importing omnipath from pypath results in AttributeError

[dmalzl]

Describe the bug
I am currently trying to use pypath in a custom pipeline. For this I created a conda environment with python 3.13.5 and tried to go through the pypath book. importing pypath works without problems but when I try to import omnipath from pypath I get the following error message (message is truncated for clarity)

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/share/curl.py:76
     74     import pysftp
     75 except:
---> 76     _logger.msg(
     77         'Module `pysftp` not available. '
     78         'Only downloading of a small number of resources '
     79         'relies on this module. '
     80         'Please install by PIP if it is necessary for you.',
     81         'curl',
     82         -1,
     83     )
     84 import codecs
     85 import gzip

AttributeError: 'NoneType' object has no attribute 'msg'

To Reproduce
Steps to reproduce the behavior:

1. run pip install pypath-omnipath
2. In python run from pypath import omnipath

Expected behavior
importing omnipath module without any errors

Traceback

In [1]: from pypath import omnipath
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/share/curl.py:74
     73 try:
---> 74     import pysftp
     75 except:

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pysftp/__init__.py:14
     13 from paramiko import SSHException, AuthenticationException   # make available
---> 14 from paramiko import AgentKey, RSAKey, DSSKey
     16 from pysftp.exceptions import (CredentialException, ConnectionException,
     17                                HostKeysException)

ImportError: cannot import name 'DSSKey' from 'paramiko' (/Users/dmalzl/miniconda3/envs/omnipath/lib/python3.13/site-packages/paramiko/__init__.py)

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
Cell In[1], line 1
----> 1 from pypath import omnipath

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/omnipath/__init__.py:25
     23 from pypath.share import session as _session_mod
     24 from pypath.share import settings as _settings_mod
---> 25 from pypath.omnipath import app as _app_mod
     28 _logger = _session_mod.Logger(name = 'omnipath.init')
     29 _log = _logger._log

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/omnipath/app.py:34
     31 import collections
     32 import itertools
---> 34 import pypath.resources.network as netres
     35 from pypath.core import annot
     36 from pypath.core import intercell

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/resources/network.py:20
      1 #!/usr/bin/env python
      2 # -*- coding: utf-8 -*-
      3
   (...)     17 #  Website: https://pypath.omnipathdb.org/
     18 #
---> 20 import pypath.resources._network as _netres
     21 import pypath.resources as _resources
     22 import pypath.internals.resource as _resfmt

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/resources/_network.py:25
     22 import copy
     24 import pypath.internals.resource as resource
---> 25 import pypath.resources.data_formats as data_formats
     26 import pypath.share.session as session_mod
     27 import pypath.share.settings as settings

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/resources/data_formats.py:26
     23 import copy
     25 # from pypath:
---> 26 import pypath.internals.input_formats as input_formats
     27 import pypath.resources.urls as urls
     28 import pypath.share.common as common

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/internals/input_formats.py:27
     25 import pypath.share.session as session
     26 import pypath_common._constants as _const
---> 27 import pypath.inputs.uniprot_idmapping as uniprot_idmapping
     28 import pypath.inputs.unichem as unichem_input
     30 _logger = session.Logger(name = 'input_formats')

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/inputs/uniprot_idmapping.py:27
     24 import pandas as pd
     26 import pypath.resources.urls as urls
---> 27 import pypath.share.curl as curl
     30 def idtypes(
     31         pairs: bool = True,
     32         raw: bool = False,
     33     ) -> dict[str, pd.DataFrame] | set[tuple[str, str]] | dict:
     34     """
     35     Identifier types in the UniProt ID mapping service.
     36
   (...)     46         otherwise a set of tuples of ID types.
     47     """

File ~/miniconda3/envs/omnipath/lib/python3.13/site-packages/pypath/share/curl.py:76
     74     import pysftp
     75 except:
---> 76     _logger.msg(
     77         'Module `pysftp` not available. '
     78         'Only downloading of a small number of resources '
     79         'relies on this module. '
     80         'Please install by PIP if it is necessary for you.',
     81         'curl',
     82         -1,
     83     )
     84 import codecs
     85 import gzip

AttributeError: 'NoneType' object has no attribute 'msg'

Log file
No other lines run

Desktop (please complete the following information):

• OS: MacOS Tahoe 26.2
• Python version: 3.13.5
• Version or commit hash 0.16.20

Additional context
None

[dmalzl]

Sorry just saw this is a duplicate. Nvm closing

[dmalzl]

or maybe not a duplicate as the other issue is quite old. reopening for now and let the maintainer decide

[dmalzl]

okay I had a bit of a deeper look and it seems that the PyPI and git are not synced. _logger is never initialised but the exception throwing code is commented out there but not in the PyPI version which is why I get the error. However, the actual reason the error occurs is an import error with pysftp which seems to be abandoned. So I will try to install from git source now and see if I can use it

[dmalzl]

Edit to above: The culprit code is commented out in the pypath git but not in the pypath-omnipath so installing from source will still throw the same error.

[dmalzl]

installing via pip install git+https://github.com/saezlab/pypath.git fixes the import error