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JeffSHF / ColabDock

Code for ColabDock paper
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TypeError: 'type' object is not subscriptable #22

Closed fabgonzal closed 6 months ago

fabgonzal commented 6 months ago

I am running the local version from the main branch and get this error when I try to run the inference

Traceback (most recent call last): File "/home/gonzalef/binaries/ColabDock/main.py", line 5, in from colabdock.model import ColabDock File "/home/gonzalef/binaries/ColabDock/colabdock/model.py", line 4, in from colabdesign.af.prep import prep_pdb File "/home/gonzalef/binaries/ColabDock/colabdesign/init.py", line 2, in from colabdesign.af.model import mk_af_model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/init.py", line 2, in from colabdesign.af.model import mk_af_model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/model.py", line 7, in from colabdesign.af.alphafold.model import data, config, model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/alphafold/model/data.py", line 20, in from colabdesign.af.alphafold.model import utils File "/home/gonzalef/binaries/ColabDock/colabdesign/af/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.8/site-packages/haiku/init.py", line 19, in from haiku import data_structures File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.8/site-packages/haiku/data_structures.py", line 18, in from haiku._src.data_structures import to_haiku_dict File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.8/site-packages/haiku/_src/data_structures.py", line 30, in from haiku._src import utils File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.8/site-packages/haiku/_src/utils.py", line 42, in def auto_repr(cls: type[Any], *args, **kwargs) -> str: TypeError: 'type' object is not subscriptable

fabgonzal commented 6 months ago

So to be compatible with dm-haiku 0.0.10 the python version needs to be upgraded to 3.9. Also unrelated but the jax version cannot exceed 0.4.23 or else you get the following error. I suggest updating the documentation and the requirements.txt to reflect this.
Traceback (most recent call last): File "/home/gonzalef/binaries/ColabDock/main.py", line 5, in from colabdock.model import ColabDock File "/home/gonzalef/binaries/ColabDock/colabdock/model.py", line 4, in from colabdesign.af.prep import prep_pdb File "/home/gonzalef/binaries/ColabDock/colabdesign/init.py", line 2, in from colabdesign.af.model import mk_af_model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/init.py", line 2, in from colabdesign.af.model import mk_af_model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/model.py", line 7, in from colabdesign.af.alphafold.model import data, config, model File "/home/gonzalef/binaries/ColabDock/colabdesign/af/alphafold/model/data.py", line 20, in from colabdesign.af.alphafold.model import utils File "/home/gonzalef/binaries/ColabDock/colabdesign/af/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.9/site-packages/haiku/init.py", line 20, in from haiku import experimental File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.9/site-packages/haiku/experimental/init.py", line 34, in from haiku._src.dot import abstract_to_dot File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.9/site-packages/haiku/_src/dot.py", line 163, in @jax.linear_util.transformation File "/home/gonzalef/miniconda3/envs/colabdock/lib/python3.9/site-packages/jax/_src/deprecations.py", line 53, in getattr raise AttributeError(f"module {module!r} has no attribute {name!r}") AttributeError: module 'jax' has no attribute 'linear_util'