SHDShim

Fix ASE problem for reading CIF

Insert the following lines to avoid error in reading CIF from ASE when you make a cif file from CrystalMaker.

_symmetry_space_group_name_H-M    "P 1"
_symmetry_int_tables_number       1

Space group number can be found in: https://en.wikipedia.org/wiki/List_of_space_groups

SHDShim

To make a shortcut to favorite folders in Mac OS

Place the following lines in .bash_profile.

X, Y, Z = change to your folder names.

# define favorite paths
if [ -f /etc/bash_completion ]; then
 . /etc/bash_completion

SHDShim

How to Make matplotlib output PDF editable in illustrator

This may not need anymore after matplotlib 3.5.

source: http://jonathansoma.com/lede/data-studio/matplotlib/exporting-from-matplotlib-to-open-in-adobe-illustrator/

import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42

SHDShim

Force reinstall pip package

pip install -I <package>

or

pip install --ignore-installed <package>

SHDShim

Installing/Packaging with requirements.txt

create an environment from requirements.txt

conda create --name <env_name> --file requirements.txt

make a requirements.txt

SHDShim

How to install Nikola in conda

conda create -n nikola python=3.6 lxml docutils Pillow MarkupSafe mako Pygments six python-dateutil cloudpickle requests unidecode natsort decorator traitlets tornado ptyprocess pexpect pickleshare appnope simplegeneric wcwidth ipython pyzmq jupyter ipykernel Jinja2 Markdown PyYAML mistune html5lib bleach jsonschema nbformat entrypoints nbconvert terminado notebook watchdog macfsevents

then activate the new environment

conda activate nikola

SHDShim

Building jupyter blog using Nikola

Nikola website: https://getnikola.com

Jupyter blog using Nikola: https://post2web.github.io/posts/jupyter-blogging/

Make a personal website: https://www.matthewallcock.co.uk/posts/creating-a-website-using-nikola/

SHDShim

If pip fails because of c compile problem in MacOS

Remove gcc in conda and run pip. gcc should be removed from the base environment.

Also, run the following in the terminal for updating xcode.

sudo open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

SHDShim

Magic commands for autoreloading packages

%load_ext autoreload
%autoreload 2

SHDShim

How to add/remove a kernel in Jupyter from a conda environment

How to add a kernel

conda activate myenv
python -m ipykernel install --user --name myenv --display-name "Python (myenv)"

If ipykernel was not found: