Dependency conflict betwen sfcalculator-torch and protenix

[DorisMai]

The conflict is upstream in the reciprocalspaceship → pandas/gemmi:

• protenix>=0.6.3 hard-pins:
  • pandas==2.3.1
  • gemmi==0.6.7
• sfcalculator-torch requires reciprocalspaceship>=0.9.18
• No reciprocalspaceship release bridges the gap:
  • rs 1.0.3–1.0.6: caps at pandas<=2.2.3 → conflicts with protenix's pandas==2.3.1`
  • rs 1.0.7: requires gemmi>=0.7.0 → conflicts with protenix's gemmi==0.6.7

This issue was discovered in PR #234 when attempting to install sfcalculator-torch to generate synthetic structure factors reward. This would block implementing and testing the corresponding new reward function for protenix.

[minhuanli]

We solved this problem when dealing with embedopt environment, now you can use protenix 2.0 codebase + sfcalculator-torch 0.3.2

see the toml file and pixi.lock file here:

https://github.com/rs-station/embedopt/blob/main/pixi.lock
https://github.com/rs-station/embedopt/blob/main/pyproject.toml