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2024-12-13 21:22:22
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zarr-developers/numcodecs | zarr-developers__numcodecs-515 | 1be12d3ae13ad900ef8f70228b30c86f225eee32 | diff --git a/docs/release.rst b/docs/release.rst
index b569015c..17f146e9 100644
--- a/docs/release.rst
+++ b/docs/release.rst
@@ -26,7 +26,8 @@ Enhancements
Fix
~~~
-
+* Fix VLenUTF8 encoding for read-only buffers.
+ By :user:`Isaac Virshup <ivirshup>`, :issue:`514`.
* Fix skip of entry points backport tests
By :user:`Elliott Sales de Andrade <QuLogic>`, :issue:`487`.
* Fix Upgrade to Zstd 1.5.5 due to potential corruption.
diff --git a/numcodecs/vlen.pyx b/numcodecs/vlen.pyx
index a1ff0e26..e1e149ee 100644
--- a/numcodecs/vlen.pyx
+++ b/numcodecs/vlen.pyx
@@ -7,6 +7,7 @@
import cython
cimport cython
+from numpy cimport ndarray
import numpy as np
from .abc import Codec
from .compat_ext cimport Buffer
@@ -74,7 +75,7 @@ class VLenUTF8(Codec):
def encode(self, buf):
cdef:
Py_ssize_t i, l, n_items, data_length, total_length
- object[:] input_values
+ ndarray[object, ndim=1] input_values
object[:] encoded_values
int[:] encoded_lengths
char* encv
diff --git a/pyproject.toml b/pyproject.toml
index 319b29d7..af8f040a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,8 @@ requires = [
"setuptools>=64",
"setuptools-scm[toml]>=6.2",
"Cython",
- "py-cpuinfo"
+ "py-cpuinfo",
+ "numpy",
]
build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
index ea8bc64c..e594a203 100644
--- a/setup.py
+++ b/setup.py
@@ -196,12 +196,13 @@ def lz4_extension():
def vlen_extension():
info('setting up vlen extension')
+ import numpy
extra_compile_args = base_compile_args.copy()
define_macros = []
# setup sources
- include_dirs = ['numcodecs']
+ include_dirs = ['numcodecs', numpy.get_include()]
# define_macros += [('CYTHON_TRACE', '1')]
sources = ['numcodecs/vlen.pyx']
| VLenUTF8().encode(buffer) fails is buffer is read-only
<!--
For bug reports, please follow the template below. For enhancement proposals, feel free
to use whatever template makes sense.
-->
#### Minimal, reproducible code sample, a copy-pastable example if possible
```python
import numpy as np
from numcodecs import VLenUTF8
codec = VLenUTF8()
a = np.array(list("abc"), dtype=object)
a.flags.writeable = False
codec.encode(a)
```
```pytb
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[39], line 9
6 a = np.array(list("abc"), dtype=object)
7 a.flags.writeable = False
----> 9 codec.encode(a)
File numcodecs/vlen.pyx:87, in numcodecs.vlen.VLenUTF8.encode()
File <stringsource>:663, in View.MemoryView.memoryview_cwrapper()
File <stringsource>:353, in View.MemoryView.memoryview.__cinit__()
ValueError: buffer source array is read-only
```
#### Problem description
Short description: this shouldn't error, as the codec shouldn't care whether it can write to the buffer it's passed.
Long description:
* Pandas 3.0 will set copy on write by default
* AnnData saves pandas dataframes to zarr stores
* Encoding string columns now errors since numcodecs throws an error
* This is made more urgent by dask-dataframe setting `copy-on-write=True` on import in the latest release
I can't think of a reason that `.encode` would need to modify the buffer, so it shouldn't care that it's read-only.
#### Version and installation information
Please provide the following:
* Value of ``numcodecs.__version__`` '0.12.1'
* Version of Python interpreter Python 3.11.7 | packaged by conda-forge | (main, Dec 23 2023, 14:43:09) [GCC 12.3.0]
* Operating system (Linux/Windows/Mac) Linux-5.15.0-100-generic-x86_64-with-glibc2.35
* How NumCodecs was installed pip into conda
Also, if you think it might be relevant, please provide the output from ``pip list`` or
``conda list`` depending on which was used to install NumCodecs.
<details>
<summary> conda list </summary>
```python
# packages in environment at /mnt/workspace/mambaforge/envs/scanpy-dev:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anndata 0.10.5.post1 pypi_0 pypi
annoy 1.17.3 pypi_0 pypi
array-api-compat 1.4.1 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
atk-1.0 2.38.0 hd4edc92_1 conda-forge
attrs 23.2.0 pypi_0 pypi
bokeh 3.3.4 pypi_0 pypi
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2023.11.17 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
click 8.1.7 pypi_0 pypi
cloudpickle 3.0.0 pypi_0 pypi
comm 0.2.1 pypi_0 pypi
contourpy 1.2.0 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
cython 3.0.8 pypi_0 pypi
dask 2024.3.0 pypi_0 pypi
dask-expr 1.0 pypi_0 pypi
dask-glm 0.3.2 pypi_0 pypi
dask-ml 2023.3.24 pypi_0 pypi
debugpy 1.8.0 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
deprecated 1.2.14 pypi_0 pypi
distributed 2024.1.1 pypi_0 pypi
execnet 2.0.2 pypi_0 pypi
executing 2.0.1 pypi_0 pypi
expat 2.5.0 hcb278e6_1 conda-forge
fasteners 0.19 pypi_0 pypi
fbpca 1.0 pypi_0 pypi
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.47.2 pypi_0 pypi
freetype 2.12.1 h267a509_2 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
fsspec 2023.12.2 pypi_0 pypi
future 0.18.3 pypi_0 pypi
gdk-pixbuf 2.42.10 h829c605_4 conda-forge
geosketch 1.2 pypi_0 pypi
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
gprof2dot 2022.7.29 pypi_0 pypi
graphite2 1.3.13 h58526e2_1001 conda-forge
graphtools 1.5.3 pypi_0 pypi
graphviz 9.0.0 h78e8752_1 conda-forge
gtk2 2.24.33 h7f000aa_3 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
h5py 3.10.0 pypi_0 pypi
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
harmonypy 0.0.9 pypi_0 pypi
icu 73.2 h59595ed_0 conda-forge
igraph 0.11.3 pypi_0 pypi
imageio 2.33.1 pypi_0 pypi
importlib-metadata 7.0.1 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
intervaltree 3.1.0 pypi_0 pypi
ipykernel 6.29.0 pypi_0 pypi
ipython 8.20.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.3 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
jupyter-client 8.6.0 pypi_0 pypi
jupyter-core 5.7.1 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
lazy-loader 0.3 pypi_0 pypi
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
legacy-api-wrap 1.4 pypi_0 pypi
leidenalg 0.10.2 pypi_0 pypi
lerc 4.0.0 h27087fc_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_4 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libgomp 13.2.0 h807b86a_4 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
librsvg 2.56.3 he3f83f7_1 conda-forge
libsqlite 3.44.2 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_4 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.3.2 h658648e_1 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.4 h232c23b_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.41.1 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
magic-impute 3.0.0 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.4 pypi_0 pypi
matplotlib 3.8.2 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
matplotx 0.3.10 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
memory-profiler 0.61.0 pypi_0 pypi
msgpack 1.0.7 pypi_0 pypi
multipledispatch 1.0.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.2.1 pypi_0 pypi
numba 0.58.1 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.26.3 pypi_0 pypi
openssl 3.2.0 hd590300_1 conda-forge
packaging 23.2 pypi_0 pypi
pandas 2.2.0 pypi_0 pypi
pango 1.50.14 ha41ecd1_2 conda-forge
parso 0.8.3 pypi_0 pypi
partd 1.4.1 pypi_0 pypi
patsy 0.5.6 pypi_0 pypi
pbr 6.0.0 pypi_0 pypi
pcre2 10.42 hcad00b1_0 conda-forge
perfplot 0.10.2 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pillow 10.2.0 pypi_0 pypi
pip 23.3.2 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
platformdirs 4.1.0 pypi_0 pypi
pluggy 1.4.0 pypi_0 pypi
profimp 0.1.0 pypi_0 pypi
prompt-toolkit 3.0.43 pypi_0 pypi
psutil 5.9.8 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pyarrow 15.0.1 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pygsp 0.5.1 pypi_0 pypi
pynndescent 0.5.11 pypi_0 pypi
pyparsing 3.1.1 pypi_0 pypi
pytest 7.4.4 pypi_0 pypi
pytest-mock 3.12.0 pypi_0 pypi
pytest-nunit 1.0.4 pypi_0 pypi
pytest-profiling 1.7.0 pypi_0 pypi
pytest-xdist 3.5.0 pypi_0 pypi
python 3.11.7 hab00c5b_1_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python-graphviz 0.20.1 pypi_0 pypi
pytz 2023.4 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 25.1.2 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
rich 13.7.1 pypi_0 pypi
scanorama 1.7.4 pypi_0 pypi
scanpy 1.10.0.dev197+g96e19540 pypi_0 pypi
scikit-image 0.22.0 pypi_0 pypi
scikit-learn 1.4.0 pypi_0 pypi
scikit-misc 0.3.1 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
scprep 1.1.0 pypi_0 pypi
scrublet 0.2.3 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
session-info 1.0.0 pypi_0 pypi
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
sparse 0.15.1 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.1 pypi_0 pypi
stdlib-list 0.10.0 pypi_0 pypi
tasklogger 1.2.0 pypi_0 pypi
tblib 3.0.0 pypi_0 pypi
texttable 1.7.0 pypi_0 pypi
threadpoolctl 3.2.0 pypi_0 pypi
tifffile 2023.12.9 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
toolz 0.12.1 pypi_0 pypi
tornado 6.4 pypi_0 pypi
tqdm 4.66.1 pypi_0 pypi
traitlets 5.14.1 pypi_0 pypi
tzdata 2023.4 pypi_0 pypi
umap-learn 0.5.5 pypi_0 pypi
urllib3 2.1.0 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 pypi_0 pypi
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xyzservices 2023.10.1 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forge
zarr 2.17.1 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.17.0 pypi_0 pypi
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
```
</details>
| Does `object[:] input_values` allow for `static` (meaning we promise not to change the values, as opposed to changing the value of the pointer) ? In true C-land, we cannot truly guarantee that code will not write to any buffer passed.
Do you mean like:
```
Error compiling Cython file:
------------------------------------------------------------
...
@cython.wraparound(False)
@cython.boundscheck(False)
def encode(self, buf):
cdef:
Py_ssize_t i, l, n_items, data_length, total_length
const object[:] values
^
------------------------------------------------------------
numcodecs/vlen.pyx:351:12: Const/volatile base type cannot be a Python object
```
Apparently not.
I would have thought that this is handleable since `pandas` is presumably passing these arrays into cython code.
Pandas has recently started wrapping the low-level arrays into immutable ones, which is maybe why you are seeing this now. I assume they internally access the low-level writable buffer somewhere. I think this is part of their move towards arrow, since arrow buffers are supposed to be immutable (which makes sense when there are offsets/indexes around, rather than just values).
> Pandas has recently started wrapping the low-level arrays into immutable ones
It looks like if you access the `.array` backing a `Series` you can get a mutable interface to the memory via the public API. Unclear if I should rely on that though.
If you're not doing any `._data` or similar, I don't see why not. It would fail for some extension array that doesn't offer that API, but some extension arrays wouldn't be appropriate input anyway.
Or we could require the caller to always provide a raw, writable numpy-like. | 2024-03-12T16:26:31 | 0.0 | [] | [] |
||
hasindu2008/slow5lib | hasindu2008__slow5lib-62 | aa2e88e2bd5f2404b5ebb49e5894cfecf4cdc4b3 | "diff --git a/.gitignore b/.gitignore\nindex c893fa00..0848971a 100644\n--- a/.gitignore\n+++ b/.git(...TRUNCATED) | initial implementation of getting a random batch
| 2022-04-21T03:19:35 | 0.0 | [] | [] |
|||
cdklabs/awscdk-appsync-utils | cdklabs__awscdk-appsync-utils-10 | 79152454be2e98a3374fecf6bfe2c995eca89c12 | "diff --git a/.projen/deps.json b/.projen/deps.json\nindex 9253ad2..d3c3d20 100644\n--- a/.projen/de(...TRUNCATED) | "Compatibility to aws-cdk v2.56+\nI really liked the CodeFirst approach which allows us to do certai(...TRUNCATED) | "So since you can't express semver ranges across multiple pre-release versions of a package as far a(...TRUNCATED) | 2023-01-12T18:14:15 | 0.0 | [] | [] |
||
machow/siuba | machow__siuba-459 | 99127df2a6bd4f0c71c624842916a2824e22ecf2 | "diff --git a/siuba/dply/verbs.py b/siuba/dply/verbs.py\nindex f138df8d..9ff7545a 100644\n--- a/siub(...TRUNCATED) | "Grouped summarize fails when a grouping col has NAs and < 2 other levels\nFor a grouped summarize, (...TRUNCATED) | 2022-11-16T17:25:38 | 0.0 | [] | [] |
|||
machow/siuba | machow__siuba-451 | ce979d90bd549176a8cb7e66547d0a02ed8c6bc4 | "diff --git a/siuba/dply/verbs.py b/siuba/dply/verbs.py\nindex 401698b0..36781fdc 100644\n--- a/siub(...TRUNCATED) | "Bug: gather does not select anything if `*args` is unspecified\nThe docs for [`gather`](https://git(...TRUNCATED) | "This would be the fix: `var_list = var_create(*args or __data.columns)`.\r\n\r\nAnd with some conte(...TRUNCATED) | 2022-09-27T23:49:03 | 0.0 | [] | [] |
||
machow/siuba | machow__siuba-440 | 73f9a2f53b57759b32c44d0f82448da5a05d1c1b | "diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml\nindex 5b353102..43322db1 100644\n(...TRUNCATED) | "Implement pivot_longer_spec\nSee PR #238 with current work. Merging it into master, so I (or anyone(...TRUNCATED) | 2022-09-10T05:02:18 | 0.0 | [] | [] |
|||
laixintao/flameshow | laixintao__flameshow-58 | 0834cfdd5079b582b38e7e408a79cbacddd82e5d | "diff --git a/flameshow/render/framedetail.py b/flameshow/render/framedetail.py\nindex 16dc306..2516(...TRUNCATED) | bug: when a frame has no more children, self should be considered as 100%
| 2023-10-19T03:50:06 | 0.0 | [] | [] |
|||
laixintao/flameshow | laixintao__flameshow-35 | db14a48daa556de8517a47d44eaf8fa29c03c244 | "diff --git a/flameshow/main.py b/flameshow/main.py\nindex ea31f07..66d9426 100644\n--- a/flameshow/(...TRUNCATED) | "support reading pprof direct from stdin\n```\r\ncurl http://localhost:6060/debug/pprof/goroutine | (...TRUNCATED) | 2023-10-04T14:32:59 | 0.0 | [] | [] |
|||
mcneel/compute.rhino3d | mcneel__compute.rhino3d-184 | ef49eb4c9889ba52de3b6d8abcd4bdb54f78c0f1 | "diff --git a/src/compute.components/RemoteDefinition.cs b/src/compute.components/RemoteDefinition.c(...TRUNCATED) | "Write sample that communicates with 3rd party app\nHops doesn't specifically need a compute instanc(...TRUNCATED) | "Linked with [COMPUTE-164](https://mcneel.myjetbrains.com/youtrack/issue/COMPUTE-164)\nPreferably a (...TRUNCATED) | 2021-01-31T23:46:55 | 0.0 | [] | [] |
||
CS-SI/eodag-cube | CS-SI__eodag-cube-38 | 5a31f7aad011377c063f192cf1494e4c793fe50f | "diff --git a/eodag_cube/api/product/drivers/stac_assets.py b/eodag_cube/api/product/drivers/stac_as(...TRUNCATED) | "standardize band identification mechanism\nUse the same band identification mechanism between drive(...TRUNCATED) | 2023-11-14T16:32:40 | 0.0 | [] | [] |
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