shenwanxiang/bidd-molmap

I cannot run molmap in Spyder IDE

mohammad-saber opened this issue · 1 comments

mohammad-saber commented

Thank you for sharing your great code.

I can run the example on the "Readme" page of the repository in Jupyter Notebook. But, when I try to run the code in Spyder IDE, I get error in several lines.

For example, when I run:

X = mp.batch_transform(smiles_list,  scale = True, 
                       scale_method = 'minmax', n_jobs=8)

I get the following error :


Traceback (most recent call last):
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 418, in _process_worker
    r = call_item()
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 272, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 567, in __call__
    return self.func(*args, **kwargs)
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/parallel.py", line 225, in __call__
    for func, args, kwargs in self.items]
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/parallel.py", line 225, in <listcomp>
    for func, args, kwargs in self.items]
  File "/Users/mohammad/Documents/Code/bidd-molmap/molmap/map.py", line 253, in transform
    print_error('please fit first!')
TypeError: func() missing 2 required keyword-only arguments: 'sep' and 'verbose'
"""

TypeError: func() missing 2 required keyword-only arguments: 'sep' and 'verbose'

Also, when I run:
mp.plot_scatter()

I get the error:
AttributeError: 'MolMap' object has no attribute 'embedded'

I don't understand the effect of IDE. This is the first time I see this phenomenon. If you have any idea how to solve this issue, I appreciate it to guide me.

shenwanxiang commented

Thank you for sharing your great code.

I can run the example on the "Readme" page of the repository in Jupyter Notebook. But, when I try to run the code in Spyder IDE, I get error in several lines.

For example, when I run:

X = mp.batch_transform(smiles_list,  scale = True, 
                       scale_method = 'minmax', n_jobs=8)

I get the following error :


Traceback (most recent call last):
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 418, in _process_worker
    r = call_item()
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 272, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 567, in __call__
    return self.func(*args, **kwargs)
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/parallel.py", line 225, in __call__
    for func, args, kwargs in self.items]
  File "/opt/anaconda3/envs/molmap/lib/python3.6/site-packages/joblib/parallel.py", line 225, in <listcomp>
    for func, args, kwargs in self.items]
  File "/Users/mohammad/Documents/Code/bidd-molmap/molmap/map.py", line 253, in transform
    print_error('please fit first!')
TypeError: func() missing 2 required keyword-only arguments: 'sep' and 'verbose'
"""

TypeError: func() missing 2 required keyword-only arguments: 'sep' and 'verbose'

Also, when I run:
mp.plot_scatter()

I get the error:
AttributeError: 'MolMap' object has no attribute 'embedded'

I don't understand the effect of IDE. This is the first time I see this phenomenon. If you have any idea how to solve this issue, I appreciate it to guide me.

Sorry, I'm not so farmilar with this, it seems that your "mp" object has not be fit yet, to transform a smiles, the mp object should be fit first

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