Non-ASCII character in .py, no encoding declared

Question

Non-ASCII character in .py, no encoding declared

greenkidneybean opened this issue 5 years ago · comments

When running snakemake --use-conda from the project root of the project directory I get the following error (line 43 of attached
snakemake.log):

SyntaxError: Non-ASCII character '\xc3' in file /spin1/users/chambersmj/snakemake_test/.snakemake/scripts/tmpmfjaxtfh.wrapper.py on line 5, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details

I thought of adding #coding=utf-8 to the head of .snakemake/scripts/tmpmfjaxtfh.wrapper.py but there are no scripts in the .snakemake/scripts directory.

Any suggestions to resolve the python source file encoding would be greatly appreciated 😊

Note: I've also attached the default config.yaml, the project tree is below, and the data directory was cloned from snakemake-workflows/ngs-test-data.

snakemake_test
├── config.txt
├── config.yaml
├── data
├── envs
├── LICENSE
├── logs
├── mapped
├── README.md
├── report
├── rules
├── samples.tsv
├── schemas
├── scripts
├── Snakefile
├── snakemake.log
├── trimmed
└── units.tsv

Michael Chambers · Answer 1 · Sat Jun 08 2019 00:29:46 GMT+0800 (China Standard Time)

This issue has been resolved.

tmux was pointing Python to the system version (2.7) and not my conda environment (3.6). Still not sure why tmux points to a different python version as opposed to when I'm detached from a session. Cheers!

Johannes Köster · Answer 2 · Tue Jun 11 2019 17:45:16 GMT+0800 (China Standard Time)

No idea, I use tmux all the time. Maybe an issue with your shell configuration?

Michael Chambers · Answer 3 · Tue Jun 11 2019 21:30:51 GMT+0800 (China Standard Time)

Starting a tmux session appended a few directories to my path, which was surpassing the conda path. I added the following line to my .tmux.conf to fix: set -g default-command "${SHELL}"