GPCR-ModSim / qfepweb

Development of the web interface to QligFEP.
GNU Lesser General Public License v2.1
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biopython dependency error #16

Closed JenkeScheen closed 3 years ago

JenkeScheen commented 3 years ago

while testing mapgen.py and test_mapgen.py (for #13) I'm getting a biopython dependency error:

Traceback (most recent call last):
  File "test_mapgen.py", line 33, in <module>
    obj = mapgen.MapGen(network_obj=net, in_sdf=sdf)
  File "/Users/jscheen/projects/modsim/qfepweb/qfepweb/networkgen/mapgen.py", line 262, in __init__
    self._set_similarity_function()
  File "/Users/jscheen/projects/modsim/qfepweb/qfepweb/networkgen/mapgen.py", line 295, in _set_similarity_function
    from Bio import pairwise2
ModuleNotFoundError: No module named 'Bio'

looks like biopython isn't installed by pip:

(qfepweb) (mbp) jscheen@macbook:$ pip list
Package              Version
-------------------- --------
asgiref              3.4.1
attrs                21.2.0
decorator            4.4.2
Django               3.2.6
django-crispy-forms  1.11.0
django-debug-toolbar 3.2.1
django-environ       0.4.5
django-extensions    3.1.3
execnet              1.9.0
gunicorn             20.1.0
importlib-metadata   4.6.3
iniconfig            1.1.1
model-bakery         1.2.1
networkx             2.5.1
numpy                1.21.1
packaging            21.0
pandas               1.2.4
Pillow               8.2.0
pip                  21.2.3
pluggy               0.13.1
py                   1.10.0
pyparsing            2.4.7
pytest               6.2.4
pytest-django        4.1.0
pytest-forked        1.3.0
pytest-timeout       1.4.2
pytest-xdist         2.2.1
python-dateutil      2.8.2
pytz                 2021.1
rdkit-pypi           2021.3.4
setuptools           41.2.0
six                  1.16.0
sqlparse             0.4.1
toml                 0.10.2
typing-extensions    3.10.0.0
vulture              2.3
zipp                 3.5.0

I'm not seeing the dependency in requirements(_devel).txt either.