Install

• Install Python
• Install Biogeme using pip
• Biogeme on GitHub
• Troubleshooting

Biogeme is an open source Python package, that relies on the version 3 of Python. Make sure that Python 3.x is installed on your computer. If you have never used Python before, you may want to consider a complete platform such as Anaconda.

If Python is already installed on your computer, verify the version. Two versions of Python are distributed: version 2 and version 3. Biogeme works only with version 3.

Biogeme is distributed using the pip package manager. There are several tutorials available on the internet such as this one or this one.

The command to install is simply

	      pip install biogeme
	    

Depending on your OS and the version of Python, pip will either directly install the executable (it is called a "wheel"), or attempt to compile the package from sources.

In the latter case, it requires a proper environment to compile C++ code. In general, it is readily available on Linux, and MacOSX (if Xcode has been installed). It may be more complicated on Windows.

The source code of Biogeme is available on GitHub. There are several tutorials available on the internet such as this one or this one.

The command to install Biogeme from source is

python setup.py install

Note that it requires a proper environment to compile C++ code. In general, it is readily available on Linux, and MacOSX (if Xcode has been installed). It may be more complicated on Windows.

ImportError

Followed by a message that looks like this:

/venv/lib/python3.6/site-packages/biogeme/cbiogeme.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE

It is likely to be caused by a conflict among versions or an installation problem. Try to uninstall biogeme:

pip uninstall biogeme

and reinstall it without using the cache:

pip install biogeme --no-cache-dir

.

Cython library not found

On Mac OSX, the following error is sometimes generated:

		  ImportError:
		  dlopen(/Users/~/anaconda3/lib/python3.6/site-packages/biogeme/cbiogeme.cpython-36m-darwin.so,
		  2): Symbol not found:
		  __ZNSt15__exception_ptr13exception_ptrD1Ev

It is likely to be due to a conflict of versions of Python packages. The best way to deal with it is to reinstall Biogeme using the following steps:

First, make sure that you have the latest version of pip:

• pip install --upgrade pip

• Uninstall biogeme:

  pip uninstall biogeme

• Install cython:

  pip install --upgrade cython

• Reinstall biogeme, without using the cache:

  pip install biogeme --no-cache-dir

If it does not work, try first to install gcc:

conda install gcc

If it does not work, try creating a new conda environment:

conda create -n python37 python=3.7 pip gcc pandas unidecode jupyter
conda activate python37
pip install biogeme


If it does not work... I don't know :-(

Trying to compile

On Mac OSX and Windows, the installation is designed to install from binaries, not sources. If you get messages that look like the following, it means that pip is trying to compile from sources. And it will most certainly fail as the environment must be properly configured.

	Running setup.py install for biogeme ... error
	Complete output from command
	c:\users\willi\anaconda3\python.exe -u -c "import setuptools,
	tokenize;
	__file__='C:\\Users\\willi\\AppData\\Local\\Temp\\pip-install-iaflhasr\\biogeme\\setup.py';
	f=getattr(tokenize, 'open', open)(__file__);
	code=f.read().replace('\r\n', '\n');
	f.close();
	exec(compile(code, __file__, 'exec'))" install --record C:\Users\willi\AppData\Local\Temp\pip-record-v6_zn0ff\install-record.txt --single-version-externally-managed --compile:
	Using Cython
	Please put "# distutils: language=c++" in your .pyx or .pxd file(s)
	running install
  

It means that there is no binaries available for your version of Python. To check which versions are supported, go to the repository

pypi.org/project/biogeme/

If you select the "Download files", you will see the list of files available. What you need to look at are the "Wheel" files. For instance, the following files are available for version 3.2.8:

• Python 3.6 for MacOSX : biogeme-3.2.8-cp36-cp36m-macosx_10_9_x86_64.whl
• Python 3.6 for Windows : biogeme-3.2.8-cp36-cp36m-win_amd64.whl
• Python 3.7 for MacOSX : biogeme-3.2.8-cp37-cp37m-macosx_10_9_x86_64.whl
• Python 3.7 for Windows : biogeme-3.2.8-cp37-cp37m-win_amd64.whl
• Python 3.8 for MacOSX : biogeme-3.2.8-cp38-cp38-macosx_10_9_x86_64.whl
• Python 3.8 for Windows : biogeme-3.2.8-cp38-cp38-win_amd64.whl
• Python 3.9 for MacOSX : biogeme-3.2.8-cp39-cp39-macosx_10_9_x86_64.whl
• Python 3.9 for Windows : biogeme-3.2.8-cp39-cp39-win_amd64.whl
• Source: biogeme-3.2.8.tar.gz

It means that you must use Python 3.6, 3.7, 3.8 or 3.9.

To verify if biogeme is correctly installed, you can print the version of Biogeme. To do so, execute the following commands in Python:

• Import the package: import biogeme.version as ver
• Print the version information: print(ver.getText())

The result should look like the following:

      Python 3.9.5 (default, May 18 2021, 12:31:01)
      [Clang 10.0.0 ] :: Anaconda, Inc. on darwin
      Type "help", "copyright", "credits" or "license" for more information.
      >>> import biogeme.version as ver
      >>> print(ver.getText())
      biogeme 3.2.8 [2021-08-05]
      Version entirely written in Python
      Home page: http://biogeme.epfl.ch
      Submit questions to https://groups.google.com/d/forum/biogeme
      Michel Bierlaire, Transport and Mobility Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL)