unable to import esm

[pengzhangzhi]

I install by pip install fair-esm. Then try the example code:

import torch
import esm

# Load ESM-2 model
model, alphabet = esm.pretrained.esm2_t48_15B_UR50D()
batch_converter = alphabet.get_batch_converter()
model.eval()  # disables dropout for deterministic results

The following error is raised:

ModuleNotFoundError                       Traceback (most recent call last)
Untitled-1.ipynb Cell 1 in <cell line: 2>()
      [1](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=0) import torch
----> [2](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=1) import esm
      [4](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=3) # Load ESM-2 model
      [5](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=4) model, alphabet = esm.pretrained.esm2_t48_15B_UR50D()

File ~/anaconda3/envs/torch/lib/python3.8/site-packages/esm/__init__.py:9, in <module>
      6 from .version import version as __version__  # noqa
      8 from .data import Alphabet, BatchConverter, FastaBatchedDataset  # noqa
----> 9 from .model.esm1 import ProteinBertModel  # noqa
     10 from .model.esm2 import ESM2  # noqa
     11 from .model.msa_transformer import MSATransformer  #noqa

ModuleNotFoundError: No module named 'esm.model.esm1'; 'esm.model' is not a package

[ptynecki]

@pengzhangzhi Reinstall the package from main branch.

[tomsercu]

Yes it sounds like a version conflict. Can you pip uninstall and then pip install again and make sure the version is 1.0.2 which just appeared on pip today?

[pengzhangzhi]

Seems like the version I install is just 1.0.2. I just install the pkg and find this error. After uninstall and re-install with pip install fair-esm==1.0.2. The same problem still show up.

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Untitled-1.ipynb Cell 1 in <cell line: 2>()
      [1](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=0) import torch
----> [2](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=1) import esm
      [4](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=3) # Load ESM-2 model
      [5](vscode-notebook-cell:Untitled-1.ipynb?jupyter-notebook#W0sdW50aXRsZWQ%3D?line=4) model, alphabet = esm.pretrained.esm2_t48_15B_UR50D()

File ~/anaconda3/envs/torch/lib/python3.8/site-packages/esm/__init__.py:9, in <module>
      6 from .version import version as __version__  # noqa
      8 from .data import Alphabet, BatchConverter, FastaBatchedDataset  # noqa
----> 9 from .model.esm1 import ProteinBertModel  # noqa
     10 from .model.esm2 import ESM2  # noqa
     11 from .model.msa_transformer import MSATransformer  #noqa

ModuleNotFoundError: No module named 'esm.model.esm1'; 'esm.model' is not a package

[donovanr]

I also have this problem, installing from main and also from pypi with fair-esm==1.0.2 into a fresh conda env with python=3.9 on linux:

Error message

```python In [1]: import torch In [2]: import esm --------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) Input In [2], in () ----> 1 import esm File ~/mambaforge/envs/fairesm/lib/python3.9/site-packages/esm/__init__.py:9, in 6 from .version import version as __version__ # noqa 8 from .data import Alphabet, BatchConverter, FastaBatchedDataset # noqa ----> 9 from .model.esm1 import ProteinBertModel # noqa 10 from .model.esm2 import ESM2 # noqa 11 from .model.msa_transformer import MSATransformer #noqa ModuleNotFoundError: No module named 'esm.model.esm1'; 'esm.model' is not a package ```

Environment

The result of ``` conda create -n fairesm python=3.9 conda activate fairesm pip install torch ipykernel pip install fair-esm==1.0.2 ``` ```bash conda list # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge asttokens 2.0.8 pypi_0 pypi backcall 0.2.0 pypi_0 pypi bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2022.6.15 ha878542_0 conda-forge debugpy 1.6.3 pypi_0 pypi decorator 5.1.1 pypi_0 pypi entrypoints 0.4 pypi_0 pypi executing 0.10.0 pypi_0 pypi fair-esm 1.0.2 pypi_0 pypi ipykernel 6.15.1 pypi_0 pypi ipython 8.4.0 pypi_0 pypi jedi 0.18.1 pypi_0 pypi jupyter-client 7.3.4 pypi_0 pypi jupyter-core 4.11.1 pypi_0 pypi ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.1.0 h8d9b700_16 conda-forge libgomp 12.1.0 h8d9b700_16 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libsqlite 3.39.2 h753d276_1 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libzlib 1.2.12 h166bdaf_2 conda-forge matplotlib-inline 0.1.6 pypi_0 pypi ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.5 pypi_0 pypi openssl 3.0.5 h166bdaf_1 conda-forge packaging 21.3 pypi_0 pypi parso 0.8.3 pypi_0 pypi pexpect 4.8.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pip 22.2.2 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.30 pypi_0 pypi psutil 5.9.1 pypi_0 pypi ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi pygments 2.13.0 pypi_0 pypi pyparsing 3.0.9 pypi_0 pypi python 3.9.13 h2660328_0_cpython conda-forge python-dateutil 2.8.2 pypi_0 pypi python_abi 3.9 2_cp39 conda-forge pyzmq 23.2.1 pypi_0 pypi readline 8.1.2 h0f457ee_0 conda-forge setuptools 65.2.0 py39hf3d152e_0 conda-forge six 1.16.0 pypi_0 pypi sqlite 3.39.2 h4ff8645_1 conda-forge stack-data 0.4.0 pypi_0 pypi tk 8.6.12 h27826a3_0 conda-forge torch 1.12.1 pypi_0 pypi tornado 6.2 pypi_0 pypi traitlets 5.3.0 pypi_0 pypi typing-extensions 4.3.0 pypi_0 pypi tzdata 2022c h191b570_0 conda-forge wcwidth 0.2.5 pypi_0 pypi wheel 0.37.1 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge ```

[dikshyantg]

I also have a similar problem when I try to run the extract.py script

File "/home/dikshyant/anaconda3/lib/python3.7/site-packages/esm/init.py", line 9, in from .model.esm1 import ProteinBertModel # noqa ModuleNotFoundError: No module named 'esm.model.esm1'; 'esm.model' is not a package

[pooriyapfn]

I had this issue too, but I could run it with a trick. first of all uninstall your package and use this command:

pip install git+https://github.com/facebookresearch/esm.git

after that if you are using Jupyter (like colab), first run this block of code, to download the model completely:

import torch
import esm

model, alphabet = esm.pretrained.esm2_t36_3B_UR50D()

after several minutes you can run rest of your code.

[tomsercu]

Hi folks thanks for flagging this issue. The build was broken due to an old file (model.py) accidentally being included in the pip wheel. Note that there was no issue on the github main branch, so as @pooriyapfn points out pip install git+https://github.com/facebookresearch/esm.git still worked.

The wheel is fixed now, so please go ahead and pip uninstall, then pip install fair-esm or pip install fair-esm==1.0.2.

Sorry for the inconvenience.

[pengzhangzhi]

Problem solved! Happy to see that!