Installing Python

AVNI requires Python and several Python packages. AVNI version 0.1.0 requires Python version 3.7 or higher. We recommend the Anaconda distribution of Python, which comes with more than 250 scientific packages pre-bundled and includes the conda command line tool for installing new packages and managing different package sets (“environments”) for different projects.

To get started, follow the installation instructions for Anaconda. When you are done, if you type the following commands in a command shell, you should see outputs similar to the following (assuming you installed conda to /home/user/anaconda3):

Linux

$ conda --version && python --version conda 4.9.2 Python 3.7.7 ::
Anaconda, Inc. $ which python /home/user/anaconda3/bin/python $
which pip /home/user/anaconda3/bin/pip

macOS

$ conda --version && python --version conda 4.9.2 Python 3.7.7 $
which python /Users/user/opt/anaconda3/bin/python $ which pip
/Users/user/opt/anaconda3/bin/pip

Windows

Most of our instructions start with $, which indicates that the commands are designed to be run from a bash command shell.

Windows command prompts do not expose the same command-line tools as bash shells, so commands like which will not work. You can test your installation in Windows cmd.exe shells with where instead:

> where python C:\Users\user\anaconda3\python.exe > where pip
C:\Users\user\anaconda3\Scripts\pip.exe

If you get an error…

If you see something like:

conda: command not found

It means that your PATH variable (what the system uses to find programs) is not set properly. In a correct installation, doing:

$ echo $PATH
...:/home/user/anaconda3/bin:...

Will show the Anaconda binary path (above) somewhere in the output (probably at or near the beginning), but the command not found error suggests that it is missing.

On Linux or macOS, the installer should have put something like the following in your ~/.bashrc or ~/.bash_profile (or your .zprofile if you’re using macOS Catalina or later, where the default shell is zsh):

# >>> conda initialize >>> # !! Contents within this block are managed
by 'conda init' !! __conda_setup= ... ... # <<< conda initialize <<<

If this is missing, it is possible that you are not on the same shell that was used during the installation. You can verify which shell you are on by using the command:

$ echo $SHELL

If you do not find this line in the configuration file for the shell you are using (bash, zsh, tcsh, etc.), try running:

conda init

in your command shell. If your shell is not cmd.exe (Windows) or bash (Linux, macOS) you will need to pass the name of the shell to the conda init command. See conda init --help for more info and supported shells.

You can also consult the Anaconda documentation and search for Anaconda install tips (Stack Overflow results are often helpful) to fix these or other problems when conda does not work.