Add examples of configuration files into the doc

Change-Id: I72001a9142d4c2eb40cc198cfb455a751753a993

README.rst

@@ -7,6 +7,8 @@ It is devided into two packages:
 	* **synthesis-workflow**, which contains the workflow tasks and tools.
 	* **MorphVal**, which is a library used for morphology validation and can be used as a standalone.
 
+The complete documentation of this project is available here:`<https://bbpteam.epfl.ch/documentation/projects/synthesis-workflow/latest/index.html>`_
+
 
 Installation
 ------------
@@ -67,16 +69,3 @@ You can get help and complete parameter description with the following command:
 .. code::
 
     morph_validation --help
-
-Workflows
----------
-
-The package ``synthesis-workflow`` contains many tasks that are organized in workflows.
-The two main workflows are the following:
-
-    * ``synthesis-workflow.tasks.ValidateVacuumSynthesis``: this workflow generates cells
-      in vacuum (e.g. with no atlas information) and compute some simple validation features.
-    * ``synthesis-workflow.tasks.ValidateSynthesis``: this workflow generates cells in a
-      given atlas and compute many validation features.
-
-More details on these workflows and their tasks can be found in the API Reference.

doc/source/config_files.rst

@@ -0,0 +1,16 @@
+Configuration files
+===================
+
+Each workflow needs a different configuration, depending on the tasks that are included in it.
+
+Example for the :py:class:`tasks.workflows.ValidateVacuumSynthesis` workflow
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. literalinclude:: ../../tests/data/in_vacuum/luigi.cfg
+  :language: ini
+
+Example for the :py:class:`tasks.workflows.ValidateSynthesis` workflow
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. literalinclude:: ../../tests/data/in_small_O1/luigi.cfg
+  :language: ini

doc/source/index.rst

@@ -1,21 +1,44 @@
 .. include:: ../../README.rst
 
 
+Workflows
+---------
+
+The package :py:mod:`synthesis_workflow` contains many tasks that are organized in workflows.
+The two main workflows are the following:
+
+    * :py:class:`tasks.workflows.ValidateVacuumSynthesis`: this workflow generates cells
+      in vacuum (e.g. with no atlas information) and compute some simple validation features.
+    * :py:class:`tasks.workflows.ValidateSynthesis`: this workflow generates cells in a
+      given atlas and compute many validation features.
+
+All workflows need configuration files. Some examples are given in :doc:`./config_files`.
+
+More details on these workflows and their tasks can be found in the :ref:`API Reference`.
+
+
+.. _API Reference:
+
 API Reference
 -------------
 
 The :doc:`./api_ref` page contains detailed documentation of:
 
 	* :py:mod:`main workflows<tasks.workflows>`
-	* :py:mod:`all tasks<tasks>`
+	* :py:mod:`all workflow tasks<tasks>`
 	* :py:mod:`all synthesis_workflow functions<synthesis_workflow>`
 	* :py:mod:`all morphval functions<morphval>`
 
+.. note::
+	:py:mod:`tasks` appears as a package in this documentation but it is actually a subpackage
+	of the :py:mod:`synthesis_workflow` package.
+
 
 .. toctree::
    :hidden:
    :maxdepth: 2
 
    Home <self>
+   config_files
    changelog
    api_ref

tests/data/in_small_O1/luigi.cfg

@@ -4,17 +4,6 @@ logging_conf_file = logging.conf
 [RunnerConfig]
 nb_jobs = 1
 
-[DiametrizerConfig]
-model = generic
-terminal_threshold = 2.0
-taper_min = -0.01
-taper_max = 1e-6
-asymmetry_threshold_basal = 1.0
-asymmetry_threhsold_apical = 0.2
-neurite_types = ["basal", "apical"]
-trunk_max_tries = 100
-s_samples = 5
-
 [CircuitConfig]
 circuit_somata_path = circuit_somata.mvd3
 atlas_path = <path_to_atlas_directory>
@@ -30,9 +19,6 @@ morphology_path = repaired_morphology_path
 density_factor = 1
 seed = 0
 
-[SliceCircuit]
-n_cells = 10
-
 [CreateAtlasPlanes]
 plane_type = aligned
 plane_count = 1