papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [10]":
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-10-c525cb273784> in <module>
      6     a_dataloader = dataloaders[next(iter(dataloaders.keys()))]["train"]
      7     x_sample, _ = next(iter(a_dataloader))
----> 8     MODEL_KWARGS["input_shape"] = ModelCls.estimate_input_shape(x_sample)
      9
     10 nn_model = ModelCls(**MODEL_KWARGS)

~/miniconda3/envs/experiments-binding-affinity/lib/python3.9/site-packages/kinoml/ml/torch_models.py in estimate_input_shape(input_sample)
     23         than a Tensor, please adapt this method accordingly.
     24         """
---> 25         return input_sample.shape[1]
     26
     27

....
        import torch
    ModuleNotFoundError: No module named 'torch'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/29/96/566ac314e796d4b07209a3b88cc7a8d2e8582d55819e33f72e6c0e8d8216/torch_scatter-0.3.0.tar.gz#sha256=9e5e5a6efa4ef45f584e8611f83690d799370dd122b862646751ae112b685b50 (from https://pypi.org/simple/torch-scatter/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement torch-scatter (from versions: 0.3.0, 1.0.2, 1.0.3, 1.0.4, 1.1.0, 1.1.1, 1.1.2, 1.2.0, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.0.7)
ERROR: No matching distribution found for torch-scatter

(experiments-binding-affinity) 31 sukrit@pillarofautumn:~/work/postdoc/kinoml-tutorial/experiments-binding-affinity$ python run_notebook.py \
> features/featurize-template.ipynb \
> features/example-ligand-only-chembl28-morgan512-1k-subsample.py \
> 
Executing:  45%|████████████████████████▏                             | 13/29 [00:07<00:09,  1.63cell/s]
Traceback (most recent call last):
  File "run_notebook.py", line 51, in <module>
    main()
  File "run_notebook.py", line 47, in main
    pm.execute_notebook(str(nbin), str(nbout), parameters)
  File "/Users/sukrit/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 118, in execute_notebook
    raise_for_execution_errors(nb, output_path)
  File "/Users/sukrit/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
    raise error
papermill.exceptions.PapermillExecutionError: 
---------------------------------------------------------------------------
Exception encountered at "In [7]":
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-7-56f51f7ca191> in <module>
----> 1 dataset = import_object(DATASET_CLS).from_source(**DATASET_KWARGS)
      2 dataset

~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/kinoml/datasets/chembl.py in from_source(cls, filename, measurement_types, sample, **kwargs)
     66                     zf.extractall(tmpdir)
     67                 cached_path.parent.mkdir(parents=True, exist_ok=True)
---> 68                 shutil.copyfile(Path(tmpdir) / csv_filename, cached_path)
     69 
     70         df = pd.read_csv(cached_path)

~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/shutil.py in copyfile(src, dst, follow_symlinks)
    262         os.symlink(os.readlink(src), dst)
    263     else:
--> 264         with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
    265             # macOS
    266             if _HAS_FCOPYFILE:

FileNotFoundError: [Errno 2] No such file or directory: '/var/folders/3q/r0xmt3qn6xq02b3p08xbr54r0000gn/T/tmpcilygxcr/activities-chembl27_v0.2.csv'

(experiments-binding-affinity) 12 singhs15@lt22:~/kinoml-workshop/openkinome/experiments-binding-affinity$ python run_notebook.py features/featurize-template.ipynb features/example-ligand-only-chembl28-morgan512-1k-subsample.py 
Executing:  28%|███████████████████▊                                                    | 8/29 [00:05<00:14,  1.48cell/s]
Traceback (most recent call last):
  File "run_notebook.py", line 51, in <module>
    main()
  File "run_notebook.py", line 47, in main
    pm.execute_notebook(str(nbin), str(nbout), parameters)
  File "/home/singhs15/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 118, in execute_notebook
    raise_for_execution_errors(nb, output_path)
  File "/home/singhs15/miniconda3/envs/experiments-binding-affinity/lib/python3.8/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
    raise error
papermill.exceptions.PapermillExecutionError: 
---------------------------------------------------------------------------
Exception encountered at "In [4]":
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-4-baec478d6de7> in <module>
     19 OUT.mkdir(parents=True, exist_ok=True)
     20 
---> 21 print(f"This notebook:           HERE = ~/{HERE.relative_to(Path.home())}")
     22 print(f"This repo:               REPO = ~/{REPO.relative_to(Path.home())}")
     23 print(f"Outputs in:               OUT = ~/{OUT.relative_to(Path.home())}")

~/miniconda3/envs/experiments-binding-affinity/lib/python3.8/pathlib.py in relative_to(self, *other)
    905         if (root or drv) if n == 0 else cf(abs_parts[:n]) != cf(to_abs_parts):
    906             formatted = self._format_parsed_parts(to_drv, to_root, to_parts)
--> 907             raise ValueError("{!r} does not start with {!r}"
    908                              .format(str(self), str(formatted)))
    909         return self._from_parsed_parts('', root if n == 1 else '',

ValueError: '/lila/home/singhs15/kinoml-workshop/openkinome/experiments-binding-affinity/features/example-ligand-only-chembl28-morgan512-1k-subsample' does not start with '/home/singhs15'

Traceback (most recent call last):
  File "/home/david/github/experiments-binding-affinity/run_notebook.py", line 51, in <module>
    main()
  File "/home/david/github/experiments-binding-affinity/run_notebook.py", line 47, in main
    pm.execute_notebook(str(nbin), str(nbout), parameters)
  File "/home/david/miniconda3/envs/test_eba/lib/python3.9/site-packages/papermill/execute.py", line 118, in execute_notebook
    raise_for_execution_errors(nb, output_path)
  File "/home/david/miniconda3/envs/test_eba/lib/python3.9/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
    raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [13]":
---------------------------------------------------------------------------
ArrowNotImplementedError                  Traceback (most recent call last)
/tmp/ipykernel_4232/462024357.py in <module>
      8     path = OUT / f"{'__'.join([g for g in group if g != 'valid'])}.parquet"
      9     parquets.append(path)
---> 10     ak.to_parquet(parquet, path)
     11     # TODO: Missing indices?

~/miniconda3/envs/test_eba/lib/python3.9/site-packages/awkward/operations/convert.py in to_parquet(array, where, explode_records, list_to32, string_to32, bytestring_to32, **options)
   3028         options["schema"] = first.schema
   3029
-> 3030     writer = pyarrow.parquet.ParquetWriter(**options)
   3031     writer.write_table(pyarrow.Table.from_batches([first]))
   3032

~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/parquet.py in __init__(self, where, schema, filesystem, flavor, version, use_dictionary, compression, write_statistics, use_deprecated_int96_timestamps, compression_level, use_byte_stream_split, writer_engine_version, data_page_version, use_compliant_nested_type, **options)
    653         self._metadata_collector = options.pop('metadata_collector', None)
    654         engine_version = 'V2'
--> 655         self.writer = _parquet.ParquetWriter(
    656             sink, schema,
    657             version=version,

~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/_parquet.pyx in pyarrow._parquet.ParquetWriter.__cinit__()

~/miniconda3/envs/test_eba/lib/python3.9/site-packages/pyarrow/error.pxi in pyarrow.lib.check_status()

ArrowNotImplementedError: Unhandled type for Arrow to Parquet schema conversion: dense_union<0: bool not null=0, 1: int64 not null=1>