tardis-sn · wkerzendorf · Jun 25, 2018 · Jun 21, 2018 · Jun 21, 2018 · Jun 21, 2018
diff --git a/docs/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst
@@ -4,6 +4,6 @@
 Atomic Data for TARDIS
 **********************
 
-For a detailed description of the datasets go to :doc:`atomic_data_description`
-
-.. include:: current_public_table.rst
+.. toctree::
+    atomic_data_description
+    current_public_table.rst
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -1,7 +1,3 @@
 .. _changelog:
 
-*********
-Changelog
-*********
-
 .. include:: ../CHANGELOG.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -59,7 +59,12 @@
                'sphinxcontrib.bibtex']
 
 
-
+nbsphinx_prolog = """
+This notebook is available at 
+https://github.com/tardis-sn/tardis/tree/master/docs/notebooks/
+{{ env.doc2path(env.docname, base=None) }}
+----
+"""
 # -- General configuration ----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.

diff --git a/docs/examples/index.rst b/docs/examples/index.rst
@@ -0,0 +1,36 @@
+**************
+Example Models
+**************
+
+The following provides some example setups for a number of typical TARDIS use
+cases. You can use these examples as blueprints for your own TARDIS
+applications.
+
+
+
+.. toctree::
+    :maxdepth: 2
+
+    modelconfig
+    tardis_example
+
+Simple Parametrized Models
+==========================
+
+These setups specify the ejecta solely via the YAML configuration file:
+
+* :doc:`tardis_example <tardis_example>`
+
+
+API demonstrations
+=========================
+
+An example on how to use the formal integrator with tardis:
+
+:ref:`notebooks/integrator.ipynb`
+
+
+Detailed Explosion Models
+=========================
+
+Coming soon
diff --git a/docs/examples/modelconfig.rst b/docs/examples/modelconfig.rst
@@ -17,12 +17,15 @@ The density and composition may be specified independently in the following ways
 Specifying the density
 ======================
 
-* :doc:`using a power-law density profile <densitypow>`
-* :doc:`using an exponential density profile <densityexp>`
-* :doc:`using a custom density profile <densitycust>`
+.. toctree::
+    densitypow
+    densityexp
+    densitycust
+
 
 Specifying the composition
 ==========================
 
-* :doc:`using a uniform composition <abundanceuni>`
-* :doc:`using a custom stratified composition <abundancecust>`
+.. toctree::
+    abundanceuni
+    abundancecust
diff --git a/docs/index.rst b/docs/index.rst
@@ -33,36 +33,45 @@ acknowledge it by citing :cite:`Kerzendorf2014`.
 Using Tardis
 ============
 
-* :doc:`Installation <installation>`
-* :doc:`Quickstart Guide <running>`
-* :doc:`Ejecta Model Setup <examples/modelconfig>`
-* :doc:`TARDIS Configuration <configuration/index>`
-* :doc:`Examples <examples/examples>`
-* :doc:`Storing simulations to HDF <to_hdf>`
-* :doc:`Helper Scripts <scripts/index>`
-* :doc:`Credit & Publication Policies <credits>`
+.. toctree::
+    :maxdepth: 2
+
+    installation
+    running
+    examples/index
+    scripts/index
+    credits
 
 ======================
 Looking under the hood
 ======================
 
-* :doc:`Physics behind TARDIS <physics/index>`
-* :doc:`Monte Carlo Primer <montecarlo/index>`
+.. toctree::
+    :maxdepth: 2
+
+    atomic
+    physics/index
+    montecarlo/index
+
 
 =================
 Developing Tardis
 =================
 
-* :doc:`Reporting Issues <issues>`
-* :doc:`How to contribute <workflow/development_workflow>`
-* :doc:`Running tests <running_tests>`
-* :doc:`Changelog <changelog>`
+.. toctree::
+    :maxdepth: 2
+
+    issues
+    workflow/development_workflow
+    runnints_tests
+    changelog
 
 ==========
 References
 ==========
 
-* :doc:`Studies using TARDIS and TARDIS references <zreferences>`
+.. toctree::
+    zreferences
 
 ====
 News

diff --git a/docs/montecarlo/index.rst b/docs/montecarlo/index.rst
@@ -9,6 +9,16 @@ can also be found in various papers by L. Lucy and in the main TARDIS publicatio
 :cite:`Long2002`, :cite:`Lucy2002`, :cite:`Lucy2003`, :cite:`Lucy2005`,
 :cite:`Kerzendorf2014`)
 
+.. toctree::
+    basicprinciples
+    discretization
+    propagation
+    lineinteraction
+    estimators
+    virtualpackets
+    sourceintegration
+    randomsampling
+
 * :doc:`Basic Principles of Monte Carlo Radiative Transfer <basicprinciples>`
 * :doc:`Monte Carlo discretization <discretization>`
 * :doc:`Propagation of Monte Carlo quanta <propagation>`

diff --git a/docs/physics/index.rst b/docs/physics/index.rst
@@ -21,7 +21,8 @@ Eventually, information about the following topics will be provided
 
 Currently some information are available for
 
-* :doc:`Plasma State Calculation <new_plasma>`
+.. toctree::
+    new_plasma
 
 
 Old Physics Section of the TARDIS Docu (Outdated)
@@ -33,8 +34,10 @@ Old Physics Section of the TARDIS Docu (Outdated)
     outdated, many basic concepts are still applicable to the current TARDIS
     version.
 
-* :doc:`physical_quantities`
-* :doc:`montecarlo`
-* :doc:`new_plasma`
-* :doc:`plasma/index`
+
+.. toctree::
+    physical_quantities
+    montecarlo
+    new_plasma
+    plasma/index
 
diff --git a/docs/physics/plasma/lte_plasma.rst b/docs/physics/plasma/lte_plasma.rst
@@ -45,6 +45,6 @@ the quantities calculated here.
 Example Calculations
 ^^^^^^^^^^^^^^^^^^^^
 
-.. plot:: physics/plasma/plasma_plots/lte_ionization_balance.py
+.. .. plot:: physics/plasma/plasma_plots/lte_ionization_balance.py
     :include-source:
 
diff --git a/docs/physics/plasma/nebular_plasma.rst b/docs/physics/plasma/nebular_plasma.rst
@@ -84,6 +84,6 @@ the quantities calculated here.
 Example Calculations
 ^^^^^^^^^^^^^^^^^^^^
 
-.. plot:: physics/plasma/plasma_plots/nebular_ionization_balance.py
+.. .. plot:: physics/plasma/plasma_plots/nebular_ionization_balance.py
     :include-source: