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Describe the bug
There was a circular import error that I believe was introduced by this commit: 05f13be
This prevents me from making use of the omnipath database.
To Reproduce
Steps to reproduce the behavior:
frompypathimportomnipathop=omnipath.db.get_db('curated', ncbi_tax_id=9606) # Circular import error here
Expected behavior
No exceptions
Traceback
Traceback (most recent call last):
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/pydevconsole.py", line 364, in runcode
coro = func()
File "<input>", line 1, in <module>
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/omnipath/__init__.py", line 25, in <module>
from pypath.omnipath import app as _app_mod
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/omnipath/app.py", line 34, in <module>
import pypath.resources.network as netres
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/resources/network.py", line 25, in <module>
import pypath.resources.data_formats as data_formats
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/resources/data_formats.py", line 26, in <module>
import pypath.internals.input_formats as input_formats
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/internals/input_formats.py", line 27, in <module>
import pypath.inputs.uniprot as uniprot_input
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/inputs/uniprot.py", line 41, in <module>
import pypath.utils.taxonomy as taxonomy
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/utils/__init__.py", line 20, in <module>
from . import orthology as homology
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/utils/orthology.py", line 45, in <module>
import pypath.utils.mapping as mapping
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/utils/mapping.py", line 65, in <module>
import pypath.internals.maps as maps
File "/Users/austinv11/Applications/PyCharm Professional Edition.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
module = self._system_import(name, *args, **kwargs)
File "/opt/homebrew/anaconda3/envs/riot/lib/python3.10/site-packages/pypath/internals/maps.py", line 31, in <module>
input_formats.UniprotMapping(
AttributeError: partially initialized module 'pypath.internals.input_formats' has no attribute 'UniprotMapping' (most likely due to a circular import)
Log file
No additional logs.
Desktop (please complete the following information):
OS: macOS
Python version: 3.10
Version or commit hash: v0.16.10
Additional context
This error goes away when downgrading to 0.16.9
The text was updated successfully, but these errors were encountered:
Describe the bug
There was a circular import error that I believe was introduced by this commit: 05f13be
This prevents me from making use of the omnipath database.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
No exceptions
Traceback
Log file
No additional logs.
Desktop (please complete the following information):
Additional context
This error goes away when downgrading to 0.16.9
The text was updated successfully, but these errors were encountered: