Branch: lyskov/rosetta-ci:main 「revision: №1」
Test: colab.none.root.ColabDesign
SubTest: ColabDesign/esm_msa/example
SubTest files: 「file-system-view」
Daemon: devel    
State: ColabDesign/esm_msa/example

Input Notebook: ColabDesign/esm_msa/example.ipynb Output Notebook: /root/working_dir/ColabDesign_esm_msa_example.ipynb Executing: 0% 0/7 [00:00<?, ?cell/s]Executing notebook with kernel: python3 Executing: 14% 1/7 [00:00<00:04, 1.40cell/s] Executing: 43% 3/7 [00:01<00:02, 1.74cell/s] Executing: 57% 4/7 [00:02<00:01, 1.74cell/s] Traceback (most recent call last): File "/usr/local/bin/papermill", line 8, in <module> sys.exit(papermill()) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill execute_notebook( File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook raise_for_execution_errors(nb, output_path) File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors raise error papermill.exceptions.PapermillExecutionError: --------------------------------------------------------------------------- Exception encountered at "In [3]": [NbConvertApp] Converting notebook /root/working_dir/ColabDesign_esm_msa_example.ipynb to html [NbConvertApp] Writing 277496 bytes to /root/working_dir/ColabDesign_esm_msa_example.html [NbConvertApp] Converting notebook /root/working_dir/ColabDesign_esm_msa_example.ipynb to asciidoc /usr/local/lib/python3.10/dist-packages/nbconvert/utils/pandoc.py:51: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1). Your version must be at least (2.14.2) but less than (4.0.0). Refer to https://pandoc.org/installing.html. Continuing with doubts... check_pandoc_version() [NbConvertApp] Writing 1307 bytes to /root/working_dir/ColabDesign_esm_msa_example.asciidoc ---------------------------------------------------------------- An Exception was encountered at `In [3]'. +*In[1]:*+ [source, ipython3] ---- import os if not os.path.exists("colabdesign"): os.system("pip -q install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1") os.system("ln -s /usr/local/lib/python3.7/dist-packages/colabdesign colabdesign") os.system("curl -fsSL https://files.ipd.uw.edu/krypton/esm_msa_jax_v1.pkl.gz | gunzip > esm_msa.pkl") ---- +*In[2]:*+ [source, ipython3] ---- from colabdesign import esm_msa import numpy as np import jax import matplotlib.pyplot as plt ---- [#papermill-error-cell]#Execution using papermill encountered an exception here and stopped:# +*In[3]:*+ [source, ipython3] ---- %shell wget -qnc https://github.com/sokrypton/ColabDesign/raw/v1.1.1/esm_msa/test_msa.npy tokens = np.load('test_msa.npy')[0] print(tokens.shape) plt.figure() plt.imshow(tokens) plt.show() ---- +*Out[3]:*+ ---- UsageError: Line magic function `%shell` not found. ---- +*In[ ]:*+ [source, ipython3] ---- model, alphabet = esm_msa.pretrained.get_model() _ = model.init(model.key, tokens) model.load_params('esm_msa.pkl') ---- +*In[ ]:*+ [source, ipython3] ---- result = model(tokens) print(result.keys()) ---- +*In[ ]:*+ [source, ipython3] ---- contacts = result['contacts'] plt.figure() plt.imshow(contacts) plt.show() ----