Commit de59035e authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

Add docstring and update readme

parent 4185c8dc
......@@ -18,28 +18,59 @@ the distribution packages library (or similar, depending on your operating syste
* libxml2-dev
* libxslt1-dev
* libgraphviz-dev
* pkg-config (fix errors when installing pygraphviz and when config is not loaded...)
* python-glade2
* python-gtk2
Fix errors when installing pygraphviz and when config is not loaded:
* pkg-config
For Matplotlib installation:
* libpng12-dev
* libfreetype6-dev
You can install these dependencies with the following command (on Debian systems):
sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2
sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev \
libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2 libpng12-dev libfreetype6-dev
## Python requirements
Before using `cadbiom` library, the following Python packages
have to be installed from pypi repository:
When `cadbiom` library is installed, the following Python packages
will be installed from pypi repository:
* lxml
* networkx
* pygraphviz
* matplotlib
* numpy
* pycryptosat
### SAT solver
Note: Cadbiom software requires a SAT solver which is
proposed as a Python wrapper by an independant library (pycryptosat).
For now, pycryptosat is not on pypi; so we use a fork from
[Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1)
Here you will find the installation of pycryptosat package:
git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev
mkdir build
cd build && cmake ../
make python_interface_install
### Cadbiom
If you want to install the library with its GUI, and command line,
after the git clone step, just do:
make install
---
For the library itself:
......@@ -134,6 +165,9 @@ The gui package exposes the command `cadbiom` to the current context.
models have the same topology, nodes & edges
attributes/roles. .. note:: You can export a graphml
file for the 2 models.
model_infos Model informations. Get number of nodes, edges,
centralities (degree, closeness, betweenness). ..
note:: You can export a graphml file for model.
### compute_macs:
......@@ -226,6 +260,21 @@ Usage in scripts:
{u'nodes': True, u'edges': True, u'topology': True}
### model_infos
usage: cadbiom_cmd model_infos [-h] [--graph] [--json] [--output [OUTPUT]]
model_file
positional arguments:
model_file
optional arguments:
-h, --help show this help message and exit
--graph
--json
--output [OUTPUT]
## Graphical User Interface
Usage:
......
......@@ -329,7 +329,7 @@ def get_places_from_condition(condition):
def parse_condition(condition, all_nodes, inhibitors_nodes):
"""
"""Return valid paths according the given logical formula and nodes.
"""
......@@ -409,8 +409,13 @@ def parse_condition(condition, all_nodes, inhibitors_nodes):
def parse_event(event):
"""
"""Decompile logical formula in event's name.
:param: Event string.
:type: <event string>
:return: A dict of events and their conditions.
:rtype: <dict>
keys: event's names; values: logical formula attached (condition)
"""
def treeToExprDefaultsList(tree):
......
......@@ -18,28 +18,59 @@ the distribution packages library (or similar, depending on your operating syste
* libxml2-dev
* libxslt1-dev
* libgraphviz-dev
* pkg-config (fix errors when installing pygraphviz and when config is not loaded...)
* python-glade2
* python-gtk2
Fix errors when installing pygraphviz and when config is not loaded:
* pkg-config
For Matplotlib installation:
* libpng12-dev
* libfreetype6-dev
You can install these dependencies with the following command (on Debian systems):
sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2
sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev \
libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2 libpng12-dev libfreetype6-dev
## Python requirements
Before using `cadbiom` library, the following Python packages
have to be installed from pypi repository:
When `cadbiom` library is installed, the following Python packages
will be installed from pypi repository:
* lxml
* networkx
* pygraphviz
* matplotlib
* numpy
* pycryptosat
### SAT solver
Note: Cadbiom software requires a SAT solver which is
proposed as a Python wrapper by an independant library (pycryptosat).
For now, pycryptosat is not on pypi; so we use a fork from
[Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1)
Here you will find the installation of pycryptosat package:
git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev
mkdir build
cd build && cmake ../
make python_interface_install
### Cadbiom
If you want to install the library with its GUI, and command line,
after the git clone step, just do:
make install
---
For the library itself:
......@@ -134,6 +165,9 @@ The gui package exposes the command `cadbiom` to the current context.
models have the same topology, nodes & edges
attributes/roles. .. note:: You can export a graphml
file for the 2 models.
model_infos Model informations. Get number of nodes, edges,
centralities (degree, closeness, betweenness). ..
note:: You can export a graphml file for model.
### compute_macs:
......@@ -226,6 +260,21 @@ Usage in scripts:
{u'nodes': True, u'edges': True, u'topology': True}
### model_infos
usage: cadbiom_cmd model_infos [-h] [--graph] [--json] [--output [OUTPUT]]
model_file
positional arguments:
model_file
optional arguments:
-h, --help show this help message and exit
--graph
--json
--output [OUTPUT]
## Graphical User Interface
Usage:
......
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