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document emacs ipython #3

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# networkscompbio
Code for the class CS 446/546 - Networks in computational biology

## Emacs Usage

Install [The Emacs IPython Notebook](http://millejoh.github.io/emacs-ipython-notebook/) (EIN) from MELPA

M-x list-packages

find `ein` and install.

Then [install Jupyter Notebook](http://jupyter.readthedocs.io/en/latest/install.html)

# pip3 install --upgrade pip
# pip3 install jupyter

And customize `.emacs`

;; Emacs IPython Notebook
;; https://github.com/millejoh/emacs-ipython-notebook
(setq ein:jupyter-default-server-command "/usr/local/bin/jupyter")
(add-hook 'ein:notebook-mode-hook
(lambda ()
(set-face-background 'ein:cell-input-area "unspecified-bg")))

To use EIN, execute `M-x ein:jupyter-server-start` and choose the appropriate directory. Use the notebook list to edit notebooks.

Useful key combinations:

Key Function Description
------------------------------------------------------------------
C-c ' ein:edit-cell-contents Edit cell
C-c C-c ein:worksheet-execute-cell Execute cell
ein:worksheet-execute-all-cell Execute all cells
C-c C-n ein:worksheet-goto-next-input Go to next
C-c C-p ein:worksheet-goto-prev-input Go to previous

Install missing Python 3 Packages with `pip3`, for example:

# pip3 install pandas
# pip3 install matplotlib
# pip3 install python-igraph
# pip3 install bintrees
# pip3 install pympler
# pip3 install pygraphviz

Run a Python 3 shell with `M-x python-shell-switch-to-shell RET /usr/bin/python3 -i RET y` or set the default interpreter `M-x set-variable RET python-shell-interpreter RET "python3" RET` to use `M-x run-python`. Run an IPython 3 shell with `M-x python-shell-switch-to-shell RET ipython3 --simple-prompt RET y`.

To revert undesirable changes, close open notebooks and then `git checkout -p -- classXX_name_python3.ipynb`.

To view local notebooks in the browser, navigate to [http://localhost:8888](http://localhost:8888). This may be necessary to debug or disable code that is not functional within Emacs such as images.