Installation Guide- MAC- Miniconda (2018)

Install miniconda: https://conda.io/miniconda.html

Installation guide is available here: https://conda.io/docs/user-guide/install/macos.html

You would have to download (for 64 bit machine) Miniconda3-latest-MacOSX-x86_64.sh file and then from your terminal browse to the folder containing this file and then run:

bash Miniconda3-latest-MacOSX-x86_64.sh

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 https://github.com/enthought/pyface/archive/master.zip
pip install https://github.com/enthought/traitsui/archive/master.zip

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

Install hyperspy:

pip install https://github.com/hyperspy/hyperspy/archive/epsic_workshop.zip#egg=hyperspy[all]

Install hyperspyUI:

pip install https://github.com/ericpre/hyperspyUI/archive/qt5.zip

Install atomap (Quantitative STEM branch):

pip install https://gitlab.com/atomap/atomap/repository/Absolute_Integrator/archive.zip

Install PyXem (master branch):

pip install spglib pymatgen transforms3d
pip install https://github.com/pyxem/pyxem/archive/master.zip

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.

Note

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

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