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This repository has been archived by the owner on Jun 17, 2024. It is now read-only.
This repository has been archived by the owner on Jun 17, 2024. It is now read-only.

Unable to re-train #22

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@nivekkagicom

Description

Attempts to run model_comparison.py to re-train for scikit-learn>=0.17.1 fail with the traceback below. There is no upper bound in the scikit-learn version so pip install azimuth installed scikit_learn==0.19.1. What is the solution (why is xlrd not a required package)?

[~]# python /Library/Python/2.7/site-packages/azimuth/model_comparison.py
/Library/Python/2.7/site-packages/sklearn/cross_validation.py:41: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. Also note that the interface of the new CV iterators are different from that of this module. This module will be removed in 0.20. "This module will be removed in 0.20.", DeprecationWarning)
/Library/Python/2.7/site-packages/sklearn/grid_search.py:42: DeprecationWarning: This module was deprecated in version 0.18 in favor of the model_selection module into which all the refactored classes and functions are moved. This module will be removed in 0.20. DeprecationWarning)
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/azimuth/model_comparison.py", line 609, in <module> save_final_model_V3(filename='saved_models/V3_model_nopos.pickle', include_position=False)
File "/Library/Python/2.7/site-packages/azimuth/model_comparison.py", line 468, in save_final_model_V3
'train_genes': azimuth.load_data.get_V3_genes(),
File "/Library/Python/2.7/site-packages/azimuth/load_data.py", line 466, in get_V3_genes
target_genes = np.concatenate((get_V1_genes(data_fileV1), get_V2_genes(data_fileV2)))
File "/Library/Python/2.7/site-packages/azimuth/load_data.py", line 456, in get_V1_genes
annotations, gene_position, target_genes, Xdf, Y = read_V1_data(data_file, learn_options=None)
File "/Library/Python/2.7/site-packages/azimuth/load_data.py", line 132, in read_V1_data
human_data = pandas.read_excel(data_file, sheetname=0, index_col=[0, 1])
File "/Library/Python/2.7/site-packages/pandas/io/excel.py", line 203, in read_excel
io = ExcelFile(io, engine=engine)
File "/Library/Python/2.7/site-packages/pandas/io/excel.py", line 232, in __init__
import xlrd # throw an ImportError if we need to
ImportError: No module named xlrd

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