Failure in installing pynwb #40
Replies: 8 comments 4 replies
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@HarelShouval what version of Python are you using? It looks like you may be using 3.11, which is not yet supported, since the h5py dependency isn't supported yet |
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I am getting the same error when specifically using pip3.10 |
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We need a little more information to help diagnose the issue. What do you get when you run the following: |
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I would recommend using conda create -n nwb python=3.9
conda activate nwb |
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I am still having problems. With Python 3.9 I was able to install the nwb package.
However, when running code I still get an error message.
This is not my code, I am just using it to read other people’s data. Therefore, I know it is indeed working.
This is the error message I get:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<string>", line 39, in <module>
File "/Users/hshouval/Documents/Papers/Ian VTA/Huijeong dataset/photometry_python/functions/load.py", line 284, in load_nwb
io = NWBHDF5IO(url, mode='r', driver='ros3')
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/utils.py", line 645, in func_call
return func(args[0], **pargs)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/pynwb/__init__.py", line 234, in __init__
super().__init__(path, manager=manager, mode=mode, file=file_obj, comm=comm, driver=driver)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/utils.py", line 645, in func_call
return func(args[0], **pargs)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 85, in __init__
super().__init__(manager, source=path)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/utils.py", line 645, in func_call
return func(args[0], **pargs)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/backends/io.py", line 23, in __init__
self.open()
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/hdmf/backends/hdf5/h5tools.py", line 729, in open
self.__file = File(self.source, open_flag, **kwargs)
File "/Users/hshouval/opt/miniconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 485, in __init__
raise ValueError(
ValueError: h5py was built without ROS3 support, can't use ros3 driver
My highlight.
Thanks
Harel
From: Ben Dichter ***@***.***>
Date: Tuesday, November 29, 2022 at 11:25 AM
To: NeurodataWithoutBorders/helpdesk ***@***.***>
Cc: Shouval, Harel ***@***.***>, Mention ***@***.***>
Subject: Re: [NeurodataWithoutBorders/helpdesk] Failure in installing pynwb (Discussion #40)
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@HarelShouval<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FHarelShouval&data=05%7C01%7Charel.shouval%40uth.tmc.edu%7C3d81d3534fc14d25314808dad22ec538%7C7b326d2441ad4f57bc6089e4a6ac721b%7C0%7C0%7C638053395572031181%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=py8prwzSgcH1kAfkf98nOIdztXNDLp3jpG7s15NwxNM%3D&reserved=0> what version of Python are you using? It looks like you may be using 3.11, which is not yet supported, since the h5py dependency isn't supported yet
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@HarelShouval it looks like you are using the ros3 driver for h5py. This is a possible way to read NWB data, but it is a pain to install h5py with ros3 enabled. A much easier (and faster!) approach is to use fsspec. See the documentation here. Try this: import fsspec
import pynwb
import h5py
# next, open the file
f = fs.open(s3_url, "rb")
file = h5py.File(f)
io = pynwb.NWBHDF5IO(file=file, load_namespaces=True)
nwbfile = io.read()
# do stuff
io.close()
file.close()
f.close() |
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See the documentation here |
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I am trying to install pynwb in order to read .nwb files.
I used pip install -U pynwb
The install fails, and i get the following message:
"...
Building h5py requires pkg-config unless the HDF5 path is explicitly specified using the environment variable HDF5_DIR. For more information and details, see https://docs.h5py.org/en/stable/build.html#custom-installation
error: pkg-config probably not installed: FileNotFoundError(2, 'No such file or directory')
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for h5py
Failed to build h5py
ERROR: Could not build wheels for h5py, which is required to install pyproject.toml-based projects
"
It seems i am missing some file, but i have no idea how to fix this.
Thanks
Harel
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