Install error with AttributeError: module 'esm.pretrained' has no attribute 'esm2_t6_8M_UR50D'.

[neptuneyt]

Dear developer, Thanks for your scuh amazing work. I did not see how to create conda environment in your page, and I did as below, but get the AttributeError: module 'esm.pretrained' has no attribute 'esm2_t6_8M_UR50D' when running the python seq2topt.py --input ../data/Tm/pred_test.csv --output tm.csv

• conda env

  $ git clone https://github.com/neptuneyt/Seq2Topt.git
  (base) [Seq2Topt]$ mamba create -n seq2topt -c conda-forge -c bioconda -c anaconda pytorch  scikit-learn seaborn requests
  (seq2topt) [Seq2Topt]$ mamba install conda-forge::fair-esm
  $ python seq2topt.py --input ../data/Tm/pred_test.csv --output tm.csv`
  File "/datanode02/yut/Seq2Topt/code/seq2topt.py", line 53, in <module>
  esm2_model, alphabet = esm.pretrained.esm2_t6_8M_UR50D() # raw code, 6 layers
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  AttributeError: module 'esm.pretrained' has no attribute 'esm2_t6_8M_UR50D'. Did you mean: 'esm1_t6_43M_UR50S'?

  Looking forward your reply.

[SizheQiu]

You should install the latest version of esm: https://github.com/facebookresearch/esm.

[neptuneyt]

Thanks for your reply in time. I try to fix as below, but it filed with as below. May I get your each dependency version? Thanks a lot.

seq2topt) [yut@io02 code]$ mamba update conda-forge::fair-esm=2.0.0                                  
Looking for: ['conda-forge::fair-esm=2.0.0']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/main/noarch                                              No change
pkgs/r/noarch                                                 No change
ursky/linux-64                                                No change
ursky/noarch                                                  No change

Pinned packages:
  - python 3.13.*

warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following package could not be installed
└─ fair-esm 2.0.0*  is installable and it requires
   └─ biotite with the potential options
      ├─ biotite [0.12.0|0.13.0|...|0.25.0] would require
      │  └─ python >=3.6,<3.7.0a0 , which can be installed;
      ├─ biotite [0.12.0|0.13.0|...|0.31.0] would require
      │  └─ python >=3.7,<3.8.0a0 , which can be installed;
      ├─ biotite [0.17.0|0.18.0|...|0.35.0] would require
      │  └─ python >=3.8,<3.9.0a0 , which can be installed;
      ├─ biotite [0.25.0|0.26.0|...|0.38.0] would require
      │  └─ python >=3.9,<3.10.0a0 , which can be installed;
      ├─ biotite [0.31.0|0.32.0|...|1.0.1] would require
      │  └─ python >=3.10,<3.11.0a0 , which can be installed;
      ├─ biotite [0.35.0|0.36.0|...|1.0.1] would require
      │  └─ python >=3.11,<3.12.0a0 , which can be installed;
      ├─ biotite [0.38.0|0.39.0|0.40.0|0.41.0|1.0.1] would require
      │  └─ python >=3.12,<3.13.0a0 , which can be installed;
      └─ biotite 0.38.0 would require
         └─ python >=3.12.0rc3,<3.13.0a0  with the potential options
            ├─ python [3.12.0|3.12.1|...|3.12.7], which can be installed;
            └─ python 3.12.0rc3 would require
               └─ _python_rc, which does not exist (perhaps a missing channel).

[SizheQiu]

Try pip install --upgrade fair-esm.