tardis-sn · andrewfullard · Dec 11, 2020 · Dec 6, 2020 · Dec 6, 2020 · Dec 6, 2020
diff --git a/docs/index.rst b/docs/index.rst
@@ -57,9 +57,9 @@ Mission Statement
     :caption: Using TARDIS
     :hidden:
 
-    running/components
-    running/tardis_widgets/index
-    running/interaction/index
+    using/components/index
+    using/gui/index
+    using/interaction/index
 
 
 .. toctree::
@@ -69,7 +69,7 @@ Mission Statement
 
     physics/montecarlo/index
     physics/plasma
-    physics/old_physics
+    physics/old_physics/index
 
 
 .. toctree::

diff --git a/...odels/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb b/...odels/examples/.ipynb_checkpoints/Custom_Density_And_Boundary_Velocities-checkpoint.ipynb
diff --git a/docs/physics/old_physics.rst → docs/physics/old_physics/index.rst b/docs/physics/old_physics.rst → docs/physics/old_physics/index.rst
@@ -11,4 +11,4 @@ Old Physics Section (Outdated)
 
 .. toctree::
     montecarlo_old
-    plasma/index
+    ../plasma/index
diff --git a/docs/physics/montecarlo_old.rst → docs/physics/old_physics/montecarlo_old.rst b/docs/physics/montecarlo_old.rst → docs/physics/old_physics/montecarlo_old.rst
diff --git a/docs/quickstart/quickstart.ipynb b/docs/quickstart/quickstart.ipynb
@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Every simulation run requires the atomic database (for more info refer to [atomic data](../atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../configuration/index.rst) ).\n",
+    "Every simulation run requires the atomic database (for more info refer to [atomic data](../using/components/atomic/atomic_data.rst) ) and a configuration file (more info at [configuration](../using/components/configuration/index.rst) ).\n",
     "You can obtain a copy of the atomic database from the\n",
     "(https://github.com/tardis-sn/tardis-refdata) repository\n",
     "(`atom_data` subfolder). We recommended to use the\n",
@@ -444,7 +444,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.10"
+   "version": "3.7.8"
   },
   "nbsphinx": {
    "execute": "always",

diff --git a/docs/atomic/atomic_data.rst → docs/using/components/atomic/atomic_data.rst b/docs/atomic/atomic_data.rst → docs/using/components/atomic/atomic_data.rst
diff --git a/docs/atomic/atomic_data_description.rst → ...onents/atomic/atomic_data_description.rst b/docs/atomic/atomic_data_description.rst → ...onents/atomic/atomic_data_description.rst
diff --git a/docs/atomic/current_public_table.rst → ...omponents/atomic/current_public_table.rst b/docs/atomic/current_public_table.rst → ...omponents/atomic/current_public_table.rst
diff --git a/docs/configuration/config_validator.rst → ...onents/configuration/config_validator.rst b/docs/configuration/config_validator.rst → ...onents/configuration/config_validator.rst
diff --git a/docs/configuration/configuration.rst → ...omponents/configuration/configuration.rst b/docs/configuration/configuration.rst → ...omponents/configuration/configuration.rst
@@ -158,8 +158,8 @@ frequency space they are switched around if necessary. The number of bins is
 just an integer. Finally, the method option selects the final spectral synthesis mode. Currently, there are three options:
 
 * real: construct spectrum from the real packet population alone
-* virtual: use the :doc:`virtual packet scheme <../montecarlo/virtualpackets>` for spectral synthesis
-* integrated: use the :doc:`formal integral method <../montecarlo/sourceintegration>` of Lucy 1999
+* virtual: use the :doc:`virtual packet scheme <../../../physics/montecarlo/virtualpackets>` for spectral synthesis
+* integrated: use the :doc:`formal integral method <../../../physics/montecarlo/sourceintegration>` of Lucy 1999
 
 .. warning::
 
@@ -168,4 +168,4 @@ just an integer. Finally, the method option selects the final spectral synthesis
   dedicated page.
 
 
-.. include:: ../running/example_data.inc
+.. include:: ../../example_data.inc
diff --git a/docs/configuration/index.rst → .../using/components/configuration/index.rst b/docs/configuration/index.rst → .../using/components/configuration/index.rst
diff --git a/docs/configuration/read_configuration.ipynb → ...ts/configuration/read_configuration.ipynb b/docs/configuration/read_configuration.ipynb → ...ts/configuration/read_configuration.ipynb
diff --git a/docs/configuration/schemas/base.yml → ...components/configuration/schemas/base.yml b/docs/configuration/schemas/base.yml → ...components/configuration/schemas/base.yml
diff --git a/docs/configuration/schemas/model.yml → ...omponents/configuration/schemas/model.yml b/docs/configuration/schemas/model.yml → ...omponents/configuration/schemas/model.yml
diff --git a/docs/configuration/schemas/montecarlo.yml → ...ents/configuration/schemas/montecarlo.yml b/docs/configuration/schemas/montecarlo.yml → ...ents/configuration/schemas/montecarlo.yml
diff --git a/docs/configuration/schemas/plasma.yml → ...mponents/configuration/schemas/plasma.yml b/docs/configuration/schemas/plasma.yml → ...mponents/configuration/schemas/plasma.yml
diff --git a/docs/configuration/schemas/spectrum.yml → ...onents/configuration/schemas/spectrum.yml b/docs/configuration/schemas/spectrum.yml → ...onents/configuration/schemas/spectrum.yml
diff --git a/docs/configuration/schemas/supernova.yml → ...nents/configuration/schemas/supernova.yml b/docs/configuration/schemas/supernova.yml → ...nents/configuration/schemas/supernova.yml
diff --git a/docs/running/components.rst → docs/using/components/index.rst b/docs/running/components.rst → docs/using/components/index.rst
@@ -8,10 +8,10 @@ The TARDIS code needs three components to calculate spectra:
 .. toctree::
     :maxdepth: 1
 
-    ../configuration/index
-    ../models/index
-    ../atomic/atomic_data
+    configuration/index
+    models/index
+    atomic/atomic_data
 
 
 A quick start guide to run TARDIS can be found
-`here <../quickstart/quickstart.ipynb>`_.
+`here <../../quickstart/quickstart.ipynb>`_.
diff --git a/docs/models/csy/csvy_test.ipynb → ...ing/components/models/csy/csvy_test.ipynb b/docs/models/csy/csvy_test.ipynb → ...ing/components/models/csy/csvy_test.ipynb
diff --git a/...tom_Density_And_Boundary_Velocities.ipynb → ...tom_Density_And_Boundary_Velocities.ipynb b/...tom_Density_And_Boundary_Velocities.ipynb → ...tom_Density_And_Boundary_Velocities.ipynb
diff --git a/docs/models/examples/abund.dat → ...sing/components/models/examples/abund.dat b/docs/models/examples/abund.dat → ...sing/components/models/examples/abund.dat
diff --git a/docs/models/examples/abundancecust.rst → ...ponents/models/examples/abundancecust.rst b/docs/models/examples/abundancecust.rst → ...ponents/models/examples/abundancecust.rst
diff --git a/docs/models/examples/abundanceuni.rst → ...mponents/models/examples/abundanceuni.rst b/docs/models/examples/abundanceuni.rst → ...mponents/models/examples/abundanceuni.rst
diff --git a/docs/models/examples/csvy_full_rad.csvy → ...onents/models/examples/csvy_full_rad.csvy b/docs/models/examples/csvy_full_rad.csvy → ...onents/models/examples/csvy_full_rad.csvy
diff --git a/docs/models/examples/density.dat → ...ng/components/models/examples/density.dat b/docs/models/examples/density.dat → ...ng/components/models/examples/density.dat
diff --git a/docs/models/examples/densitycust.rst → ...omponents/models/examples/densitycust.rst b/docs/models/examples/densitycust.rst → ...omponents/models/examples/densitycust.rst
diff --git a/docs/models/examples/densityexp.rst → ...components/models/examples/densityexp.rst b/docs/models/examples/densityexp.rst → ...components/models/examples/densityexp.rst
diff --git a/docs/models/examples/densitypow.rst → ...components/models/examples/densitypow.rst b/docs/models/examples/densitypow.rst → ...components/models/examples/densitypow.rst
diff --git a/docs/models/examples/examples.rst → ...g/components/models/examples/examples.rst b/docs/models/examples/examples.rst → ...g/components/models/examples/examples.rst
diff --git a/docs/models/examples/index.rst → ...sing/components/models/examples/index.rst b/docs/models/examples/index.rst → ...sing/components/models/examples/index.rst
diff --git a/docs/models/examples/modelconfig.rst → ...omponents/models/examples/modelconfig.rst b/docs/models/examples/modelconfig.rst → ...omponents/models/examples/modelconfig.rst
diff --git a/.../models/examples/run_simple_example.ipynb → .../models/examples/run_simple_example.ipynb b/.../models/examples/run_simple_example.ipynb → .../models/examples/run_simple_example.ipynb
diff --git a/...ardis_configv1_abundance_cust_example.yml → ...ardis_configv1_abundance_cust_example.yml b/...ardis_configv1_abundance_cust_example.yml → ...ardis_configv1_abundance_cust_example.yml
diff --git a/...is_configv1_abundance_uniform_example.yml → ...is_configv1_abundance_uniform_example.yml b/...is_configv1_abundance_uniform_example.yml → ...is_configv1_abundance_uniform_example.yml
diff --git a/.../tardis_configv1_density_cust_example.yml → .../tardis_configv1_density_cust_example.yml b/.../tardis_configv1_density_cust_example.yml → .../tardis_configv1_density_cust_example.yml
diff --git a/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml b/..._configv1_density_exponential_example.yml → ..._configv1_density_exponential_example.yml
diff --git a/...is_configv1_density_power_law_example.yml → ...is_configv1_density_power_law_example.yml b/...is_configv1_density_power_law_example.yml → ...is_configv1_density_power_law_example.yml
diff --git a/...nfigv1_isotope_abundance_cust_example.yml → ...nfigv1_isotope_abundance_cust_example.yml b/...nfigv1_isotope_abundance_cust_example.yml → ...nfigv1_isotope_abundance_cust_example.yml
diff --git a/docs/models/examples/tardis_example.rst → ...onents/models/examples/tardis_example.rst b/docs/models/examples/tardis_example.rst → ...onents/models/examples/tardis_example.rst
diff --git a/docs/models/examples/tardis_example.yml → ...onents/models/examples/tardis_example.yml b/docs/models/examples/tardis_example.yml → ...onents/models/examples/tardis_example.yml
diff --git a/docs/models/examples/tardis_model_abund.csv → ...ts/models/examples/tardis_model_abund.csv b/docs/models/examples/tardis_model_abund.csv → ...ts/models/examples/tardis_model_abund.csv
diff --git a/docs/models/examples/test_abund.dat → ...components/models/examples/test_abund.dat b/docs/models/examples/test_abund.dat → ...components/models/examples/test_abund.dat
diff --git a/docs/models/examples/test_density.txt → ...mponents/models/examples/test_density.txt b/docs/models/examples/test_density.txt → ...mponents/models/examples/test_density.txt
diff --git a/docs/models/index.rst → docs/using/components/models/index.rst b/docs/models/index.rst → docs/using/components/models/index.rst
diff --git a/...ning/configuration/schemas/csvy_model.yml → ...sing/configuration/schemas/csvy_model.yml b/...ning/configuration/schemas/csvy_model.yml → ...sing/configuration/schemas/csvy_model.yml
diff --git a/docs/running/example_data.inc → docs/using/example_data.inc b/docs/running/example_data.inc → docs/using/example_data.inc
diff --git a/...g/tardis_widgets/generating_widgets.ipynb → docs/using/gui/generating_widgets.ipynb b/...g/tardis_widgets/generating_widgets.ipynb → docs/using/gui/generating_widgets.ipynb
diff --git a/docs/running/tardis_widgets/index.rst → docs/using/gui/index.rst b/docs/running/tardis_widgets/index.rst → docs/using/gui/index.rst
diff --git a/.../running/tardis_widgets/using_widgets.rst → docs/using/gui/using_widgets.rst b/.../running/tardis_widgets/using_widgets.rst → docs/using/gui/using_widgets.rst
diff --git a/docs/running/images/LineInfo.png → docs/using/images/LineInfo.png b/docs/running/images/LineInfo.png → docs/using/images/LineInfo.png
diff --git a/docs/running/images/OpeningScreen.png → docs/using/images/OpeningScreen.png b/docs/running/images/OpeningScreen.png → docs/using/images/OpeningScreen.png
diff --git a/docs/running/images/ShellInfo.png → docs/using/images/ShellInfo.png b/docs/running/images/ShellInfo.png → docs/using/images/ShellInfo.png
diff --git a/...ing/images/line_info_spectrum_modebar.gif → ...ing/images/line_info_spectrum_modebar.gif b/...ing/images/line_info_spectrum_modebar.gif → ...ing/images/line_info_spectrum_modebar.gif
diff --git a/...images/line_info_spectrum_rangeslider.gif → ...images/line_info_spectrum_rangeslider.gif b/...images/line_info_spectrum_rangeslider.gif → ...images/line_info_spectrum_rangeslider.gif
diff --git a/...g/images/line_info_spectrum_selection.gif → ...g/images/line_info_spectrum_selection.gif b/...g/images/line_info_spectrum_selection.gif → ...g/images/line_info_spectrum_selection.gif
diff --git a/.../running/images/line_info_widget_demo.gif → docs/using/images/line_info_widget_demo.gif b/.../running/images/line_info_widget_demo.gif → docs/using/images/line_info_widget_demo.gif
diff --git a/...running/images/shell_info_widget_demo.gif → docs/using/images/shell_info_widget_demo.gif b/...running/images/shell_info_widget_demo.gif → docs/using/images/shell_info_widget_demo.gif
diff --git a/...action/Custom_TARDIS_Model_Tutorial.ipynb → ...action/Custom_TARDIS_Model_Tutorial.ipynb b/...action/Custom_TARDIS_Model_Tutorial.ipynb → ...action/Custom_TARDIS_Model_Tutorial.ipynb
diff --git a/docs/running/interaction/access.rst → docs/using/interaction/access.rst b/docs/running/interaction/access.rst → docs/using/interaction/access.rst
diff --git a/...running/interaction/access_iterations.rst → docs/using/interaction/access_iterations.rst b/...running/interaction/access_iterations.rst → docs/using/interaction/access_iterations.rst
diff --git a/...unning/interaction/callback_example.ipynb → .../using/interaction/callback_example.ipynb b/...unning/interaction/callback_example.ipynb → .../using/interaction/callback_example.ipynb
diff --git a/docs/running/interaction/commandline.rst → docs/using/interaction/commandline.rst b/docs/running/interaction/commandline.rst → docs/using/interaction/commandline.rst
diff --git a/...running/interaction/converters/cmfgen.rst → docs/using/interaction/converters/cmfgen.rst b/...running/interaction/converters/cmfgen.rst → docs/using/interaction/converters/cmfgen.rst
diff --git a/.../running/interaction/converters/index.rst → docs/using/interaction/converters/index.rst b/.../running/interaction/converters/index.rst → docs/using/interaction/converters/index.rst
diff --git a/...ng/interaction/converters/mesa.stella.dat → ...ng/interaction/converters/mesa.stella.dat b/...ng/interaction/converters/mesa.stella.dat → ...ng/interaction/converters/mesa.stella.dat
diff --git a/...raction/converters/stella_to_tardis.ipynb → ...raction/converters/stella_to_tardis.ipynb b/...raction/converters/stella_to_tardis.ipynb → ...raction/converters/stella_to_tardis.ipynb
diff --git a/docs/running/interaction/custom_source.ipynb → docs/using/interaction/custom_source.ipynb b/docs/running/interaction/custom_source.ipynb → docs/using/interaction/custom_source.ipynb
diff --git a/docs/running/interaction/data/abund.dat → docs/using/interaction/data/abund.dat b/docs/running/interaction/data/abund.dat → docs/using/interaction/data/abund.dat
diff --git a/...ing/interaction/data/config_init_trad.yml → ...ing/interaction/data/config_init_trad.yml b/...ing/interaction/data/config_init_trad.yml → ...ing/interaction/data/config_init_trad.yml
diff --git a/.../interaction/data/config_no_init_trad.yml → .../interaction/data/config_no_init_trad.yml b/.../interaction/data/config_no_init_trad.yml → .../interaction/data/config_no_init_trad.yml
diff --git a/docs/running/interaction/data/density.txt → docs/using/interaction/data/density.txt b/docs/running/interaction/data/density.txt → docs/using/interaction/data/density.txt
diff --git a/docs/running/interaction/hdf_writer.ipynb → docs/using/interaction/hdf_writer.ipynb b/docs/running/interaction/hdf_writer.ipynb → docs/using/interaction/hdf_writer.ipynb
diff --git a/docs/running/interaction/index.rst → docs/using/interaction/index.rst b/docs/running/interaction/index.rst → docs/using/interaction/index.rst
diff --git a/docs/running/interaction/init_trad_bug.ipynb → docs/using/interaction/init_trad_bug.ipynb b/docs/running/interaction/init_trad_bug.ipynb → docs/using/interaction/init_trad_bug.ipynb
diff --git a/docs/running/interaction/integrator.ipynb → docs/using/interaction/integrator.ipynb b/docs/running/interaction/integrator.ipynb → docs/using/interaction/integrator.ipynb
diff --git a/...ing/interaction/isotope_pd_subclass.ipynb → ...ing/interaction/isotope_pd_subclass.ipynb b/...ing/interaction/isotope_pd_subclass.ipynb → ...ing/interaction/isotope_pd_subclass.ipynb
diff --git a/docs/running/interaction/old_gui.rst → docs/using/interaction/old_gui.rst b/docs/running/interaction/old_gui.rst → docs/using/interaction/old_gui.rst
diff --git a/...ing/interaction/physical_quantities.ipynb → ...ing/interaction/physical_quantities.ipynb b/...ing/interaction/physical_quantities.ipynb → ...ing/interaction/physical_quantities.ipynb
diff --git a/docs/running/interaction/tardis_example.yml → docs/using/interaction/tardis_example.yml b/docs/running/interaction/tardis_example.yml → docs/using/interaction/tardis_example.yml
diff --git a/docs/running/interaction/to_hdf.ipynb → docs/using/interaction/to_hdf.ipynb b/docs/running/interaction/to_hdf.ipynb → docs/using/interaction/to_hdf.ipynb
diff --git a/docs/running/interaction/to_hdf.rst → docs/using/interaction/to_hdf.rst b/docs/running/interaction/to_hdf.rst → docs/using/interaction/to_hdf.rst
diff --git a/...ing/interaction/using_formal_integral.rst → ...ing/interaction/using_formal_integral.rst b/...ing/interaction/using_formal_integral.rst → ...ing/interaction/using_formal_integral.rst
diff --git a/docs/running/tardis_example.yml → docs/using/tardis_example.yml b/docs/running/tardis_example.yml → docs/using/tardis_example.yml