NumPy 2.0.0 support #259
Description
A major new NumPy version 2.0.0 was released on 16th June 2024. (Release notes and migration guide)
It seems that as of 2024-07-02 the latest available pyEDFlib version 0.1.37 is not compatible with NumPy 2.0.0.
Could support for the latest NumPy be added? Thanks in advance. Also, I'd be happy to help if further information is required or if running some additional debugging would be considered useful.
Steps to reproduce
Environment:
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 24.04 LTS
Release: 24.04
Codename: noble
$ uname -a
Linux <redacted> 6.8.0-36-generic #36-Ubuntu SMP PREEMPT_DYNAMIC Mon Jun 10 10:49:14 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
The created virtual environment edfvenv was removed with rm -rf edfvenv between each of the following attempts.
Using pyEDFlib package from PyPI
Installation (doesn't crash)
$ python3.12 -m venv edfvenv
$ source edfvenv/bin/activate
$ pip install numpy==2.0.0
$ pip install pyedflib
Importing (crashes)
$ python
Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.version.full_version
'2.0.0'
>>> import pyedflib
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<stdin>", line 1, in <module>
File "/<redacted>/edfvenv/lib/python3.12/site-packages/pyedflib/__init__.py", line 9, in <module>
from ._extensions._pyedflib import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/<redacted>/edfvenv/lib/python3.12/site-packages/pyedflib/__init__.py", line 9, in <module>
from ._extensions._pyedflib import *
File "pyedflib/_extensions/_pyedflib.pyx", line 1, in init pyedflib._extensions._pyedflib
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
Using pyEDFlib cloned from this GitHub repository
Installation (doesn't crash)
$ git clone https://github.com/holgern/pyedflib.git
$ python3.12 -m venv edfvenv
$ source edfvenv/bin/activate
$ pip install numpy==2.0.0
$ pip install pyedflib/
Processing ./pyedflib
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.9.1 in ./edfvenv/lib/python3.12/site-packages (from pyEDFlib==0.1.37) (2.0.0)
Building wheels for collected packages: pyEDFlib
Building wheel for pyEDFlib (pyproject.toml) ... done
Created wheel for pyEDFlib: filename=pyEDFlib-0.1.37-cp312-cp312-linux_x86_64.whl size=2658315 sha256=d97838bdaf14142ab58d6cf56a96f97199fdb8c729004373763a2ee7120ae415
Stored in directory: /tmp/pip-ephem-wheel-cache-zyj5e7mw/wheels/ec/68/85/248f36407621f2ecfd82dc765dabfc6419a617faffed1ee3ad
Successfully built pyEDFlib
Installing collected packages: pyEDFlib
Successfully installed pyEDFlib-0.1.37
Importing (crashes in the same way as above)
$ python
Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.version.full_version
'2.0.0'
>>> import pyedflib
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<stdin>", line 1, in <module>
File "/<redacted>/edfvenv/lib/python3.12/site-packages/pyedflib/__init__.py", line 9, in <module>
from ._extensions._pyedflib import *
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/<redacted>/edfvenv/lib/python3.12/site-packages/pyedflib/__init__.py", line 9, in <module>
from ._extensions._pyedflib import *
File "pyedflib/_extensions/_pyedflib.pyx", line 1, in init pyedflib._extensions._pyedflib
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
Using pyEDFlib cloned from the repository and applying a small change
Installation (doesn't crash)
$ git clone https://github.com/holgern/pyedflib.git
Add the following change (literally what was suggested in the ImportError above):
diff --git a/pyedflib/_extensions/_pyedflib.pyx b/pyedflib/_extensions/_pyedflib.pyx
index 6087453..7297e01 100644
--- a/pyedflib/_extensions/_pyedflib.pyx
+++ b/pyedflib/_extensions/_pyedflib.pyx
@@ -25,6 +25,7 @@ from . cimport c_edf
cimport cpython
import numpy as np
cimport numpy as np
+np.import_array()
from datetime import datetime, date
from cpython.version cimport PY_MAJOR_VERSION
include "edf.pxi"
$ python3.12 -m venv edfvenv
$ source edfvenv/bin/activate
$ pip install numpy==2.0.0
$ pip install pyedflib/
Processing ./pyedflib
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.9.1 in ./edfvenv/lib/python3.12/site-packages (from pyEDFlib==0.1.37) (2.0.0)
Building wheels for collected packages: pyEDFlib
Building wheel for pyEDFlib (pyproject.toml) ... done
Created wheel for pyEDFlib: filename=pyEDFlib-0.1.37-cp312-cp312-linux_x86_64.whl size=2658315 sha256=d97838bdaf14142ab58d6cf56a96f97199fdb8c729004373763a2ee7120ae415
Stored in directory: /tmp/pip-ephem-wheel-cache-zyj5e7mw/wheels/ec/68/85/248f36407621f2ecfd82dc765dabfc6419a617faffed1ee3ad
Successfully built pyEDFlib
Installing collected packages: pyEDFlib
Successfully installed pyEDFlib-0.1.37
Importing (crashes in a different way)
$ python
Python 3.12.3 (main, Apr 10 2024, 05:33:47) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> np.version.full_version
'2.0.0'
>>> import pyedflib
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/<redacted>/edfvenv/lib/python3.12/site-packages/pyedflib/__init__.py", line 9, in <module>
from ._extensions._pyedflib import *
File "pyedflib/_extensions/_pyedflib.pyx", line 1, in init pyedflib._extensions._pyedflib
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject