Introductory Python

We’ll be looking at the following IPython Notebooks, all of which are under the python/ directory of the git repository:

Scientific Python basics: python-full.ipynb

Plotting with matplotlib: matplotlib-full.ipynb

Reading and writing files: readwrite-full.ipynb

—

Loading and plotting files: loading-and-plotting-data.ipynb

make_figure.py script

End of day data Analysis mix: end-of-day-data-analysis.ipynb

Running IPython Notebook

Honestly, the hardest part is just getting things running :(. Pick whichever one of the solutions below works...

Running the notebook on Mac OS X using Anaconda CE

Once you get the Anaconda CE file (see Installation and setup instructions for download links!), go run it at the command line – double clicking it doesn’t seem to work :(.

This should be as simple as opening up a Terminal window and typing:

bash ~/Downloads/AnacondaCE-1.2.0-macosx.sh

and answering all the questions with the defaults (‘yes’ where appropriate).

Then, once it’s all done installing, cd to the git directory that you downloaded earlier, cd into the python/ subdirectory, and type

~/anaconda/bin/ipython notebook --pylab=inline

Your Web browser should pop up. Tada!

Running the notebooks in the Virtual Box virtual machine

Start up your virtual machine (see Installation and setup instructions for instructions on installing VirtualBox), and then click ‘Terminal’. Inside of terminal, run the following commands:

git clone https://github.com/swcarpentry/2012-11-scripps
ls
cd 2012-11-scripps/
ls
cd python
ls
./run-in-vm.sh

(You can copy on your Web browser, and then paste into the Terminal in your VM with ‘ctrl-shift-V’.)

This will start up a Firefox browser pointing at IPython Notebook

Extra – upgrading ipython notebook

You can upgrade ipython notebook to a newer version like so. Type:

sudo apt-get install python-pip
sudo pip install --upgrade ipython

This will take a few minutes to do, because it has to download some files...

IPython Notebook, a brief intro

The IPython Notebook (ipynb for short) is a simple notebook interface to Python that lets you interactively run Python code and view figures and graphics. You can load, save, and download notebooks as a record of your research as well as for interaction with colleagues.

The main thing you need to know about IPython is that to execute code in a cell, you hit Shift-ENTER.

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