This setup tutorial will walk you through installing the software you will need for this workshop. We will cover the following topics. Click on a particular topic to skip to that section.
condaPython 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, however, so we recommend the all-in-one installer Anaconda.
Throughout the rest of this set-up, we will assume that you are using Anaconda and the conda package manager.
Please set up your python environment at least a day in advance of the workshop. If you encounter problems with the installation procedure, ask your workshop organizers via e-mail for assistance so you are ready to go as soon as the workshop begins.
Open https://www.anaconda.com/download with your web browser.
Download the Python 3 installer for Windows.
Double-click the executable and install Python 3 using MOST of the default settings. The only exception is to check the Make Anaconda the default Python option.
Alternatively, if you are running Windows 10, you can install the Windows Subsystem for Linux and follow the Linux tutorial.
Open https://www.anaconda.com/download with your web browser.
Download the Python 3 installer for OS X.
Install Python 3 using all of the defaults for installation.
Note that the following installation steps require you to work from the shell. If you run into any difficulties, please request help before the workshop begins.
Open https://www.anaconda.com/download with your web browser.
Download the Python 3 installer for Linux.
Install Python 3 using all of the defaults for installation.
a. Open a terminal window.
b. Navigate to the folder where you downloaded the installer
c. Type
$ bash Anaconda3-
and press tab. The name of the file you just downloaded should appear.
d. Press enter.
e. Follow the text-only prompts. When the license agreement appears (a colon
will be present at the bottom of the screen) hold the down arrow until the
bottom of the text. Type yes and press enter to approve the license. Press
enter again 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).
Use of Anaconda with its package manager, conda, greatly simplifies package installation and environment management.
conda is a general package manager, meaning that it can install dependencies and packages in languages besides Python, unlike pip (which is Python’s package manager). Both pip and conda can be used to install packages.
A conda environment contains a specific collection of packages you have installed. This means that packages are isolated, and installed only for a specific environment – you can have several environments each with different installed packages, or different versions of installed packages in different environments.
It’s considered a best practice to create a new Python environment for each project you work on.
To create an environment for this project using conda,
$ conda create --name molssi_devops python=3.6
For other projects, you should replace molssi_devops with a descriptive name for your project. conda also allows you to specify the python version to use with the environment. Here, python=3.6 specifies that we want to use Python 3.6 in this environment. Executing this command will list the environment location and a list of Python packages to be installed. Choose y(es) when prompted.
Activate the environment using the command
$ conda activate molssi_devops`
Once you’ve activated an environment, the name of the environment will be in parenthesis at the front of your command line prompt.
If you wanted to create an environment for testing your code in Python 2.7, for example, you could use the command
$ conda create --name molssi_devops27 python=2.7
When this environment is activated, Python 2.7 will be used instead of Python 3.6.
To see a list of all your environments
$ conda info --envs
To deactivate an environment, type
$ conda deactivate
Using conda, we can install packages to our environments. Note: Make sure you have activated the environment where you want to install packages.
To list all the Python packages installed in an environment, first activate it, then type
$ conda list
Packages can be installed using the conda install package_name command. For example, to install NumPy,
$ conda install numpy
Further, the desired version of NumPy can be specified:
$ conda install numpy=1.15
For this workshop, we will create the structure of our Python package using the CMS CookieCutter. Please have this package installed in your molssi_devops environment.
First, switch to your environment for this workshop if you are not in it.
$ conda activate molssi_devops
Install the general cookiecutter with the following commands.
$ conda config --add channels conda-forge
$ conda install cookiecutter
Create an account on github.com. Remember your username and password for configuring git in the next section.
Download and install git for your operating system.
The first time you use Git on a particular computer, you need to configure some things.
First, you should set your identity. One of the most important things that version control like Git does is to keep track of who changes what. This helps repository maintainers coordinate the efforts of all the people who contribute to the project. Most importantly, it makes it easier to figure out who to blame when something goes wrong. You can provide git your name and contact information with the following commands:
$ git config --global user.name "<Firstname> <Lastname>"
$ git config --global user.email "<email address>"
Next, you might want to change the Git text editor. As we will see later, certain Git commands will open text files. When this happens, Git will use your environment’s default text editor, which might not be the editor you are most comfortable using. Using configuration commands, you can tell Git to use your favorite editor. To use Emacs as your text editor, you can do:
$ git config --global core.editor "emacs"
Alternatively, to use Vim as your text editor, do:
$ git config --global core.editor "vim"
A more complete list of possible editors is available here.
You can check the configuration commands that you have set using:
$ git config --list
Finally, we want to upload an ssh key to GitHub so that it doesn’t ask for our password every time we try to do something.
Check for existing keys using:
$ ls -al ~/.ssh
If you see something like id_rsa.pub, then you don’t need to generate a new key.
Otherwise, do:
$ ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
Generating public/private rsa key pair.
Enter a file in which to save the key (/Users/you/.ssh/id_rsa): (Press enter)
Enter same passphrase again: (Type passphrase again)
On a Mac, do:
$ eval "$(ssh-agent -s)"
Agent pid 59566
If using macOS Sierra 10.12.2 or later, also add this to the end of ~/.ssh/config
Host *
AddKeysToAgent yes
UseKeychain yes
IdentityFile ~/.ssh/id_rsa
$ ssh-add -K ~/.ssh/id_rsa
On a Windows machine, do:
$ eval $(ssh-agent -s)
Agent pid 59566
$ ssh-add ~/.ssh/id_rsa
On Linux, do:
$ eval "$(ssh-agent -s)"
Agent pid 59566
$ ssh-add ~/.ssh/id_rsa
Now copy the SSH key to your clipboard:
On Mac:
$ pbcopy < ~/.ssh/id_rsa.pub
On Windows:
$ clip < ~/.ssh/id_rsa.pub
On Linux:
$ sudo apt-get install xclip
$ xclip -sel clip < ~/.ssh/id_rsa.pub
Now we will upload the ssh key to GitHub.
Go to GitHub using a web browser, click on your user image on the top right, and then select “settings” from the drop-down menu.
Click “SSH and GPG keys” on the left.
Click “New SSH key on the top right.
Add a title that will remind you which machine this is for, then paste the key into the “Key” field.
Click “Add SSH key”
Alternatively, if you don’t want to setup ssh keys, you can decrease the number of times git asks you for your password by using:
$ git config --global credential.helper cache
At the end of this set-up, you should have created a Python environment (molssi_devops) which has Python 3.6, numpy, and cookiecutter installed. You should also have installed and created an account on GitHub and configured git.