEADER_LENGTH > data_end:
raise ValueError('corrupt buffer, data seem truncated')
l = load_le32(<uint8_t*>data)
data += 4
data += HEADER_LENGTH
if data + l > data_end:
raise ValueError('corrupt buffer, data seem truncated')
out[i] = PyUnicode_FromStringAndSize(data, l)
Expand Down Expand Up @@ -247,7 +251,7 @@ class VLenBytes(Codec):
elif not PyBytes_Check(b):
raise TypeError('expected byte string, found %r' % b)
l = PyBytes_GET_SIZE(b)
data_length += l + 4 # 4 bytes to store item length
data_length += l + HEADER_LENGTH
lengths[i] = l

# setup output
Expand All @@ -263,7 +267,7 @@ class VLenBytes(Codec):
for i in range(n_items):
l = lengths[i]
store_le32(<uint8_t*>data, l)
data += 4
data += HEADER_LENGTH
encv = PyBytes_AS_STRING(values[i])
memcpy(data, encv, l)
data += l
Expand Down Expand Up @@ -309,10 +313,10 @@ class VLenBytes(Codec):
# https://github.com/cython/cython/issues/1608
data += HEADER_LENGTH
for i in range(n_items):
if data + 4 > data_end:
if data + HEADER_LENGTH > data_end:
raise ValueError('corrupt buffer, data seem truncated')
l = load_le32(<uint8_t*>data)
data += 4
data += HEADER_LENGTH
if data + l > data_end:
raise ValueError('corrupt buffer, data seem truncated')
out[i] = PyBytes_FromStringAndSize(data, l)
Expand Down Expand Up @@ -399,7 +403,7 @@ class VLenArray(Codec):
raise ValueError('only 1-dimensional arrays are supported')
l = v.nbytes
normed_values[i] = v
data_length += l + 4 # 4 bytes to store item length
data_length += l + HEADER_LENGTH
lengths[i] = l

# setup output
Expand All @@ -415,7 +419,7 @@ class VLenArray(Codec):
for i in range(n_items):
l = lengths[i]
store_le32(<uint8_t*>data, l)
data += 4
data += HEADER_LENGTH

value_mv = ensure_continguous_memoryview(normed_values[i])
value_pb = PyMemoryView_GET_BUFFER(value_mv)
Expand Down Expand Up @@ -468,10 +472,10 @@ class VLenArray(Codec):
# https://github.com/cython/cython/issues/1608
data += HEADER_LENGTH
for i in range(n_items):
if data + 4 > data_end:
if data + HEADER_LENGTH > data_end:
raise ValueError('corrupt buffer, data seem truncated')
l = load_le32(<uint8_t*>data)
data += 4
data += HEADER_LENGTH
if data + l > data_end:
raise ValueError('corrupt buffer, data seem truncated')

Expand Down
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