Software Carpentry: USGS Flagstaff Science Campus

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed scientists and engineers affiliated with the USGS. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 2255 N. Gemini Dr., Flagstaff, Arizona. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail dbuscombe@usgs.gov for more information.

Schedule

Day 1

09:00	Automating tasks with the Unix shell
10:30	Coffee
12:00	Lunch break
13:00	Building programs with Python
14:30	Coffee
16:30	Wrap-up

Day 2

09:00	Version control with Git
10:30	Coffee
12:00	Lunch break
13:00	Managing data with SQL
14:30	Coffee
16:30	Wrap-up

Etherpad: http://pad.software-carpentry.org/2016-02-04-flagstaff.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code. Keep the etherpad open in your browser during the workshop so you can quickly access it.

Syllabus

The Unix Shell

Files and directories
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things
Reference...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals
Defensive programming
Using Python from the command line
Reference...

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
Reference...

Managing Data with SQL

Reading and sorting data
Filtering with where
Calculating new values on the fly
Handling missing values
Combining values using aggregation
Combining information from multiple tables using join
Creating, modifying, and deleting data
Programming with databases
Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

Please install the software below even if you already have a working version of Python in your computer. A common set of software assures that everyone is working in the same environment as the instructors and minimizes time lost to troubleshooting.

Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.

Contact the instructors if you run into trouble during installation. We also maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

These instructions will install both Git and Bash (as the application Git Bash).

Download the Git for Windows installer.
Run the installer and follow the steps bellow:
1. Click on "Next".
2. Click on "Next".
3. Click on "Next".
4. Click on "Next".
5. Click on "Next".
6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you do not select this option, the programs that you need for the workshop will not work properly. If this happens, rerun the installer and select the appropriate option.
7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
8. Select "Use Windows' default console window" and click on "Next".
9. Click on "Next".
10. Click on "Finish".

Mac OS X

All versions of Mac OS X use bash as the default shell, so no installation is necessary. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

The default shell in Linux is usually bash. If your machine is set up differently, you can run bash by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that allows you to track changes made to documents, the author of those changes, and when they were made. It is most often used for coding projects, but almost any type of file can be tracked using git. It is also a powerful collaboration tool and can be used to easily share documents with the public through github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above, are supported browsers).

Windows

Git should have installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Git is a command line program, so this installation won't create any new files in the /Applications folder.
For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Linux

If Git is not already available on your machine, you should install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Text Editors

The text editors most of us regularly use are not optimized for writing code. An editor with features like automatic color-coding of key words and language-specific commenting make code much easier to read and edit, greatly increasing your productivity as a programmer and reducing frustration. We suggest you install one of several code-friendly text editors, but any simple text editor (that can save as plain text) will work.

There are also many situations where you might need to use a text editor within the command line. These programs don't have a GUI (Graphical User Interface) -- you interact with them exclusively by typing into the terminal. The text editor nano is easy to use and the one that instructors will use in the workshop.

The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

To install nano, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

If you want to install a text editor optimized for code, you can use Notepad++ or Sublime Text.

Mac OS X

The text editor nano should be pre-installed in Mac OS X.

If you want to install a text editor optimized for code, you can use Text Wrangler or Sublime Text.

Linux

The text editor nano should be pre-installed in Mac OS X.

If you want to install a text editor optimized for code, you can use Gedit, Kate or Sublime Text.

Python

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we use Anaconda, an all-in-one installer. Make sure you install Python version 2.7.

Please install Anaconda even if you already have a working version of Python on your computer. Using a common environment helps workshops run smoothly and facilitate learning. It is easy to uninstall Anaconda after the workshop if you choose to not use it.

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. You will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Open http://continuum.io/downloads with your web browser.
Download the Python 2.7 installer for Windows.
Install Python 2.7 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Download the Python 2.7 installer for OS X.
Install Python 2.7 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Download the Python 2.7 installer for Linux.
Install Python 2.7 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help from the instructors, preferably before the workshop!).
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

The Software Carpentry Windows Installer installs SQLite for Windows. You don't need to run the installer again if you used it to install nano.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.