move configuration again

cleanup in running
tardis-sn · Jul 22, 2019 · 6d35962 · 6d35962
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diff --git a/...unning/configuration/config_validator.rst → docs/configuration/config_validator.rst b/...unning/configuration/config_validator.rst → docs/configuration/config_validator.rst
diff --git a/docs/running/configuration/configuration.rst → docs/configuration/configuration.rst b/docs/running/configuration/configuration.rst → docs/configuration/configuration.rst
@@ -7,8 +7,7 @@ Configuration File
 TARDIS uses the `YAML markup language <https://en.wikipedia.org/wiki/YAML>`_
 for its configuration files. There are several sections which allow different
 settings for the different aspects of the TARDIS calculation. An example
-configuration file (with a small subset of the options that can be specified) can be downloaded :download:`here
-<../examples/tardis_example.yml>`.
+configuration file (with a small subset of the options that can be specified) can be downloaded at `example_yml`_.
 
 .. warning::
     One should note that currently floats in YAML need to be specified in a special format:
@@ -24,6 +23,10 @@ can be seen here:
     The following shows all the options (and their default settings) that are available for TARDIS. No other options
     are allowed or available
 
+
+.. contents:: Overview
+    :local:
+
 Configuration Schema
 ====================
 
@@ -159,3 +162,5 @@ just an integer. Finally, the method option selects the final spectral synthesis
   interaction mode. Note also the limitations listed at the bottom of the
   dedicated page.
 
+
+.. include:: ../running/example_data.inc
diff --git a/docs/running/configuration/index.rst → docs/configuration/index.rst b/docs/running/configuration/index.rst → docs/configuration/index.rst
diff --git a/...ng/configuration/read_configuration.ipynb → docs/configuration/read_configuration.ipynb b/...ng/configuration/read_configuration.ipynb → docs/configuration/read_configuration.ipynb
diff --git a/docs/configuration/schemas/base.yml b/docs/configuration/schemas/base.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/base.yml
diff --git a/docs/configuration/schemas/model.yml b/docs/configuration/schemas/model.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/model.yml
diff --git a/docs/configuration/schemas/montecarlo.yml b/docs/configuration/schemas/montecarlo.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/montecarlo.yml
diff --git a/docs/configuration/schemas/plasma.yml b/docs/configuration/schemas/plasma.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/plasma.yml
diff --git a/docs/configuration/schemas/spectrum.yml b/docs/configuration/schemas/spectrum.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/spectrum.yml
diff --git a/docs/configuration/schemas/supernova.yml b/docs/configuration/schemas/supernova.yml
@@ -0,0 +1 @@
+../../../tardis/io/schemas/supernova.yml
diff --git a/docs/yml_files/integration.yml → docs/development/integration.yml b/docs/yml_files/integration.yml → docs/development/integration.yml
diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb
diff --git a/docs/running/configuration/schemas/base.yml b/docs/running/configuration/schemas/base.yml
diff --git a/docs/running/configuration/schemas/model.yml b/docs/running/configuration/schemas/model.yml
diff --git a/docs/running/configuration/schemas/montecarlo.yml b/docs/running/configuration/schemas/montecarlo.yml
diff --git a/docs/running/configuration/schemas/plasma.yml b/docs/running/configuration/schemas/plasma.yml
diff --git a/docs/running/configuration/schemas/spectrum.yml b/docs/running/configuration/schemas/spectrum.yml
diff --git a/docs/running/configuration/schemas/supernova.yml b/docs/running/configuration/schemas/supernova.yml
diff --git a/docs/running/example_data.inc b/docs/running/example_data.inc
@@ -0,0 +1,2 @@
+.. _example_yml: https://github.com/tardis-sn/tardis-setups/blob/master/2014/2014_kerzendorf_sim/appendix_A1/tardis_example.yml
+.. _example_atomic_database: https://github.com/tardis-sn/tardis-refdata/raw/master/atom_data/kurucz_cd23_chianti_H_He.h5
diff --git a/docs/running/index.rst b/docs/running/index.rst
@@ -2,18 +2,29 @@
 Running TARDIS
 **************
 
-The TARDIS code needs three components to calculate spectra: 1) an atom database
-2) a model 3) a configuration file. The Atom Database is created by the
-`Carsus <https://tardis-sn.github.io/carsus/>`_ subpackage. A quick start guide
-to run TARDIS can be found :ref:`here <quickstart>`
+The TARDIS code needs three components to calculate spectra:
 
 
+.. toctree::
+    :maxdepth: 1
+    :numbered:
+
+    ../models/index.rst
+    ../configuration/index.rst
+    3. Atom Database <https://tardis-sn.github.io/carsus/>
+
+
+A quick start guide to run TARDIS can be found
+`here <../quickstart/quickstart.ipynb>`_.
+
 
 .. toctree::
     :maxdepth: 2
+    :caption: Running TARDIS and interactivity
 
     commandline
     gui
+    notebooks/index.rst
 
 .. _quickstart:
 

diff --git a/docs/running/notebooks/index.rst b/docs/running/notebooks/index.rst
@@ -0,0 +1,4 @@
+Interactive TARDIS runs
+=======================
+
+xxx
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		@@ -0,0 +1,2 @@
		.. _example_yml: https://github.com/tardis-sn/tardis-setups/blob/master/2014/2014_kerzendorf_sim/appendix_A1/tardis_example.yml
		.. _example_atomic_database: https://github.com/tardis-sn/tardis-refdata/raw/master/atom_data/kurucz_cd23_chianti_H_He.h5