blimpy.waterfall WARNING Could not import bitshuffle, using hdf5plugin failover. Write access disabled.
cmorsoc opened this issue · comments
Hi, I'm running the blimpy tutorial and we get this warning:
blimpy.waterfall WARNING Could not import bitshuffle, using hdf5plugin failover. Write access disabled.
When running these lines:
import pylab as plt
from blimpy import Waterfall
And:
/home/cmorsoc/.local/lib/python3.7/site-packages/blimpy/io/file_wrapper.py:323: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
self.h5 = h5py.File(self.filename)
When running:
file_path = 'Voyager1.single_coarse.fine_res.h5'
obs = Waterfall(file_path)
Setup
- Python version: 3.X
- Blimpy version? Latest (pip3 install blimpy)
Thanks @cmorsoc -- in the short term, these are safe to ignore in terms of functionality, but longer term we should change the code so the warnings don't get raised.
The first is a warning that the bitshuffle package isn't installed. A lot of people have had issues installing it, so we started using a package hdf5plugin. Early versions of hdf5plugin couldn't write out bitshuffle-compressed datasets, but this might have been added, so time to revisit.
The second is a warning from h5py, that in future versions they will open files as read-only by default. This might break stuff for other people who rely on its old behaviour, hence the message. This is also easy enough to fix, just adding mode='r' to a few calls.
Ok. Thanks!
I believe this is now fixed, hdf5plugin does read/write and bitshuffle package requirement has been dropped.