I have a folder structure of
- src
- Snakefile
- scripts
- scripts_A
- A.py
- A2.py
- scripts_B
- B.py
- scripts_A
In A.py I have the import statements
import A2 from src.scripts.scripts_B.B import B
This works when I run A as a script normally. However when I try a snakefile with rule
rule stuff: input: a_in output: b_out script: scripts/scripts_A/A.py
it fails with ModuleNotFoundError: No module named 'src'
I've tried changing location of Snakefile to be above and below src