tardis-sn · andrewfullard · Dec 9, 2020 · Dec 1, 2020 · Dec 3, 2020 · Dec 3, 2020
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,4 +1,4 @@
-# Contributing to TARDIS
+# Contribution Guidelines
 
 So you are wondering how can you contribute to TARDIS? Congrats, you've landed on the right page!
 

diff --git a/docs/governance.rst b/docs/governance.rst
diff --git a/docs/physics/index.rst b/docs/physics/index.rst
diff --git a/docs/physics/new_plasma.rst b/docs/physics/new_plasma.rst
@@ -2,6 +2,7 @@
 Plasma
 ******
 
+
 The role of the plasma module is to determine the ionisation and excitation states of the elements of the 
 supernova ejecta, given the basic structure, including the elemental abundances, densities and radiation temperature.
 After the calculation of the plasma state, the :math:`\tau_{\textrm{sobolev}}` values can be calculated.
@@ -40,9 +41,9 @@ Updating the Plasma
 -------------------
 During each iteration of the main code, TARDIS updates the plasma using the `update_radiationfield` function. This requires, at minimum, new values for `t_rad` (the radiation temperature), `w` (the dilution factor) and `j_blues` (the intensity in the blue part of each line).
 
-
-
+Plasma Calculations
+-------------------
 .. toctree::
     :maxdepth: 2
 
-    plasma/index
+    plasma/index
diff --git a/docs/physics/old_physics.rst b/docs/physics/old_physics.rst
@@ -1,6 +1,6 @@
-*********************
-Old Physics Section of the TARDIS Docu (Outdated)
-*********************
+******************************
+Old Physics Section (Outdated)
+******************************
 
 .. note::
     The following entries reflects the physics section of the old TARDIS
@@ -10,6 +10,5 @@ Old Physics Section of the TARDIS Docu (Outdated)
 
 
 .. toctree::
-    physical_quantities
     montecarlo_old
     plasma/index
diff --git a/docs/running/index.rst b/docs/running/index.rst
diff --git a/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb b/docs/running/interaction/Custom_TARDIS_Model_Tutorial.ipynb
@@ -788,7 +788,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,

diff --git a/docs/running/commandline.rst → docs/running/interaction/commandline.rst b/docs/running/commandline.rst → docs/running/interaction/commandline.rst
diff --git a/docs/running/converters/cmfgen.rst → ...running/interaction/converters/cmfgen.rst b/docs/running/converters/cmfgen.rst → ...running/interaction/converters/cmfgen.rst
diff --git a/docs/running/converters/index.rst → .../running/interaction/converters/index.rst b/docs/running/converters/index.rst → .../running/interaction/converters/index.rst
diff --git a/docs/running/converters/mesa.stella.dat → ...ng/interaction/converters/mesa.stella.dat b/docs/running/converters/mesa.stella.dat → ...ng/interaction/converters/mesa.stella.dat
diff --git a/...running/converters/stella_to_tardis.ipynb → ...raction/converters/stella_to_tardis.ipynb b/...running/converters/stella_to_tardis.ipynb → ...raction/converters/stella_to_tardis.ipynb
diff --git a/docs/running/custom_source.ipynb → docs/running/interaction/custom_source.ipynb b/docs/running/custom_source.ipynb → docs/running/interaction/custom_source.ipynb
diff --git a/docs/running/interaction/index.rst b/docs/running/interaction/index.rst
@@ -8,17 +8,20 @@ have full access to the model properties (as described in :ref:`physical_quantit
     :maxdepth: 1 
 
 
-    ../commandline
+    commandline
     callback_example
-    ../converters/index
+    converters/index
     Custom_TARDIS_Model_Tutorial
-    ../gui
+    custom_source
+    old_gui
     access
     init_trad_bug
     integrator
     isotope_pd_subclass
-    to_hdf
+    to_hdf.rst
     hdf_writer
+    physical_quantities
+    using_formal_integral
 
 ..    examples/run_simple_example.ipynb
 

diff --git a/docs/running/interaction/integrator.ipynb b/docs/running/interaction/integrator.ipynb
@@ -60,19 +60,19 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[\u001B[1mtardis.plasma.standard_plasmas\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001B[1mstandard_plasmas.py\u001B[0m:72)\n",
-      "tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
+      "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n",
+      "tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
       "tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n",
-      "[\u001B[1mtardis.plasma.base  \u001B[0m][\u001B[1;34mDEBUG\u001B[0m  ]  Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n",
-      "tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n",
-      "[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m  ]  Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n",
-      "tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Simulation finished in 1 iterations and took 0.90 s (\u001B[1mbase.py\u001B[0m:221)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 0.90 s\n"
+      "[\u001b[1mtardis.plasma.base  \u001b[0m][\u001b[1;34mDEBUG\u001b[0m  ]  Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n",
+      "tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
+      "[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m  ]  Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n",
+      "tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/1\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:271)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Simulation finished in 1 iterations and took 0.90 s (\u001b[1mbase.py\u001b[0m:221)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 1 iterations and took 0.90 s\n"
      ]
     }
    ],
@@ -919,21 +919,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[\u001B[1mtardis.plasma.standard_plasmas\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001B[1mstandard_plasmas.py\u001B[0m:72)\n",
-      "tardis.plasma.standard_plasmas - \u001B[1;37mINFO\u001B[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
+      "[\u001b[1mtardis.plasma.standard_plasmas\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5 (\u001b[1mstandard_plasmas.py\u001b[0m:72)\n",
+      "tardis.plasma.standard_plasmas - \u001b[1;37mINFO\u001b[0m - Reading Atomic Data from /media/data/projects/tardis/tardis-code/tardis/../../data/tardis_example/kurucz_cd23_chianti_H_He.h5\n",
       "tardis.atomic - INFO - Read Atom Data with UUID=5ca3035ca8b311e3bb684437e69d75d7 and MD5=21095dd25faa1683f4c90c911a00c3f8\n",
-      "[\u001B[1mtardis.plasma.base  \u001B[0m][\u001B[1;34mDEBUG\u001B[0m  ]  Updating modules in the following order: (\u001B[1mbase.py\u001B[0m:195)\n",
-      "tardis.plasma.base - \u001B[1;34mDEBUG\u001B[0m - Updating modules in the following order:\n",
-      "[\u001B[1mtardis.montecarlo.base\u001B[0m][\u001B[1;34mDEBUG\u001B[0m  ]  Electron scattering switched on (\u001B[1mbase.py\u001B[0m:411)\n",
-      "tardis.montecarlo.base - \u001B[1;34mDEBUG\u001B[0m - Electron scattering switched on\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Starting iteration 1/1 (\u001B[1mbase.py\u001B[0m:194)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Starting iteration 1/1\n",
+      "[\u001b[1mtardis.plasma.base  \u001b[0m][\u001b[1;34mDEBUG\u001b[0m  ]  Updating modules in the following order: (\u001b[1mbase.py\u001b[0m:195)\n",
+      "tardis.plasma.base - \u001b[1;34mDEBUG\u001b[0m - Updating modules in the following order:\n",
+      "[\u001b[1mtardis.montecarlo.base\u001b[0m][\u001b[1;34mDEBUG\u001b[0m  ]  Electron scattering switched on (\u001b[1mbase.py\u001b[0m:411)\n",
+      "tardis.montecarlo.base - \u001b[1;34mDEBUG\u001b[0m - Electron scattering switched on\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Starting iteration 1/1 (\u001b[1mbase.py\u001b[0m:194)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Starting iteration 1/1\n",
       "Running with OpenMP - 4 threads\n",
-      "\u001B[2K\t[100%] Packets(finished/total): 10000/10000\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001B[1mbase.py\u001B[0m:271)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
-      "[\u001B[1mtardis.simulation.base\u001B[0m][\u001B[1;37mINFO\u001B[0m   ]  Simulation finished in 1 iterations and took 1.05 s (\u001B[1mbase.py\u001B[0m:221)\n",
-      "tardis.simulation.base - \u001B[1;37mINFO\u001B[0m - Simulation finished in 1 iterations and took 1.05 s\n",
+      "\u001b[2K\t[100%] Packets(finished/total): 10000/10000\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s (\u001b[1mbase.py\u001b[0m:271)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Luminosity emitted = 8.03041e+42 erg / s Luminosity absorbed = 2.57695e+42 erg / s Luminosity requested = 1.05928e+43 erg / s\n",
+      "[\u001b[1mtardis.simulation.base\u001b[0m][\u001b[1;37mINFO\u001b[0m   ]  Simulation finished in 1 iterations and took 1.05 s (\u001b[1mbase.py\u001b[0m:221)\n",
+      "tardis.simulation.base - \u001b[1;37mINFO\u001b[0m - Simulation finished in 1 iterations and took 1.05 s\n",
       "Saving the integrated spectrum.\n",
       "Doing the formal integral with 4 threads\n",
       "\n",
@@ -1720,23 +1720,23 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 3
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.12"
+   "pygments_lexer": "ipython3",
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}
diff --git a/docs/running/interaction/isotope_pd_subclass.ipynb b/docs/running/interaction/isotope_pd_subclass.ipynb
@@ -217,7 +217,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.8"
   }
  },
  "nbformat": 4,

diff --git a/docs/running/gui.rst → docs/running/interaction/old_gui.rst b/docs/running/gui.rst → docs/running/interaction/old_gui.rst
@@ -1,6 +1,6 @@
-*************************************
-Old Graphical User Interface Section
-*************************************
+***************************************
+Old Graphical User Interface (Outdated)
+***************************************
 
 TARDIS uses the `PyQt5 framework <http://www.riverbankcomputing.com/software/pyqt/download5>`_ for its cross-platform
 interface.

diff --git a/docs/physics/physical_quantities.ipynb → ...ing/interaction/physical_quantities.ipynb b/docs/physics/physical_quantities.ipynb → ...ing/interaction/physical_quantities.ipynb
diff --git a/docs/running/to_hdf.rst → docs/running/interaction/to_hdf.rst b/docs/running/to_hdf.rst → docs/running/interaction/to_hdf.rst
diff --git a/docs/running/using_formal_integral.rst → ...ing/interaction/using_formal_integral.rst b/docs/running/using_formal_integral.rst → ...ing/interaction/using_formal_integral.rst