Setup Python virtual environment
The purpose is to setup a Python virtual environment for code development and testing. This is realized by using the Anaconda environment.
Steps
Step 1: Use Anaconda
Start the Linux Workstation tool. A default terminal should be opened automatically. The command prompt is something like the following:
user_name@cdmhub_session:~$
To use the Anaconda environment, run
use anaconda-6
Then for the follow-up question, input y for yes:
Do you want to make 'use anaconda-6' persistent? (y/n) y
You can type conda to check if Anaconda is used properly.
If not, you may need to restart the terminal.
Step 2: Create a virtual environment
Suppose that we want to create a Python 3.8 virtual environment with the name myenv.
In the terminal, run
conda create --name myenv python=3.8
Anaconda will list all packages that will be downloaded and installed.
Type y (or just press ‘enter’) to proceed:
Proceed ([y]/n)? y
Once finished, if there is no error, you can follow the instruction printed on screen to activate the virtual environment:
conda activate myenv
If this is the first time of activation, an error message could pops up:
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
Then go to Step 2.
Otherwise, the command prompt should be something like this:
(myenv) user_name@cdmhub_session:~$
Step 3: Configure the shell start-up file
Following the printed instruction after the error message, run
conda init bash
A short piece of script will be added to the file ~/.bashrc.
Then close and re-open the current shell.
If the command prompt is updated by prepending (base):
(base) user_name@cdmhub_session:~$
Then this step is done and you can proceed to Step 3.
Otherwise, one more thing needs to be done.
Since the default terminal on the workstation starts from the file ~/.bash_profile, we need to add scripts to let ~/.bashrc be executed when start the shell.
Use any text editor you are familiar with to open the file ~/.bash_profile.
Add the following script at the beginning of the file:
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
Then close and re-open the shell. Try activate the virtual environment again and everything should work now. The command prompt should now looks like
(myenv) user_name@cdmhub_session:~$
Step 4: Install packages
To install Python packages, activate and switch to the desired virtual environment first.
Suppose we want to install NumPy and SciPy, run
conda install numpy scipy
Anaconda will list all dependences that will be downloaded and installed.
Type y to proceed.
If no error occurs, then done.
Other useful commands
To check all installed packages in the currently active virtual environment, run
conda list
To delete the virtual environment named myenv, run
conda remove --name myenv --all
To check all created virtual environments, run
conda env list