The pip recipe is to build the openbabel python bindings from source. That requires that openbabel has been built and installed from source before you run the pip build.
Personally, I’d suggest using mamba-forge and their openbabel package. Best, -Geoff On Jul 31, 2023 at 5:04:11 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > Problems similar to this have been asked, but I've not seen an answer. > In my case I'm trying to pip install openbabel but it's failing. > I have a dockerfile like this: > > FROM python:3.10.12-slim-bullseye > RUN apt-get update && apt-get -y install gcc swig &&\ > apt-get clean > RUN pip install openbabel==3.1.1.1 > > > Running this generates this error: > > Sending build context to Docker daemon 50.4MB > Step 1/3 : FROM python:3.10.12-slim-bullseye > ---> 00e023604615 > Step 2/3 : RUN apt-get update && apt-get -y install gcc swig && apt-get > clean > ---> Using cache > ---> 1c4ea5b6e7a6 > Step 3/3 : RUN pip install openbabel==3.1.1.1 > ---> Running in 8ec19781b2b5 > Collecting openbabel==3.1.1.1 > Downloading openbabel-3.1.1.1.tar.gz (82 kB) > ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 kB 849.1 kB/s eta > 0:00:00 > Preparing metadata (setup.py): started > Preparing metadata (setup.py): finished with status 'done' > Building wheels for collected packages: openbabel > Building wheel for openbabel (setup.py): started > Building wheel for openbabel (setup.py): finished with status 'error' > error: subprocess-exited-with-error > > × python setup.py bdist_wheel did not run successfully. > │ exit code: 1 > ╰─> [66 lines of output] > running bdist_wheel > running build > running build_ext > Warning: invalid version number '3.1.1.1'. > Guessing Open Babel location: > - include_dirs: ['/usr/local/include/python3.10', > '/usr/local/include/openbabel3'] > - library_dirs: ['/usr/local/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/local/include/python3.10 -I/usr/local/include/openbabel3 -o > openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i > openbabel/openbabel-python.i:246: Error: Unable to find > 'openbabel/babelconfig.h' > openbabel/openbabel-python.i:248: Error: Unable to find > 'openbabel/data.h' > openbabel/openbabel-python.i:249: Error: Unable to find > 'openbabel/obutil.h' > openbabel/openbabel-python.i:250: Error: Unable to find > 'openbabel/math/vector3.h' > openbabel/openbabel-python.i:252: Error: Unable to find > 'openbabel/math/matrix3x3.h' > openbabel/openbabel-python.i:253: Error: Unable to find > 'openbabel/math/transform3d.h' > openbabel/openbabel-python.i:254: Error: Unable to find > 'openbabel/math/spacegroup.h' > openbabel/openbabel-python.i:256: Error: Unable to find > 'openbabel/bitvec.h' > openbabel/openbabel-python.i:260: Error: Unable to find > 'openbabel/base.h' > openbabel/openbabel-python.i:262: Error: Unable to find > 'openbabel/generic.h' > openbabel/openbabel-python.i:265: Error: Unable to find > 'openbabel/griddata.h' > openbabel/openbabel-python.i:267: Error: Unable to find > 'openbabel/chains.h' > openbabel/openbabel-python.i:268: Error: Unable to find > 'openbabel/typer.h' > openbabel/openbabel-python.i:276: Error: Unable to find > 'openbabel/plugin.h' > openbabel/openbabel-python.i:281: Error: Unable to find > 'openbabel/oberror.h' > openbabel/openbabel-python.i:282: Error: Unable to find > 'openbabel/format.h' > openbabel/openbabel-python.i:283: Error: Unable to find > 'openbabel/obconversion.h' > openbabel/openbabel-python.i:284: Error: Unable to find > 'openbabel/obfunctions.h' > openbabel/openbabel-python.i:295: Error: Unable to find > 'openbabel/elements.h' > openbabel/openbabel-python.i:296: Error: Unable to find > 'openbabel/residue.h' > openbabel/openbabel-python.i:297: Error: Unable to find > 'openbabel/internalcoord.h' > openbabel/openbabel-python.i:298: Error: Unable to find > 'openbabel/atom.h' > openbabel/openbabel-python.i:299: Error: Unable to find > 'openbabel/bond.h' > openbabel/openbabel-python.i:300: Error: Unable to find > 'openbabel/reaction.h' > openbabel/openbabel-python.i:301: Error: Unable to find > 'openbabel/reactionfacade.h' > openbabel/openbabel-python.i:319: Error: Unable to find > 'openbabel/mol.h' > openbabel/openbabel-python.i:326: Error: Unable to find > 'openbabel/ring.h' > openbabel/openbabel-python.i:327: Error: Unable to find > 'openbabel/parsmart.h' > openbabel/openbabel-python.i:328: Error: Unable to find > 'openbabel/alias.h' > openbabel/openbabel-python.i:330: Error: Unable to find > 'openbabel/fingerprint.h' > openbabel/openbabel-python.i:332: Error: Unable to find > 'openbabel/descriptor.h' > openbabel/openbabel-python.i:343: Error: Unable to find > 'openbabel/forcefield.h' > openbabel/openbabel-python.i:345: Error: Unable to find > 'openbabel/builder.h' > openbabel/openbabel-python.i:346: Error: Unable to find > 'openbabel/op.h' > openbabel/openbabel-python.i:348: Error: Unable to find > 'openbabel/chargemodel.h' > openbabel/openbabel-python.i:351: Error: Unable to find > 'openbabel/phmodel.h' > openbabel/openbabel-python.i:352: Error: Unable to find > 'openbabel/graphsym.h' > openbabel/openbabel-python.i:353: Error: Unable to find > 'openbabel/isomorphism.h' > openbabel/openbabel-python.i:354: Error: Unable to find > 'openbabel/query.h' > openbabel/openbabel-python.i:355: Error: Unable to find > 'openbabel/canon.h' > openbabel/openbabel-python.i:357: Error: Unable to find > 'openbabel/stereo/stereo.h' > openbabel/openbabel-python.i:361: Error: Unable to find > 'openbabel/rotor.h' > openbabel/openbabel-python.i:363: Error: Unable to find > 'openbabel/rotamer.h' > openbabel/openbabel-python.i:364: Error: Unable to find > 'openbabel/spectrophore.h' > openbabel/openbabel-python.i:435: Error: Unable to find > 'openbabel/obiter.h' > openbabel/stereo.i:1: Error: Unable to find > 'openbabel/stereo/tetranonplanar.h' > openbabel/stereo.i:2: Error: Unable to find > 'openbabel/stereo/tetraplanar.h' > openbabel/stereo.i:3: Error: Unable to find > 'openbabel/stereo/tetrahedral.h' > openbabel/stereo.i:4: Error: Unable to find > 'openbabel/stereo/cistrans.h' > openbabel/stereo.i:5: Error: Unable to find > 'openbabel/stereo/squareplanar.h' > openbabel/stereo.i:6: Error: Unable to find > 'openbabel/stereo/bindings.h' > > 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 > [end of output] > > note: This error originates from a subprocess, and is likely not a > problem with pip. > ERROR: Failed building wheel for openbabel > > Any idea what's wrong? > > Tim > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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