ViennaRNA / ernwin

Sample and predict coarse grain 3D RNA structures
GNU Affero General Public License v3.0
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Installation fails for python 3.10 #9

Closed MartGro closed 3 months ago

MartGro commented 1 year ago

Hello, I tried to install ernwin in a new python 3.10 conda environment. However, the installation does not work when running pip install -r requirenments.txt

After some time, i got it to work by manually installing Cython and numpy first before the rest.

Still, when trying to run the example, the program crashes:


Traceback (most recent call last):
  File "ernwin_env/bin/ernwin.py", line 17, in <module>
    import forgi.utilities.commandline_utils as fuc
  File "ernwin_env/lib/python3.10/site-packages/forgi/__init__.py", line 30, in <module>
    from forgi.utilities.commandline_utils import load_rna
  File "ernwin_env/lib/python3.10/site-packages/forgi/utilities/commandline_utils.py", line 21, in <module>
    import forgi.threedee.model.coarse_grain as ftmc
  File "ernwin_env/lib/python3.10/site-packages/forgi/threedee/model/coarse_grain.py", line 67, in <module>
    from .linecloud import CoordinateStorage, LineSegmentStorage
  File "ernwin_env/lib/python3.10/site-packages/forgi/threedee/model/linecloud.py", line 12, in <module>
    from collections import Mapping
ImportError: cannot import name 'Mapping' from 'collections' `(ernwin_env/lib/python3.10/collections/__init__.py)```
Bernhard10 commented 1 year ago

Hello, Please try to install the latest version of forgi from the master branch (https://github.com/ViennaRNA/forgi). I still need to publish a release with the latest fixes.

Good point about numpy and cython, I should add this to the documentation.

Bernhard10 commented 3 months ago

With the latest release of ernwin and forgi the installation should be fixed.