Hello all, I have the following script which I want to run on Python 3.8:
import pybel import openbabel from pybel import ob, readfile, Outputfile # NOT WORKING Now, I'm trying to build an image for Singularity with all the dependencies but I don't manage to make it work. I'm doing this that I found in the documentation: # install openbabel 3 git clone https://github.com/openbabel/openbabel.git cd openbabel mkdir build cd build cmake .. -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 make -j24 make install export PYTHONPATH=/usr/local/lib:$PYTHONPATH cd ../scripts/python cp ../stereo.i ../openbabel-python.i openbabel/ cp openbabel/__init__.py.in openbabel/__init__.py export BABEL_VERSION=$(obabel -V | awk '{print $3}') python3 setup.py install But I get this error: + python3 setup.py install /usr/local/lib/python3.8/dist-packages/setuptools/dist.py:545: UserWarning: The version specified ('${BABEL_VERSION}') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details. warnings.warn( running install /usr/local/lib/python3.8/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build_ext Warning: invalid version number '${BABEL_VERSION}'. Guessing Open Babel location: - include_dirs: ['/usr/include/python3.8', '/usr/local/include/openbabel3'] - library_dirs: ['/usr/lib', '/usr/local/lib'] building 'openbabel._openbabel' extension swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp swig -python -c++ -small -O -templatereduce -naturalvar -I/usr/include/python3.8 -I/usr/local/include/openbabel3 -o openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i Error: SWIG failed. Is Open Babel installed? You may need to manually specify the location of Open Babel include and library directories. For example: python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib python setup.py install FATAL: While performing build: while running engine: exit status 1 Can anyone help me to make my script work? Thanks a lot -- Antonio Jesús Banegas Luna Docente e Investigador *UCAM Universidad Católica de Murcia* Teléfono: 821 Email: ajbane...@ucam.edu <https://scholar.google.es/citations?user=EWtHIUMAAAAJ> <http://orcid.org/0000-0003-1158-8877> <https://www.researchgate.net/profile/Antonio_Jesus_Banegas_Luna> *UCAM Universidad Católica San Antonio de Murcia* Departamento de Grado en Ingeniería Informática Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) <https://bio-hpc.eu> -- "Este mensaje es privado y confidencial y se dirige exclusivamente a su destinatario. Si usted recibe este mensaje por error, no debe revelar, distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la confidencialidad ni a ningún privilegio a causa de una transmisión errónea o por mal funcionamiento". "This message is private and confidential and it is intended exclusively for the addressee. If your receive this message by mistake, you should not disseminate, distribute or copy this e-mail. Please inform the sender and delete the message and attachments from your system. No confidentiality or any privilege regarding the information is waived or lost by any mistransmission or malfunction". No me imprimas si no es necesario.Don't print me unless it's necessary.
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
