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README.md

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+# README
+ARGoS3-AutoMoDe
+=====================
+
+All useful information about the ARGoS3-AutoMoDe package, including
+installation and utilization instructions, are regrouped in the
+following technical report ([techrep](#bibliography)). Please cite this report if
+you use the ARGoS3-AutoMoDe package.
+
+## Package content
+
+- `bin` This empty folder will contain the executable automode_main
+after compilation.
+- `experiments` The folder where all experiments configuration files
+  (.argos or .xml) are located
+    - `chocolate` The experiment configuration files of the
+        experiments described in [chocolate](#bibliography)
+    - `example` The experiment configuration file used as example in
+        the technical report of the package.
+- `optimization` The folder where one should place files regarding
+    the optimization algorithm used (including grammar generator for
+    the irace algorithm)
+    - `example` The necessary elements to launch irace on a small example described in the technical report.
+- `src` The source files of ARGoS3-AutoMoDe package.
+    - `cmake` The .cmake files for ARGoS3.
+    - `core` The core classes of ARGoS3-AutoMoDe.
+    - `modules` The behaviors and conditions modules described in [chocolate](#bibliography)
+- `AutoMoDeMain.cpp` :: The main procedure to launch ARGoS3-AutoMoDe.
+
+
+## Installation
+### Dependencies:
+- [ARGoS3](https://github.com/ilpincy/argos3) (3.0.0-beta48)
+- [argos3-epuck](https://github.com/demiurge-project/argos3-epuck) (v48)
+- [experiments-loop-functions](https://github.com/demiurge-project/experiments-loop-functions) (master)
+- [demiurge-epuck-dao](https://github.com/demiurge-project/demiurge-epuck-dao) (master)
+
+### Compiling AutoMoDe:
+    $ git clone https://github.com/demiurge-project/ARGoS3-AutoMoDe.git
+    $ cd argos3-AutoMoDe
+    $ mkdir build
+    $ cmake ..
+    $ make
+
+Once compiled, the `bin/` folder should contain the `automode_main`
+executable.
+
+## How to use
+### Run a single experiment:
+To run a single experiment, you need to use the `automode_main`
+as follows:
+
+    usage: automode_main [-r | --readable] [-c | --config-file configfile] [-m | --method method] [-s | --seed seed] [--fsm-config fsmconfig]
+        options:
+            [-c | --config-file configfile] Path to the .argos|.xml experiment file to use [REQUIRED]
+            [-r | --readable] Prints an URL containing a DOT representation of the finite state machine [OPTIONAL]
+            [-s | --seed seed] The random seed for the ARGoS3 simulator [OPTIONAL]
+            [--fsm-config fsmconfig] the description of the finite state machine in the AutoMoDe format [REQUIRED]
+
+
+### Run the design process
+To run the design process you will need the
+[`irace` package](http://iridia.ulb.ac.be/irace/) and a
+fonctional `R` distribution.
+
+If you are using an MPI capable computing cluster you can use the
+`parallel-irace-mpi` located in the `optimization/` folder.
+Otherwise, you can directly launch irace with the command:
+
+    irace --exec-dir=EXECDIR --seed SEED --scenario scenario
+        options:
+            [--exec-dir=execdir] the execution folder
+            [--seed seed] the random seed for the optimization algorithm
+            [--scenario scenario] the scenario file of the experiment
+
+For example (in the `optimization/` folder):
+
+    irace --exec-dir=aggregation --seed 1234 --scenario scenario.txt
+
+This will run the optimization algorithm for 200k simulation in order
+to train for the aggregation mission (see [chocolate](#bibliography) for details
+on missions).
+
+
+
+## References
+### Bibliography
+
+- [techrep] Ligot, A., Hasselmann, K., Delhaisse, B., Garattoni, L., Francesca, G., & Birattari, M. (2017). AutoMoDe, NEAT, and EvoStick: implementations for the E-puck robot in ARGoS3. Technical report TR/IRIDIA/2017-002, IRIDIA, Université libre de Bruxelles, Belgium.
+- [chocolate] Francesca, G., Brambilla, M., Brutschy, A., Garattoni, L., Miletitch, R., Podevijn, G., ... & Mascia, F. (2015). AutoMoDe-Chocolate: automatic design of control software for robot swarms. Swarm Intelligence, 9(2-3), 125-152.