Exception executing moFF in fresh installations

[CarlosHorro]

Hi all,

I have installed moFF some hours ago and It seems that there is a problem caused by an update of Pandas library. My execution of moFF gives an error like this:

Starting Apex for ./ident_inputs/Label-PSM-ToDelete.raw ...
moff Input file: ./ident_inputs/Label-PSM-ToDelete.raw  XIC_tol 10.0 XIC_win 3.0000 moff_rtWin_peak 1.0000 
RAW file  :  ['./raws/qExactive01819.raw.raw']
Output file in :  ./out
starting  peptide quantification (ms2 / matched ) ..
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
end apex quantification (ms2 / matched ) peptides
computational time (sec):  0.2071 
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 888, in apex_multithr
    raise e
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 133, in save_moff_apex_result
    if result[df_index].get()[1] == -1:
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/multiprocessing/pool.py", line 670, in get
    raise self._value
AttributeError: 'DataFrame' object has no attribute 'ix'
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 888, in apex_multithr
    raise e
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/site-packages/pandas/core/generic.py", line 5274, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/bin/moff_all.py", line 447, in <module>
    result = moff.save_moff_apex_result(result)
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 144, in save_moff_apex_result
    raise e
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/share/moff-2.0.2-2/moff.py", line 133, in save_moff_apex_result
    if result[df_index].get()[1] == -1:
  File "/home/carlos/GitHub/galaxy/database/dependencies/_conda/envs/__moff@2.0.2/lib/python3.6/multiprocessing/pool.py", line 670, in get
    raise self._value
AttributeError: 'DataFrame' object has no attribute 'ix'

Reading about it, it looks like Pandas 1.0.0 has removed support for DataFrame.ix , and all installations later than 2020/01/30 will install Pandas 1.0.0 instead of the previous ones which just showed a warning (pandas-dev/pandas#26438) about the future removal of it:

https://www.google.com/url?q=https://stackoverflow.com/questions/59991397/attributeerror-dataframe-object-has-no-attribute-ix&sa=D&source=hangouts&ust=1581513473589000&usg=AFQjCNFEGjVIrr7Qu4p5FbTWfRG8JYGygw

As I don't know so much about .ix , I've just checked what could be done about it and found some suggestions which may be of interest:
https://www.google.com/url?q=https://stackoverflow.com/questions/43838999/pandas-replacement-for-ix&sa=D&source=hangouts&ust=1581513285770000&usg=AFQjCNHkQjL0cJp9RNuvDlwo0oEjn23XKg

Greetings,
Carlos