Commit a6dac999 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

Big update of the documentation

parent 8c7f9d54
......@@ -3,7 +3,7 @@ Based on Guarded transition semantic, it gives a formal framework to help the mo
biological systems such as cell signaling network.
Official website: [link](http://cadbiom.genouest.org/)
Full documentation: [link](http://cadbiom.genouest.org/doc/cadbiom/index.html)
# Installation
......
# Installation
This program is tested on python 2.7
(Indeed, the GUI is based on GTK2, and sadly, can not be easily ported to GTK3 with Python 3).
Please check the system requirements on the
[Main website](http://cadbiom.genouest.org/download.html) or [Gitlab](https://gitlab.inria.fr/pvignet/cadbiom).
As always, the use of a Python virtual environment
(via [virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/)) is **strongly advised**.
## From PyPI
pip install cadbiom_cmd
## From sources for developers
cd command_line/
python2.7 setup.py develop
python2.7 setup.py develop --uninstall
......@@ -4,6 +4,5 @@ Command line package
.. toctree::
command_line_install
command_line_usage
command_line_doc
\ No newline at end of file
# GUI package
## Installation
This program is tested on python 2.7
(Indeed, the GUI is based on GTK2, and sadly, can not be easily ported to GTK3 with Python 3).
Please check the system requirements on the
[Main website](http://cadbiom.genouest.org/download.html) or [Gitlab](https://gitlab.inria.fr/pvignet/cadbiom).
As always, the use of a Python virtual environment
(via [virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/)) is **strongly advised**.
### From PyPI
pip install cadbiom_gui
### From sources for developers
cd gui/
python2.7 setup.py develop
python2.7 setup.py develop --uninstall
## Usage
Just type:
$ cadbiom
TODO
====
\ No newline at end of file
......@@ -6,6 +6,10 @@
Welcome to CADBIOM's documentation!
===================================
CADBIOM (Computer Aided Design of Biological Models) is an open source modelling software.
Based on Guarded transition semantic, it gives a formal framework to help the modelling of
biological systems such as cell signaling network.
Cadbiom is freely available on cadbiom.genouest.org, distributed
under the terms of the GNU General Public License.
The website also provides a broad range of informations, model library
......@@ -13,13 +17,14 @@ and documentation.
The user manual is available in `html <../../manual/manual.html>`_ or `pdf <../../manual/manual.pdf>`_ formats.
The main repository is available on the `INRIA Gitlab <https://gitlab.inria.fr/pvignet/cadbiom/>`_
.. toctree::
:maxdepth: 2
:caption: Contents:
installation
command_line_package
library_package
gui_package
examples
......
Installation
============
This program is tested on python 2.7 on a GNU/Linux operating system.
It uses Python bindings to the SAT solver `CryptoMiniSat <>`_,
which comes with the Cadbiom library.
We do not plan to port Cadbiom on Python 3.
The first reason is that the GUI of Cadbiom is based on GTK2 that works
exclusively with Python 2.7, and sadly, can not be easily ported
without heavy design changes to GTK3 that is specific to Python 3.
.. https://stackoverflow.com/questions/27542828/is-it-possible-to-create-gtk2-x-applications-using-python-3
For a comfortable use on Microsoft Windows systems we recommend the use of virtual machines like Virtual Box.
In a general way, if you need to perform computationally intensive uses,
you will probably want to move to a cluster-like infrastructure running a GNU/Linux operating system.
However, it should be possible to install the software suite under Microsoft Windows via `Cygwin <https://www.cygwin.com/>`_
which is a large collection of GNU and Open Source tools which provide functionality
similar to a GNU/Linux distribution on Microsoft Windows.
The porting to a native Python 2.7 application for Microsoft Windows is impossible,
because of the age of this version of Python now deprecated,
and the design of the C and C++ libraries of this platform
(more information `here <https://blogs.msdn.microsoft.com/vcblog/2014/06/10/the-great-c-runtime-crt-refactoring/>`_).
System requirements
-------------------
Please check the system requirements on the
`Main website <http://cadbiom.genouest.org/download.html>`_ or `Gitlab <https://gitlab.inria.fr/pvignet/cadbiom>`_.
Virtual environment
-------------------
As always, the use of a Python virtual environment
(via `virtualenvwrapper <https://virtualenvwrapper.readthedocs.io/en/latest/>`_) is **strongly advised**.
This is not a mandatory step but it is a good practice to use virtual environments
to separate projects from each other.
* Install virtualenvwrapper:
.. code-block:: bash
pip install virtualenvwrapper
* Edit your ``.bashrc`` or ``.zshrc`` file to source the ``virtualenvwrapper.sh`` script with these lines:
.. code-block:: bash
export WORKON_HOME=~/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/bin/virtualenvwrapper.sh
The location of this script may vary depending on your Linux distro
* Restart your terminal or run:
.. code-block:: bash
source /usr/bin/virtualenvwrapper.sh
* Create your virtualenv:
.. code-block:: bash
mkvirtualenv cadbiom -p /usr/bin/python2.7
* Later if you want to reactivate the virtualenv:
.. code-block:: bash
workon cadbiom
Installation
------------
Cadbiom package is available on PyPI (Python Package Index), the official third-party software repository for Python language.
* `Library <https://pypi.python.org/pypi/cadbiom>`_
* `Command line <https://pypi.python.org/pypi/cadbiom-cmd>`_
* `GUI <https://pypi.python.org/pypi/cadbiom-gui>`_
You can install these packages with the following command on all systems that run Python interpreter:
.. code-block:: bash
pip install cadbiom-cmd cadbiom-gui
.. note:: The package of the library itself (``cadbiom``) is automatically installed as a dependency
when the gui or the command line is installed via pip.
For developers
--------------
Install from sources
~~~~~~~~~~~~~~~~~~~~
If you want to install from the sources, the library with its GUI and command line,
just do:
.. code-block:: bash
git clone https://gitlab.inria.fr/pvignet/cadbiom
and then:
.. code-block:: bash
make install
If you want to make changes in the code without having to reinstall the packages,
it is **strongly advised** to use the following command:
.. code-block:: bash
make dev_install
Uninstall
~~~~~~~~~
Depending on the installation method you have chosen in the previous chapter:
.. code-block:: bash
make uninstall
# or
make dev_uninstall
# Library package
## Installation
```eval_rst
.. note:: The library is installed when the gui or the command line is installed via pip.
```
This program is tested on python 2.7
(Indeed, the GUI is based on GTK2, and sadly, can not be easily ported to GTK3 with Python 3).
Please check the system requirements on the
[Main website](http://cadbiom.genouest.org/download.html) or [Gitlab](https://gitlab.inria.fr/pvignet/cadbiom).
As always, the use of a Python virtual environment
(via [virtualenvwrapper](https://virtualenvwrapper.readthedocs.io/en/latest/)) is **strongly advised**.
### From PyPI
pip install cadbiom
### From sources for developers
cd library/
python2.7 setup.py develop
python2.7 setup.py develop --uninstall
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