How do I use python-openbabel in Travis CI?

问题

I use Travis CI as part of a Toxicology mapping project. For this project I require python-openbabel as a dependency. As such, I have added the apt-get installer to the .travis.yml file, shown below ( comments removed ).

language: python
python: 
  - "2.7"
before_install:
  - sudo apt-get update -qq
  - sudo apt-get install python-openbabel
install: "pip install -r requirements.txt"
script: nosetests tox.py

However, all these attempts failed with the error message Error: SWIG failed. Is Open Babel installed?. I have tried adding SWIG to the list of applications to be installed, to no avail.

Additionally, I have attempted to add the entire build process as proposed by Openbabel itself, this yields the following travis.yml:

language: python
python: 
  - "2.7"
before_install:
  - sudo apt-get update -qq
  - sudo apt-get install python-openbabel
  - wget http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.1/openbabel-2.3.1.tar.gz?r=http://%3A%2F%2Fsourceforge.net%2Fprojects%2Fopenbabel%2Fopenbabel%2F2.3.1%2Fts=1393727248&use_mirror=switch
  - tar zxf openbabel-2.3.1.tar.gz
  - mkdir build
  - cd build
  - cmake ../openbabel-2.3.1 -DPYTHON_BINDINGS=ON
  - make
  - make install
  - export PYTHONPATH=/usr/local/lib:$PYTHONPATH
install: "pip install -r requirements.txt"
script: nosetests tox.py

This fails when trying to untar the downloaded file.

All the failed builds can be seen on Travis-CI: https://travis-ci.org/ToxProject/ToxProject
The Github repo is here: https://github.com/ToxProject/ToxProject

In short, how do I get python-openbabel working with Travis-CI?

回答1:

The version of openbabel installed via apt-get is 1.7 while the version specified in setup.py in requirements.txt is openbabel>=1.8. ~~This make makes the package installed by apt-get not satisfy the requirements.txt and pip is trying install it regardless the installed old version of openbabel.~~ And virtualenv doesn't use the already installed system packages.

~~And when install openbabel via pip, it needs the header files of libopenbabel which is not included in libopenbabel4 which is automatically installed by python-openbabel~~ The version of libopenbabel-dev in ubuntu 12.04 used by travisCI doesn't satisfy the needs of openbabel==1.8.

Solution:

install newer version of libopenbabel-dev and libopenbabel4 manually:

before_install:
  - sudo apt-get install -qq -y swig python-dev
  - wget http://mirrors.kernel.org/ubuntu/pool/universe/o/openbabel/libopenbabel4_2.3.2+dfsg-1.1_amd64.deb
  - sudo dpkg -i libopenbabel4_2.3.2+dfsg-1.1_amd64.deb
  - wget http://mirrors.kernel.org/ubuntu/pool/universe/o/openbabel/libopenbabel-dev_2.3.2+dfsg-1.1_amd64.deb
  - sudo dpkg -i libopenbabel-dev_2.3.2+dfsg-1.1_amd64.deb

回答2:

I see that now the build fails at the pip install requirements stage. Travis creates a virtual environment for running python. By default, python packages installed on the system (ie via apt-get) will not be available, unless you add this to your travils.yml:

virtualenv:
      system_site_packages: true

I had the same problem with python-qt4 and python-qgis, here is a travis.yml file I used recently: https://github.com/anitagraser/TimeManager/blob/master/.travis.yml

来源：https://stackoverflow.com/questions/22128856/how-do-i-use-python-openbabel-in-travis-ci

标签

python

travis-ci

openbabel