To participate in PS239T, you will need access to the software described below. In addition, you will need an up-to-date web browser. I recommend Google Chrome.
Once you've installed all of the software below, test your installation by following the instructions at the bottom on this page.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program. NOTE: on the ~6th step of installation, you will need to select the option "Use Windows' default console window" rather than the default of "Use MinTTY" in order for nano to work correctly.
After the installer does its thing, it leaves the window open, so that you can play with the "Git Bash".
Chances are that you want to have an easy way to restart that Git Bash. You can install shortcuts in the start menu, on the desktop or in the QuickStart bar by calling the script /share/msysGit/add-shortcut.tcl (call it without parameters to see a short help text).
If you receive an "xcrun" error message, take a look at https://stackoverflow.com/questions/32893412/command-line-tools-not-working-os-x-el-capitan-macos-sierra-macos-high-sierra/32894314#32894314.
The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this class.
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.
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).
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. 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 yum install git.
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 recommend an all-in-one installer.
Regardless of how you choose to install it, please make sure you install Python version 3.x and not version 2.x (e.g., 3.5 is fine, but not 2.7).
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).
- Download and install Anaconda.
- Select Windows operating system.
- Click the link for the most recent Python 3 version and the Graphical Installer. Run the installer.
- Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
- Download and install Anaconda.
- Select Mac operating system.
- Click the link for the most recent Python 3 version and the Graphical Installer. Run the installer.
- Download the default Python 3 installer (do not follow the link to version 2). Use all of the defaults for installation.
We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you during the class.)
- Download the installer that matches your operating system and save it in your home folder. Download the default Python 3 installer (do not follow the link to version 2).
- 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
yesand press enter to approve the license. Press enter to approve the default location for the files. Typeyesand press enter to prepend Anaconda to yourPATH(this makes the Anaconda distribution the default Python).
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. All you need is RStudio Desktop.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE. All you need is RStudio Desktop. Please note that if you already have R and update to a newer version, you will have to reinstall any previously installed packages.
You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE. All you need is RStudio Desktop.
When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. 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.
For this class, we use nano as a default in the terminal. But I also really like Sublime Text to write markdown and other basic text files. I recommend you download both.
nano is a basic editor and the default that we use in this class. To install it, download the Software Carpentry Windows installer[http://files.software-carpentry.org/SWCarpentryInstaller.exe] and double click on the file to run it. This installer requires an active internet connection.
Sublime Text is a more advanced editor. Download Sublime Text 3 here.
nano is a basic editor and the default that we use in this class. It should be pre-installed.
Sublime Text is a more advanced editor. Download Sublime Text 3 here.
nano is a basic editor and the default that we use in this class. It should be pre-installed.
Sublime Text is a more advanced editor. Download Sublime Text 3 here.
Pandoc is a universal document converter. It can be used to convert scripts (like in jupyter notebooks) into pdfs for assignments. For PDF output, you’ll also need to install LaTeX, a type-setting system. We recommend that you do the MacTex full install.
Install Pandoc and Latex using the instructions here.
Install Pandoc and Latex using the instructions here.
Install Pandoc and Latex using the instructions here.
If you have trouble with installation, please come to the Installfest.
Open a command line window ('terminal' or, on windows, 'git bash'), and enter the following commands (without the $ sign):
$ R --version
$ git --version
$ python --version
$ nano --version
$ pdflatex --version
$ pandoc --versionIf git and python and nano (a text editor) have been installed, those commands should print output version information. The python version should include "Anaconda" and its version information.
NB: If you're using git bash (Windows), the R --version command may not work. In this case, just make sure you can open up RStudio. One possible solution: The Software Carpentry installer may need to run as Administrator. (Right click the install app, select “Run as administrator”).
Double-check that you are able to open a jupyter notebook (a document that combines computer code and rich-text elements like photos in an application that uses your browser window):
$ jupyter notebookThis should open a programming interface in your default web browser. It may take a few minutes the first time. To close, just close your browser and then CTRL-C to end the process in the command line.
Software Carpentry maintains a list of common issues that occur during installation may be useful for our class here: Configuration Problems and Solutions wiki page.
Credit: Thanks to Software Carpentry for providing installation guidelines.