running the benchmark script

[pojeda]

Hi,

I have done the setup suggested in the Readme file for importing demystifying, then I moved to the folder bpj_paper_input and tried the command:

python run_benchmarks.py --extractor_type PCA

this gives the error:

2022-03-20 10:37:43 Extracting features-DEBUG: Done with feature extraction for auto-cutoff
2022-03-20 10:37:43 benchmarking-ERROR: 'numpy.ndarray' object is not callable
Traceback (most recent call last):
  File "/demystifying/bpj_paper_input/run_benchmarks.py", line 76, in do_run
    postprocessors = computing.compute(extractor_type=et,
  File "/demystifying/benchmarking/computing.py", line 108, in compute
    feature_to_resids=dg.feature_to_resids())
TypeError: 'numpy.ndarray' object is not callable
/demystifying/bpj_paper_input/run_benchmarks.py:97: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
  logger.warn("Failed for extractor %s ", et)

Some information about my setup, I am using pip, python 3.9.6, and the following dependencies' versions:

pip show numpy
Name: numpy
Version: 1.22.3
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: 
License: BSD
Location: /env-demys/lib/python3.9/site-packages
Requires: 
Required-by: scipy, scikit-learn, pandas, mdtraj, matplotlib, biopandas

pip show mdtraj
Name: mdtraj
Version: 1.9.7
Summary: MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
Home-page: http://mdtraj.org
Author: Robert McGibbon
Author-email: [email protected]
License: LGPLv2.1+
Location: /env-demys/lib/python3.9/site-packages
Requires: scipy, numpy, pyparsing, astunparse
Required-by: 

pip show scikit-learn 
Name: scikit-learn
Version: 1.0.2
Summary: A set of python modules for machine learning and data mining
Home-page: http://scikit-learn.org
Author: 
Author-email: 
License: new BSD
Location: /env-demys/lib/python3.9/site-packages
Requires: threadpoolctl, numpy, joblib, scipy
Required-by: 

pip show biopandas
Name: biopandas
Version: 0.2.9
Summary: Machine Learning Library Extensions
Home-page: https://github.com/rasbt/biopandas
Author: Sebastian Raschka
Author-email: [email protected]
License: BSD 3-Clause
Location: /env-demys/lib/python3.9/site-packages
Requires: setuptools, pandas, numpy
Required-by: