pyedfread
pyedfread copied to clipboard
nwilming
import error after installation
Great to see new life in this package!
Unfortunately, we are failing to import (after successful installation) on two different machines.
1. Macbook, EyeLink Dev Kit installed:
installing in base env (first creating dedicated conda env leads to the same issue)
(base) m0043843:~ uraiae$ pip install git+https://github.com/s-ccs/pyedfread
Collecting git+https://github.com/s-ccs/pyedfread
Cloning https://github.com/s-ccs/pyedfread to /private/var/folders/ly/drwv1q0j4t977rvf2rqyvvq8gsq3lc/T/pip-req-build-zh_glvm7
Running command git clone --filter=blob:none --quiet https://github.com/s-ccs/pyedfread /private/var/folders/ly/drwv1q0j4t977rvf2rqyvvq8gsq3lc/T/pip-req-build-zh_glvm7
Resolved https://github.com/s-ccs/pyedfread to commit 475cf0feded65c69cadaa4aa8ec5ed892b8844a3
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy (from pyedfread==0.3.0)
Using cached numpy-2.1.0-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Collecting pandas (from pyedfread==0.3.0)
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl.metadata (19 kB)
Collecting h5py (from pyedfread==0.3.0)
Using cached h5py-3.11.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (2.5 kB)
Collecting python-dateutil>=2.8.2 (from pandas->pyedfread==0.3.0)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->pyedfread==0.3.0)
Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas->pyedfread==0.3.0)
Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas->pyedfread==0.3.0)
Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Using cached h5py-3.11.0-cp312-cp312-macosx_11_0_arm64.whl (2.9 MB)
Using cached numpy-2.1.0-cp312-cp312-macosx_14_0_arm64.whl (5.1 MB)
Using cached pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl (11.3 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: pyedfread
Building wheel for pyedfread (pyproject.toml) ... done
Created wheel for pyedfread: filename=pyedfread-0.3.0-cp312-cp312-macosx_11_0_arm64.whl size=3441241 sha256=aa12c418e2eda7556b777088e1ff6418c0aa13f006f9a1495ad633d05e819078
Stored in directory: /private/var/folders/ly/drwv1q0j4t977rvf2rqyvvq8gsq3lc/T/pip-ephem-wheel-cache-mrnbu8d1/wheels/71/01/be/6437965794e8879933ae0e9f876a1163814a70d80320f928f9
Successfully built pyedfread
Installing collected packages: pytz, tzdata, six, numpy, python-dateutil, h5py, pandas, pyedfread
Successfully installed h5py-3.11.0 numpy-2.1.0 pandas-2.2.2 pyedfread-0.3.0 python-dateutil-2.9.0.post0 pytz-2024.1 six-1.16.0 tzdata-2024.1
then:
(base) m0043843:~ uraiae$ python
Python 3.12.3 | packaged by Anaconda, Inc. | (main, May 6 2024, 14:46:42) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyedfread
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/miniconda3/lib/python3.12/site-packages/pyedfread/__init__.py", line 3, in <module>
from pyedfread.parse import read_edf
File "/opt/miniconda3/lib/python3.12/site-packages/pyedfread/parse.py", line 1, in <module>
from pyedfread import edf_read
ImportError: dlopen(/opt/miniconda3/lib/python3.12/site-packages/pyedfread/edf_read.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/edfapi.framework/Versions/A/edfapi
Referenced from: <9807F4DB-F490-3A45-B3DA-549D3065025D> /opt/miniconda3/lib/python3.12/site-packages/pyedfread/edf_read.cpython-312-darwin.so
Reason: tried: '/opt/miniconda3/lib/edfapi.framework/Versions/A/edfapi' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/miniconda3/lib/edfapi.framework/Versions/A/edfapi' (no such file), '/opt/miniconda3/lib/edfapi.framework/Versions/A/edfapi' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/miniconda3/lib/edfapi.framework/Versions/A/edfapi' (no such file), '/opt/miniconda3/bin/../lib/edfapi.framework/Versions/A/edfapi' (no such file), '/opt/miniconda3/bin/../lib/edfapi.framework/Versions/A/edfapi' (no such file)
>>>
2. Windows (after following these instructions)
import pyedfread
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[2], line 5
2 from pathlib import Path
3 import numpy as np
----> 5 import pyedfread
File c:\Users\Philippa\miniconda3\envs\iblenv\lib\site-packages\pyedfread\__init__.py:3
1 """Read eye-tracking information from EyeLink EDF files."""
----> 3 from pyedfread.parse import read_edf
4 from pyedfread.edf_read import read_preamble, read_messages, read_calibration
File c:\Users\Philippa\miniconda3\envs\iblenv\lib\site-packages\pyedfread\parse.py:1
----> 1 from pyedfread import edf_read
2 import numpy as np
3 import pandas as pd
ImportError: DLL load failed while importing edf_read: The specified module could not be found.
Any idea as to what's going wrong in both cases (where the install doesn't throw any errors)?
I finally made some progress here - for some reason in newer python versions, some systempath is not added, and surprisingly, it cannot find python311.dll (on windows).
I'll try to look further later
PS: Linux still works ;-)
ok,I think that was a red hering - I now think it has to do with Python3.8 and a change in cython where some paths are not added automatically anymore. In python 3.7 iirc it worked. I'm close I think :D
ok at least the windows one is fixed now. For the mac one I draw a blank for now, because I simply have no mac environment available :|
I found that if I set the environment variable DYLD_FRAMEWORK_PATH on macOS, I am able to load the edfapi.
(hippocampus) roger@work29 PyHippocampus % export DYLD_FRAMEWORK_PATH=/Library/Frameworks
(hippocampus) roger@work29 PyHippocampus % ipython
Python 3.11.0 (main, Mar 1 2023, 12:33:14) [Clang 14.0.6 ]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.29.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import pyedfread
I haven't found a way to set this from within python, though.
