Feb. 23-24, 2019
8:30-17:00
Instructors: Phillip Benoit, Upendra Devisetty, Dawson Fairbanks, Blake Joyce, Chun Ly, Susan Miller, Kristina Riemer
Helpers: Jiali Han, Matt Miller, Noah Nelson, Cristian Palacios, Austen Stewart, Travis Struck, Derrick Yoo, Meghan Balk, Marnee Dearman
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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 at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
Where: Please check your email for the workshop location!. Get directions with OpenStreetMap or Google Maps.
When: Feb. 23-24, 2019. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Links to workshop materials are being provided below. If we can provide additional resources to help making learning easier for you (e.g. large-font hand-outs, sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email the workshop administrator at hilgert@bio5.org for more information.
Please be sure to complete these surveys before and after the workshop.
| 08:30 | Access and navigate the command line / Bash Shell |
| 10:30 | Break |
| 10:45 | Manage data with git/GitHub |
| 12:00 | Break |
| 13:00 | Automate tasks with shell scripts |
| 14:45 | Break |
| 15:00 | Automate tasks with shell scripts, cont. |
| 17:00 | End of Day |
| 08:30 | Analyze scientific data with Python and git/GitHub |
| 10:30 | Break |
| 11:00 | Analyze scientific data with Python and git/GitHub, cont. |
| 12:00 | Break |
| 13:00 | Analyze scientific data with Python and git/GitHub, cont. |
| 14:45 | Break |
| 15:00 | Analyze scientific data with Python and git/GitHub, cont. |
| 17:00 | End of Day |
Schedule subject to change if necessary.
We will use the collaborative document at https://pad.carpentries.org/2019-02-23-Tucson for chatting, taking notes, and sharing URLs and bits of code.
Find, create, copy, move and delete folders and filesadd, commit, ...status, diff, ...clone, pull, push, ...Syllabus subject to change if necessary.
To participate in a Software Carpentry workshop, you will need access to the software described below. Unless you prepare your laptop as described below you will be unable to follow along. In addition, you will need an up-to-date web browser, we recommend Firefox, Chrome or Safari as Internet Explorer/Edge can be buggy.
Should you encounter issues while installing the software below, please look for a solution in our Configuration Problems and Solutions wiki page. If even this does not help, please get in touch with us at the contact email listed above and we will attempt to provide a solution.
Bash is a commonly-used shell environment that gives you the power to quickly do simple tasks on your computer. Bash stands for 'Bourne Again Shell'; if you are interested in the history of the term and the underlying technological development, please search the Web for 'Bash Shell'.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then pressing [Enter]This will provide you with both Bash and Git in the Git Bash program.
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities).
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.
Writing code is much easier with respectively optimized text editors that include features such as automatic color-coding of key words and syntax-highlighting. We will use the basic editor 'nano' in the workshop; it comes pre-installed with the git-bash download above for Windows, Mac and Linux.
Click the Start button and type 'git bash' into the search window.
Click on the "Git Bash" icon to open the shell.
Type 'nano test.txt' to open a text editor. IF this does not open the nano text editor contact the workshop administrator at the email listed above.
Type 'Test'.
To exit the nano editor press Ctrl and type 'x' (a.k.a. '^X'; additional commands are listed at the bottom of the text edito window.
During the workshop we will be using the basic editor nano. nano should be pre-installed; see the Git installation video tutorial for an example on how to open nano.
During the workshop we will be using the basic editor nano. nano should be pre-installed
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
For the workshop you will need a GitHub account, if you don't have one already please get it at github.com. Basic GitHub accounts are free. However, please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private at GitHub.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo dnf install git.
Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).
We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work 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).
bash Anaconda3-and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:
cd DownloadsThen, try again.
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).
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.