Participation in the MolSSI Best Practices Workshop will require use of your own personal computer or laptop and installation of some software.
Windows users take note
If you are working on a Windows computer, participation in this workshop will require you to install the Windows Subsystem for Linux (WSL). You should install WSL 2, you will need to have the Windows 10 or Windows 11 OS with the following version requirements:
For x64 systems: Version 1903 or higher, with Build 18362 or higher.
For ARM64 systems: Version 2004 or higher, with Build 19041 or higher.
If you haven’t updated your computer in a while, these updates could take a considerable amount of time. Plan accordingly!
If you are on Windows 11, you can also set up WSL to be able to use graphical interfaces.
Please follow the instructions given here to make sure you have the necessary software installed. We will be using Python and the conda package manager. If you are on MacOS, Linux, or WSL and you already have Anaconda (or miniconda) installed, skip to the environment creation portion of these set-up instructions. If you do not have Anaconda or miniconda installed please see the appropriate section below. Note If you are on Windows miniconda has to be installed on WSL (not Windows). This might be a separate installation.
Anaconda vs. Minconda
Anaconda is a distribution of Python, the conda package manager, and several third-party libraries which are commonly used in data science. Miniconda contains only Python and the conda package manager. You will be able to install any package you would like later using miniconda. Miniconda will take up a lot less space on your computer. We will be learning to manage conda environments and install the packages we need, so we consider miniconda to be the better option between the two. If you already have Anaconda installed, however, there is no need to install miniconda.
Installing WSL (Windows users only)#
If your computer uses the Windows operating system, we require installing Windows Subsystem for Linux (WSL). Follow the installation instructions at this link. If you don’t have a preference on Linux distribution, we recommend installing Ubuntu 20.04.
Once WSL is installed, open your ‘Start’ menu and choose ‘Ubuntu’. This will open a terminal window. A terminal is an interface you can use to interact with your computer using text. The first time you have opened Ubuntu, you may see a message which says “Installing, this may take a few minutes…”. After the installation is done, you will have to create a username and password. After these are created, you should be able to use the terminal.
The Windows Subsystem for Linux is like running another computer inside your computer. It is a different operating system and has different software installed than your Windows computer. For the WSL, you have to install miniconda from the terminal in your Linux operating system. Note that if you are using the WSL, your Linux OS is completely separated from your Windows operating system. This means that software installed on one operating system is not available in the other. If you are running the Windows 11 operating system, you can set up WSL to use graphical interfaces on your computer. Otherwise, you will only be able to interact with WSL through the terminal (and the text editor VSCode, see later in the set-up for information on how to use VS Code in WSL)
You can install miniconda through a graphical interface or using your terminal. Pick either “Graphical Installation” or “Text-based (terminal) Installation”. If you are using WSL, it may be easiest to complete this using the terminal installation.
Obtain the latest version of miniconda for your OS at this link. This will download an installer you can run to install miniconda on your system. Note that if you are using WSL, you will need the Linux installer, and you will have to move this file to WSL before running.
Text-based (terminal) Installation#
You can also use the terminal to download and install the miniconda compilers using the terminal. If you are using Linux or WSL, type the following into your terminal.
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh
If you are using Mac, you should pick the appropriate link for your architecture from the miniconda installer page.
close and reopen your terminal window.
If you do not see
(base) before your username on the command line, type
Creating a conda environment#
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.
This section uses the command line interface (CLI), or terminal, to create an environment using
If you are on Mac or Linux, you will type these commands into your terminal.
If you are on Windows, you will use WSL.
To create an environment for this project using
conda create --name molssi_best_practices "python=3.10"
For other projects, you should replace
molssi_best_practices with a descriptive name for your project.
conda also allows you to specify the Python version to use with the environment.
python=3.10 specifies that we want to use Python 3.10 in this environment.
Executing this command will list the environment location and a list of Python packages to be installed.
y(es) when prompted.
Activate the environment using the command
conda activate molssi_best_practices
To see a list of all your environments,
conda info --envs
To deactivate an environment, type
$ conda deactivate
You can use
conda to create environments with different Python versions.
You might be able to see how this could be useful for running old code
(you can change
3.10 in the command above to any version you want),
or testing your code in different Python versions.
Package installation using conda#
conda, we can install packages to our environments.
Note: Make sure you have activated the environment where you want to install packages.
$ conda activate molssi_best_practices
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 (do not execute this, we will install NumPy later),
$ conda install numpy
Further, the desired version of NumPy can be specified by adding this following the package name.
For example, if you wanted to install NumPy version 1.15:
conda install numpy=1.15
For this workshop, you will need to install the following packages into your environment
Packages available to Conda are stored within
Some packages are not stored in the default Conda channel, so we need to specify where Conda can find the package with
-c followed by a channel name in our installation command.
We will install all of our packages from the
so we include the syntax
-c conda-forge in our installation command.
You can install multiple libraries at the same time by listing them one after another.
$ conda install -c conda-forge numpy matplotlib notebook
Installing and configuring git#
We will be using the
git software for version control during this workshop.
This portion walks you through installing and configuring
If you do not have the environment activated, activate it first:
conda activate molssi_best_practices
Next, make sure you have git installed.
You can check if git is installed using the following command in your terminal:
Make sure that this outputs at least version 2.28. If you do not have git installed, or if it is an older version of git, you can install git using conda:
conda install -c conda-forge git
Note that because of the solver that conda uses to decide which version of a package to install you may end up with a version that is < 2.28.
you can use the same command from above
git --version to see what version has been installed.
If the output of that command is < 2.28 you will want to use the following command to specify the version to install. Any version >=2.28 is acceptable.
conda install -c conda-forge git">=2.28"
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:
In the command below, you do not need to put your name or your email address in all caps.
git config --global user.name "YOUR_FIRSTNAME YOUR_LASTNAME" git config --global user.email "YOUR_EMAIL_ADDRESS"
Next, you will need to set the name of the default branch git uses. The following command will set your default branch name to be “main”
git config --global init.defaultBranch main
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.
We recommend installing Visual Studio Code as your text editor in the last portion of this set-up.
Note that using VS Code on Windows or Mac requires additional set-up, which is outlined in the section
Installing a text editor.
To make VS Code your default editor for git, do
$ git config --global core.editor "code --wait"
A more complete list of possible editors is available here.
You can check the configuration commands that you have set using:
$ git config --list
If you do not yet have a GitHub account, you will need to create one. To create an account, navigate to github.com, and click “Sign up”. When creating your GitHub username, remember that this is a professional profile where you can showcase your work. Keeping this in mind, make sure that your GitHub username is both professional and recognizable.
We will be using the command line interface for GitHub. GitHub very recently deprecated using a username and password from the command line. Instead, you will need to create something called an ssh key to verify your account.
Follow the instructions given by GitHub to create an SSH key and add it to your account.
Everyone should have a text editor they can use to edit code. If you do not have a preference for text editors, we recommend Visual Studio Code. If you are using WSL, see these instructions for installing Visual Studio Code for use with WSL. If you are using Mac, follow these instructions to set-up VS Code so that you can use it from the command line.
You should also install the Microsoft Python Extension Plugin for VSCode.
When enabled, the Python extension will allow you to set the Python environment that VS Code will use to run static checks of your code.
You can set the Python environment when you have a Python project open by clicking the Python version (will likely be 3.something) on
in the blue ribbon at the botton of the editor on the right.
Downloading Workshop Materials#
In this workshop, we will be moving code from a Jupyter notebook into a Python package that we can install and import into other scripts.
Downloading materials from the command line
If you are on WSL, or would like to use the command line, you can download the workshop materials using
(similar to how you downloaded the miniconda installer)
Create a folder called
molssi_best_practicesand add the file you downloaded from the step above.
The file you download as starting materials will be a
zipfile. You should unzip this file into the folder you have created. (On the command line, you can type
unzip data.zip) After downloading and unzipping, verify that you see the following directory structure.
molssi_best_practices └── starting_material ├── data │ ├── pdb │ │ ├── 1bna.pdb │ │ ├── benzene.pdb │ │ └── water.pdb │ └── xyz │ ├── 1bna.xyz │ ├── benzene.xyz │ └── water.xyz └── starting_notebook.ipynb
At the end of this set-up, you should have created a Python environment (
molssi_best_practices) which has Python 3.10,
You should also have downloaded starting material, installed and created an account on GitHub, and configured Git.