BioEmu.ipynb: "AssertionError: Something went wrong during colabfold install"

[hughhigin]

Hello,

I'm writing because I have been unable to run the BioEmu colab notebook due to an apparent error with colabfold installation, which appears separate from the recently resolved issue here. Just to test I also tried to run the BioEmu Hpacker notebook on colab, but with that notebook for some reason bioemu is not installing (plus I do not have access to the requested A100 GPUs anyway.

Please let me know if more information is required or if there is a quick fix on my end - after first encountering the error I have been trying to use the default initialization with lysozyme to troubleshoot.

Here is the full text of the error message:

/usr/local/lib/python3.11/site-packages/huggingface_hub/utils/_auth.py:94: UserWarning:
The secret HF_TOKEN does not exist in your Colab secrets.
To authenticate with the Hugging Face Hub, create a token in your settings tab (https://huggingface.co/settings/tokens), set it as secret in your Google Colab and restart your session.
You will be able to reuse this secret in all of your notebooks.
Please note that authentication is recommended but still optional to access public models or datasets.
warnings.warn(
Sampling batches...: 0%| | 0/167 [00:00<?, ?it/s]
Stackprinter failed while formatting <FrameInfo , line 17, scope <cell line: 0>>:
File "/usr/local/lib/python3.11/site-packages/stackprinter/frame_formatting.py", line 225, in select_scope
raise Exception("Picked an invalid source context: %s" % info)
Exception: Picked an invalid source context: [17], [], dict_keys([1])

So here is your original traceback at least:

Traceback (most recent call last):
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3553, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 17, in <cell line: 0>
sample(sequence=Sequence, num_samples=int(number_of_samples), output_dir=os.path.join(workDir, output), filter_samples=filter_samples)
File "/usr/local/lib/python3.11/site-packages/torch/utils/_contextlib.py", line 116, in decorate_context
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bioemu/sample.py", line 169, in main
batch = generate_batch(
^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bioemu/sample.py", line 230, in generate_batch
single_embeds_file, pair_embeds_file = get_colabfold_embeds(
^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bioemu/get_embeds.py", line 163, in get_colabfold_embeds
colabfold_bin_dir = ensure_colabfold_install()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/bioemu/get_embeds.py", line 78, in ensure_colabfold_install
result.returncode == 0
AssertionError: Something went wrong during colabfold install: + echo 'Setting up colabfold...'
Setting up colabfold...

• BASE_PYTHON=/usr/bin/python3.real
• VENV_FOLDER=/root/.bioemu_colabfold
• /usr/bin/python3.real -m venv /root/.bioemu_colabfold
  Error: Command '['/root/.bioemu_colabfold/bin/python3.real', '-m', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1.

[pablo-arantes]

Hi,

Thank you for letting me know about the issue. I've fixed the code, please, try again and let me know if everything is working fine.

Best,

Pablo

[pablo-arantes]

I've fixed the issue. Can you please try again and letting me know if everything is working fine?