trouble with anaconda install

[Eric Leroy]

Hi,
I work on MacOS and I want to use hyperspy with Anaconda distribution.
I proceeded like this :

1. install Anaconda
2. create hyperspy environment with the following command : conda create -n hyperspy python=3.5 anaconda
3. switch to hyperspy environment : conda activate hyperspy
4. install hyperspy : conda install hyperspy -c conda-forge
5. launch a Jupyter notebook (jupyter noteook) then create a python 3 notebook
6. then launch the commands to start hyperspy as written in the documentation :
1. %matplotlib qt
2. import numpy as np
3. import matplotlib.pyplot as plt
4. import hyperspy.api as hs
7. for the last command, I have the following message from python :

1. /Users/ericleroy/anaconda3/envs/hspy35/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
     from ._conv import register_converters as _register_converters
   WARNING:hyperspy.api:The ipywidgets GUI elements are not available, probably because the hyperspy_gui_ipywidgets package is not installed.
   WARNING:hyperspy.api:The traitsui GUI elements are not available, probably because the hyperspy_gui_traitui package is not installed.

8. If I continue and for exampla want to load data with s=hs.load(), I have the following error message :

1. ---------------------------------------------------------------------------
   ImportError                               Traceback (most recent call last)
   <ipython-input-7-190d830d3818> in <module>()
   ----> 1 s=hs.load()
   
   ~/anaconda3/envs/hspy35/lib/python3.5/site-packages/hyperspy/io.py in load(filenames, signal_type, stack, stack_axis, new_axis_name, lazy, **kwds)
       166         from hyperspy.signal_tools import Load
       167         load_ui = Load()
   --> 168         get_gui(load_ui, toolkey="load")
       169         if load_ui.filename:
       170             filenames = load_ui.filename
   
   ~/anaconda3/envs/hspy35/lib/python3.5/site-packages/hyperspy/ui_registry.py in get_gui(self, toolkey, display, toolkit, **kwargs)
        87     if not TOOLKIT_REGISTRY:
        88         raise ImportError(
   ---> 89             "No toolkit registered. Install hyperspy_gui_ipywidgets or "
        90             "hyperspy_gui_traitsui GUI elements. If hyperspy_gui_traits"
        91             "is installed, initialize a toolkit supported by traitsui "
   
   ImportError: No toolkit registered. Install hyperspy_gui_ipywidgets or hyperspy_gui_traitsui GUI elements. If hyperspy_gui_traitsis installed, initialize a toolkit supported by traitsui before importing HyperSpy.

2. I tried to install hyperspy_gui_traitsui and hyperpy_gui_ipywidgets with pip and the error is not solved.

Do ou have any idea on how to solve the problem or can you tell me what I am doing worng?

Thank you

Best regards,

Eric

[Thomas Aarholt]

Can you try running it in the notebook again, but replacing the @matplotlib qt with @matplotlib notebook ? 

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[Eric Leroy]

if I do this, I have no warning when I import hyperspy but when I want to open data with s=hs.load(), I have this error message :

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
<ipython-input-9-190d830d3818> in <module>()
----> 1 s=hs.load()

~/anaconda3/envs/hs14/lib/python3.5/site-packages/hyperspy/io.py in load(filenames, signal_type, stack, stack_axis, new_axis_name, lazy, **kwds)

    166         from hyperspy.signal_tools import Load
    167         load_ui = Load()
--> 168         get_gui(load_ui, toolkey="load")
    169         if load_ui.filename:
    170             filenames = load_ui.filename

~/anaconda3/envs/hs14/lib/python3.5/site-packages/hyperspy/ui_registry.py in get_gui(self, toolkey, display, toolkit, **kwargs)
    144         raise NotImplementedError(
    145             "There is no user interface registered for this feature."
--> 146             "Try installing {}.".format(propose))
    147     if not display:
    148         widgets = {}

NotImplementedError: There is no user interface registered for this feature.Try installing hyperspy_gui_traitsui.

[Josh Taillon]

Eric, that sounds like it might be working, because we do not have a loader implemented using the "ipywidgets" GUI base. You have to provide a string to the file path like hs.load("my_file.dm3").

If you want to get the traitsui working, can you try uninstalling through pip (pip uninstall hyperspy_gui_traitsui) and installing through conda (conda install hyperspy-gui-traitsui -c conda-forge). Assuming that works, try running `import hyperspy_gui_traitsui` directly to see if it generates any errors that could help explain the situation.

Also, feel free to jump onto the gitter chat (https://gitter.im/hyperspy/hyperspy) for more interactive assistance.

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Joshua Taillon

www.joshuataillon.com

[Eric Leroy]

Hi,
When I type import hyperspy_gui_traitsui, I have this error :

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)

<ipython-input-8-be6e20052baf> in <module>()
----> 1 import hyperspy_gui_traitsui

ImportError: No module named 'hyperspy_gui_traitsui'

[Josh Taillon]

Interesting... Even after installing through conda?

Can you post the output of `conda list | grep hyper` and `pip show hyperspy-gui-traitsui`?

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