Installation Guide- MAC- Miniconda (2018)

Installation guide is available here:

You would have to download (for 64 bit machine) file and then from your terminal browse to the folder containing this file and then run:

  • Install dependencies using conda by running the following lines - one after the other- in Terminal:
conda install pip numpy scipy matplotlib=2.1.2 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython ipyparallel dask numba qtconsole notebook
pip install blosc
pip install
pip install

pip install blosc requires installing “Command Lines Developers Tools”. If that is needed, please install these tools before proceeding.

  • Install hyperspy:
pip install[all]
  • Install hyperspyUI:
pip install
  • Install atomap (Quantitative STEM branch):
pip install
  • Install PyXem (master branch):
pip install spglib pymatgen transforms3d
pip install

To check that all is well with your install, open a Jupyter Notebook by running:

Jupyter notebook

 from the terminal. 

This will open the Jupyter home screen in a web browser.

To create a new blank notebook in the current folder select new > python3

Test the install by executing the following code in Jupyter Notebook (copy the code in the box and press the Run button at the top, or press Shift + Enter):

%matplotlib qt
import hyperspy.api as hs
import atomap.api as am
import pyxem as px

You should not get any error messages.


There will be a warning as below that can be ignored:

site-packages/h5py/ 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