• make a script that does it for you

Create the virtual environment so pip is allowed to run

cd ~/pdf_to_md
python -m venv venv
source venv/bin/activate
pip install pymupdf
python pdf_to_md.py

*note pipx doesn't work in this context because it's isolated and pdf_to_md.py is just a file not available on pipx

Stopping

deactivate

Reusing it afterwards

cd ~/pdf_to_md
source venv/bin/activate
python pdf_to_md.py