installing isicle

[samuelcajahuaringa]

Hello ISICLE developers, I try to install ISICLE inside a python venv but I have de following problem to installing the requirements:

""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Installing collected packages: toposort, throttler, stopit, pytz, pulp, plac, openbabel, fastjsonschema, connection-pool, appdirs, wrapt, urllib3, tzdata, traitlets, tabulate, smmap, smart-open, six, rpds-py, reretry, pyyaml, psutil, platformdirs, Pillow, packaging, numpy, MarkupSafe, joblib, idna, humanfriendly, dpath, docutils, datrie, configargparse, charset-normalizer, certifi, attrs, yte, scipy, requests, referencing, rdkit, python-dateutil, patsy, jupyter-core, jinja2, gitdb, pandas, jsonschema-specifications, gitpython, statsmodels, jsonschema, nbformat, snakemake Running setup.py install for openbabel ... error error: subprocess-exited-with-error

× Running setup.py install for openbabel did not run successfully. │ exit code: 1 ╰─> [16 lines of output] running install /home/samuel/Documents/CCS_database/isicle/isicle_venv/lib/python3.10/site-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 '3.1.1.1'. Guessing Open Babel location:

• include_dirs: ['/home/samuel/Documents/CCS_database/isicle/isicle_venv/include', '/usr/include/python3.10', '/usr/local/include/openbabel3']

• library_dirs: ['/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/home/samuel/Documents/CCS_database/isicle/isicle_venv/include -I/usr/include/python3.10 -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 [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> openbabel

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" can help me to install the ISICLE please.

Thanks

[smcolby]

Please try the instructions on Read the Docs: https://isicle.readthedocs.io/en/latest/getting_started/installation.html

[samuelcajahuaringa]

Thank a lot @smcolby , after successfully installing:

Installing collected packages: isicle Running setup.py develop for isicle Successfully installed isicle-2.0.0"

I run the example collision_cross_section.py the code finished with follow message:

---

Overall wall time : 0h : 0m :55s

CREST terminated normally.

but not finished all calculations until to obtain the CCS, and When I try the example of read the docs and have the follow problems: with the function "isicle.io.load", and not is possible continue the calculations, is possible send a example similar to the file collision_cross_section.py to test the new version of ISICLE.

Thanks a lot, Samuel

[smcolby]

Apologies for the delay, this dropped off my radar. You can use isicle.load instead of isicle.io.load, which should resolve the issue. The docs have unfortunately not been updated to reflect this yet.