Library and executable code can be used with python3
.
The chlamymodel library relies on pre-calculated friction matrices
that are saved in the python_internal pickle format. Those are
provided in the folder install_data and have to be copied into your
${HOME}
folder:
mkdir -p ~/.chlamymodel
cp install_data/*.pickle ~/.chlamymodel
The friction matrices themselves are created with a pre-compiled program utilizing the fast-multipole boundary element method. Executable files for Windows and Linux as well as two configuration files are installed as follows:
mkdir -p ~/.FMBEM
cp install_data/*.exe ~/.FMBEM
cp install_data/*.cnd ~/.FMBEM
The sperm cell, analyzed by Ben:
cp -r install_data/sperm_data ~/.sperm_data
Chlamydomonas cell, measured by Christian, analyzed by myself:
cp -r install_data/chlamy_data ~/.chlamy_data
To use the python libraries, set the python path accordingly
export PYTHONPATH=${PYTHONPATH}:${this_install}
with ${this_install}
being the folder in which this README file is
saved.
The folders example_*
contain python files that can be executed when
the files in install_data
are copied to their appropriate places,
see install intructions.
A documentation web-page can be generated using sphinx. For this
aim, install sphinx. Then execute sphinx-quickstart
from within the
doc
folder. It is important, that you do not overwrite the file
doc/index/rst
. Also, make use of the autodoc
feature. Then, execute
from within the doc
folder:
./apidoc-everything # creates the documentation files for the modules
make html # generates html from them
Then, there should be a folder _build/html
containing the file
index.html
, which is to be opened in a web browser.