README inacuracies

[shannog2]

The README says to run:

protenix pred -i input.json -o ./output -n protenix_base_default_v1.0.0

pred is not an option. predict is
-i is not an option. -input is
-o is not an option. --out_dir is

[zhangyuxuann]

@shannog2 No! I think you shoud update to latest protenix version and retry. https://github.com/bytedance/Protenix/blob/main/inference_demo.sh

[zhangyuxuann]

@shannog2 Just a quick reminder: -i and --input are aliases for the same option in Click. They refer to the exact same parameter—you can use either form interchangeably:

Protenix/runner/batch_inference.py

Line 540 in bda4145

@click.option(

[shannog2]

I installed with pip as the README instructed. Maybe keep pypi up to date with the repo

[zhangyuxuann]

@shannog2
Thanks for reporting this issue!
Just to clarify: Protenix's GitHub release tags and PyPI packages are automatically synchronized by github workflow. The latest version (v1.0.4) has been published to PyPI.

1. Explicitly install the latest version

pip install protenix==1.0.4

2. Check your PyPI index source (mirrors may have delays):

pip install protenix==1.0.4 --index-url https://pypi.org/simple

Thanks for using Protenix! 😊