Workflow

1. Open terminal
2. Set up python environment: conda activate myenv
3. Coding using your favorate editor/ using jupyter notebook: jupyter notebook
4. Run python code in terminal: python code.py

Environment management in conda

• create a blank conda environment: conda create --name myenv python=3.9.16
• create a conda environment from yml file: conda create myenv —-file myenv.yml
• update the current environment using yml file: conda env update --name myenv --file myenv.yml --prune
• list all conda environments on the machine: conda env list
• copy an exisiting environment myenv 1, name it as myenv2: conda create --clone myenv1 --name myenv2
• display active conda channels: conda config --show channels
• update conda: conda update --all
• activate a conda environemnt: conda activate myenv
• check conda version: conda --version
• check python version: python --version

Argument Parser

In shell/terminal:

python main.py --arg1 2 --arg2 "arg2_alt"

In main.py:

import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--arg1", type=int, help="integer argument 1", default = 1)
parser.add_argument("--arg2", type=str, help="string argument 2", default = "arg2_default")
args = parser.parse_args()
arg1 = args.arg1
arg2 = args.arg2