Introduction & Method

We can control the flow of execution of shell commands/scripts with Python. If we want to use gdalwarp, mrf2isis (USGS/ISIS software), etc. in the shell script, the related conda environment should be activated first. The subprocess module of Python and the following codes can be used:

import subprocess

# activate conda environment
subprocess.run(". ~/anaconda3/etc/profile.d/conda.sh && conda activate <env_name>",
    shell=True, check=True)

# Other shell command goes here, e.g.:
subprocess.run("gdalwarp --help",
    shell=True, check=True)

Exceptional Case

The story here can be ended. However, some errors might occur:

/bin/sh: 6: /home/zhaofei/anaconda3/envs/isis/etc/conda/activate.d/geotiff-activate.sh: [[: not found

This is because the version of Python in the conda base environment is 3.11. The version of Python in the is 3.9. The ...activate.d/geotiff-activate.sh is too old for ...profile.d/conda.sh in the base. Therefore, I modified the problematical line:

if [[ -n "$GEOTIFF_CSV" ]]; then
    export _CONDA_SET_GEOTIFF_CSV=$GEOTIFF_CSV"
fi

to:

if [ -n "${GEOTIFF_CSV:-}" ]; then
    export _CONDA_SET_GEOTIFF_CSV=$GEOTIFF_CSV"
fi