Merge pull request #1379 from smithis7/reorganizing_2

Reorganizing files in docs (2/2)
tardis-sn · Dec 11, 2020 · ce5b665 · ce5b665
2 parents 6565a80 + 9ffee87
commit ce5b665
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Showing 84 changed files with 14 additions and 824 deletions.
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@@ -11,4 +11,4 @@ Old Physics Section (Outdated)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