several changes to the structure

tardis-sn · Jul 19, 2019 · 470c081 · 470c081
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Showing 14 changed files with 32 additions and 22 deletions.
diff --git a/docs/index.rst b/docs/index.rst
@@ -32,15 +32,20 @@ assistance.
 
 
 
+.. toctree::
+    :maxdepth: 2
+
+    installation
+
+
 ============
-Using Tardis
+Using TARDIS
 ============
 
 .. toctree::
     :maxdepth: 2
+    :caption: Using TARDIS
 
-    installation
-    CHANGELOG.md
     quickstart
     running/index
     examples/index
@@ -52,37 +57,40 @@ Physics of TARDIS
 
 .. toctree::
     :maxdepth: 2
+    :caption: The Physics of TARDIS
 
-    atomic/atomic_data
     physics/index
-    montecarlo/index
 
 ====
 Team
 ====
 
 .. toctree::
     :maxdepth: 2
+    :caption: Team & Credits
 
     team
     credits
 
-=================
-Developing Tardis
-=================
+================
+Developers Guide
+================
 
 .. toctree::
     :maxdepth: 2
+    :caption: Developers Guide
 
     issues
     workflow/development_workflow
     running_tests
+    CHANGELOG.md
 
 ==========
 References
 ==========
 
 .. toctree::
+    :caption: References
     zreferences
 
 ====

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -16,19 +16,19 @@ simple TARDIS calculations.
 
 .. warning::
 
-    TARDIS is currently only compatbile with Python 2.7.
+    TARDIS is only compatbile with Python >3.6
 
 .. note::
-    We strongly recommond to install TARDIS within an Anaconda environment and
+    We strongly recommend to install TARDIS within an Anaconda environment and
     to always use the lastest github development version.
 
 Requirements
 ============
 
-You can see a list of all the requirements of TARDIS in the `environment definition file <https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env27.yml>`_.
+You can see a list of all the requirements of TARDIS in the `environment definition file <https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env3.yml>`_.
 
-TARDIS is using astropy's excellent installation helpers and thus uses similar
-instructions to astropy.
+TARDIS is using Astropy's excellent installation helpers and thus uses similar
+instructions to Astropy.
 
 .. _anaconda_inst_label:
 
@@ -45,13 +45,13 @@ machine. The next step is to create an environment for TARDIS that contains all
 of the necessary packages (this ensures that TARDIS requirements won't clash
 with any other python installs on disc::
 
-First, download the `environment definition file <https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env27.yml>`_ from::
+First, download the `environment definition file <https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env3.yml>`_ from::
 
-    https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env27.yml
+    https://raw.githubusercontent.com/tardis-sn/tardis/master/tardis_env3.yml
 
 To create the environment, change to the directory that you downloaded the environment definition file and run::
 
-    conda env create -f tardis_env27.yml
+    conda env create -f tardis_env3.yml
 
 Then to activate this environment simply do::
 

diff --git a/docs/news.rst b/docs/news.rst
@@ -1,3 +1,5 @@
+
+
 GSOC 2017
 ---------
 

diff --git a/docs/physics/index.rst b/docs/physics/index.rst
@@ -1,6 +1,6 @@
-************************************
-Behind the scenes: Physics of TARDIS
-************************************
+*****************
+Physics of TARDIS
+*****************
 
 .. warning::
 
@@ -23,10 +23,11 @@ Currently some information are available for
 
 .. toctree::
     new_plasma
+    montecarlo/index
 
 
 Old Physics Section of the TARDIS Docu (Outdated)
-======================================
+=================================================
 
 .. note::
     The following entries reflects the physics section of the old TARDIS
@@ -37,7 +38,6 @@ Old Physics Section of the TARDIS Docu (Outdated)
 
 .. toctree::
     physical_quantities
-    montecarlo
-    new_plasma
+    montecarlo_old
     plasma/index
 
diff --git a/docs/montecarlo/basicprinciples.rst → docs/physics/montecarlo/basicprinciples.rst b/docs/montecarlo/basicprinciples.rst → docs/physics/montecarlo/basicprinciples.rst
diff --git a/docs/montecarlo/discretization.rst → docs/physics/montecarlo/discretization.rst b/docs/montecarlo/discretization.rst → docs/physics/montecarlo/discretization.rst
diff --git a/docs/montecarlo/estimators.rst → docs/physics/montecarlo/estimators.rst b/docs/montecarlo/estimators.rst → docs/physics/montecarlo/estimators.rst
diff --git a/docs/montecarlo/index.rst → docs/physics/montecarlo/index.rst b/docs/montecarlo/index.rst → docs/physics/montecarlo/index.rst
diff --git a/docs/montecarlo/lineinteraction.rst → docs/physics/montecarlo/lineinteraction.rst b/docs/montecarlo/lineinteraction.rst → docs/physics/montecarlo/lineinteraction.rst
diff --git a/docs/montecarlo/propagation.rst → docs/physics/montecarlo/propagation.rst b/docs/montecarlo/propagation.rst → docs/physics/montecarlo/propagation.rst
diff --git a/docs/montecarlo/randomsampling.rst → docs/physics/montecarlo/randomsampling.rst b/docs/montecarlo/randomsampling.rst → docs/physics/montecarlo/randomsampling.rst
diff --git a/docs/montecarlo/sourceintegration.rst → .../physics/montecarlo/sourceintegration.rst b/docs/montecarlo/sourceintegration.rst → .../physics/montecarlo/sourceintegration.rst
diff --git a/docs/montecarlo/virtualpackets.rst → docs/physics/montecarlo/virtualpackets.rst b/docs/montecarlo/virtualpackets.rst → docs/physics/montecarlo/virtualpackets.rst
diff --git a/docs/physics/montecarlo.rst → docs/physics/montecarlo_old.rst b/docs/physics/montecarlo.rst → docs/physics/montecarlo_old.rst