Commit 12cf18f9 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

[doc] Move website doc to this doc; add troubleshooting section

parent 2835d94e
......@@ -32,12 +32,48 @@ and the design of the C and C++ libraries of this platform
System requirements
-------------------
Please check the system requirements on the
`main website <http://cadbiom.genouest.org/download.html>`_ or on the `Gitlab repository <https://gitlab.inria.fr/pvignet/cadbiom>`_.
CADBIOM is mainly developed in Python 2.7. Before running Cadbiom, the following system packages have to be installed from the distribution packages library (or similar, depending on your operating system).
**Most of these packages are already installed on basic GNU/Linux systems.**
Debian-like systems (Ubuntu)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- python2.7-dev
- libxml2-dev
- libxslt1-dev (Library providing the Gnome XSLT engine)
- pkg-config (Fix errors when installing pygraphviz and when config is not loaded)
- libgraphviz-dev (GUI layouts)
- python-gtk2 (GUI)
- python-glade2 (GUI)
- python-gtksourceview2 (GUI)
- python-tk (GUI)
You can install these dependencies with the following shell command::
$ sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev \
libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2 python-tk
Red Hat-like systems (Fedora/CentOS)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- python-devel
- libxml-devel
- redhat-rpm-config (lxml config)
- libxslt-devel (Library providing the Gnome XSLT engine)
- graphviz-devel (GUI layouts)
- pygtk2 (GUI)
- pygtk2-libglade (GUI)
- pygtksourceview (GUI)
You can install these dependencies with the following command::
$ sudo dnf install python-devel libxml-devel redhat-rpm-config libxslt-devel graphviz-devel \
pygtk2 pygtk2-libglade pygtksourceview
Virtual environment
-------------------
Setting up a virtual environment
--------------------------------
As always, the use of a Python virtual environment
(via `virtualenvwrapper <https://virtualenvwrapper.readthedocs.io/en/latest/>`_) is **strongly advised**.
......@@ -57,13 +93,15 @@ This is not a mandatory step but it is a good practice to separate projects from
export WORKON_HOME=~/.virtualenvs
mkdir -p $WORKON_HOME
# The location of this script may vary depending on your Linux distro.
# See also ~.local/bin/
# Maybe you would better to add this directory to your $PATH variable.
source /usr/bin/virtualenvwrapper.sh
* Restart your terminal or run:
.. code-block:: bash
source /usr/bin/virtualenvwrapper.sh
source ~/.bashrc
* Create your virtualenv:
......@@ -71,7 +109,7 @@ This is not a mandatory step but it is a good practice to separate projects from
mkvirtualenv cadbiom -p /usr/bin/python2.7
* Later if you want to reactivate the virtualenv:
* Later if you want to work in the virtualenv:
.. code-block:: bash
......@@ -81,7 +119,8 @@ This is not a mandatory step but it is a good practice to separate projects from
Installation
------------
Cadbiom package is available on PyPI (Python Package Index), the official third-party software repository for Python language.
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>`_
......@@ -98,6 +137,12 @@ You can install these packages with the following command on all systems that ru
when the gui or the command line is installed via pip.
At this point 2 commands are available in your shell:
- ``cadbiom``: Launch the GUI program.
- ``cadbiom_cmd``: Launch the command line program.
For developers
--------------
......@@ -117,7 +162,6 @@ and then:
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:
......@@ -136,3 +180,45 @@ Depending on the installation method you have chosen in the previous chapter:
make uninstall
# or
make dev_uninstall
Very outdated release (archived)
--------------------------------
To download Cadbiom on your Linux distribution, click on the following link: `Download <annexe/cadbiom.tar.gz>`_.
Please note that this version is still available on the `INRIA Gitlab (branch 1.1.x) <https://gitlab.inria.fr/pvignet/cadbiom/tree/1.1.x>`_.
You will have to install the following packages:
- python-pygraphviz
- python-lxml
- python-networkx
- python-gtksourceview2
If you encounter some problems with the precompiled solver (`2bits <annexe/solver_32.tar>`_ or `64bits <annexe/solver_64.tar.gz>`_), we provide the sources of the `2.9 (recommended) <annexe/source_solver_2_9.tar.gz>`_ and `2.7 <annexe/source_solver_2_7.tar.gz>`_ versions.
The solver CryptoMiniSat is an LGPL-licenced SAT solver, more information on `cryptominisat2 <http://www.msoos.org/cryptominisat2/>`_.
Troubleshooting
---------------
pip command is missing
~~~~~~~~~~~~~~~~~~~~~~
On some very old systems you may have to install also the system package ``python-pip``.
matplotlib is missing
~~~~~~~~~~~~~~~~~~~~~
To be solved: Some (deprecated) functions may require matplotlib::
$ pip install matplotlib==1.5
pygraphviz error: ``_graphviz.so: undefined symbol``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When installing pygraphviz on some systems, you may have this error::
_graphviz.so: undefined symbol: Agundirected
...which is solved by::
$ pip install --upgrade pygraphviz --install-option="--include-path=/usr/include/graphviz" \
--install-option="--library-path=/usr/lib/graphviz/"
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