further restructure

add quickstart
tardis-sn · Jul 22, 2019 · 595aba5 · 595aba5
1 parent 4101163
commit 595aba5
Show file tree

Hide file tree

Showing 32 changed files with 1,245 additions and 139 deletions.
diff --git a/docs/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst
@@ -4,8 +4,8 @@
 Atomic Data
 ***********
 
-The Atom Database for TARDIS is generated by the
+The Atom Database for TARDIS is generated by the Carsus package.
 
 .. toctree::
     atomic_data_description
-    current_public_table.rst
+    current_public_table
diff --git a/docs/conf.py b/docs/conf.py
@@ -77,7 +77,7 @@
 templates_path = ['_templates']
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_templates']
+exclude_patterns = ['_build', '_templates',  '**.ipynb_checkpoints']
 #exclude_patterns.append('_templates')
 
 # This is added to the end of RST files - a good place to put substitutions to

diff --git a/docs/configuration/schemas/base.yml b/docs/configuration/schemas/base.yml
diff --git a/docs/configuration/schemas/model.yml b/docs/configuration/schemas/model.yml
diff --git a/docs/configuration/schemas/montecarlo.yml b/docs/configuration/schemas/montecarlo.yml
diff --git a/docs/configuration/schemas/plasma.yml b/docs/configuration/schemas/plasma.yml
diff --git a/docs/configuration/schemas/spectrum.yml b/docs/configuration/schemas/spectrum.yml
diff --git a/docs/configuration/schemas/supernova.yml b/docs/configuration/schemas/supernova.yml
diff --git a/docs/developer_faq.rst → docs/development/developer_faq.rst b/docs/developer_faq.rst → docs/development/developer_faq.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -37,6 +37,7 @@ assistance.
     :hidden:
 
     installation
+    quickstart/quickstart
 
 
 
@@ -45,8 +46,11 @@ assistance.
     :caption: Using TARDIS
     :hidden:
 
-    quickstart
+
     running/index
+    running/configuration/configuration
+    atomic/atomic_data
+    models/index
     examples/index
     scripts/index
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -68,7 +68,8 @@ and after you are done with TARDIS you can deactivate::
 One does not need to recreate the environment, but simply activate it every time
 TARDIS is used.
 
-Since TARDIS has reached a mature state, we recommend always installing the latest development version::
+Since TARDIS has reached a mature state, we recommend always installing the
+latest development version::
 
     pip install git+https://github.com/tardis-sn/tardis
 
@@ -78,6 +79,12 @@ Alternatively, you can manually clone our repository and install TARDIS by
     cd tardis
     python setup.py install
 
+
+.. _install_openmp:
+Enabling parallel execution with OpenMP
+---------------------------------------
+
+
 Manually, cloning the repository enables other options such as running the code in parallel (enabling OpenMP).
 In general we encourage to download the compilers from `conda` as we then can ensure that they work with TARDIS.
 Within the TARDIS conda environment do::
@@ -92,13 +99,12 @@ For Linux::
 
     conda install -c conda-forge openmp
 
-To compile TARDIS for parallel execution:
+To compile TARDIS for parallel execution::
 
     python setup.py install --with-openmp
 
 
 .. _troubleshooting_inst_label:
-
 Installation Troubles (FAQ)
 ===========================
 

diff --git a/docs/physics/montecarlo/sourceintegration.rst b/docs/physics/montecarlo/sourceintegration.rst
@@ -1,6 +1,8 @@
-******************************** 
+.. _source_integration:
+
+*****************************************
 Direct integration of the radiation field
-********************************
+*****************************************
 
 :cite:`Lucy1999a` describes an alternative method for the generation of
 synthetic supernova spectra. Instead of using the frequency and energy of

diff --git a/docs/physics/montecarlo/virtualpackets.rst b/docs/physics/montecarlo/virtualpackets.rst
@@ -1,3 +1,5 @@
+.. _virtual_packets:
+
 ****************************************
 Spectrum Generation with Virtual Packets
 ****************************************

diff --git a/docs/quickstart.rst b/docs/quickstart.rst