Updating embedded links in docs with new file names "tutorial_" and "…

…how_to_" (#2578)

* updated embedded links with new file names, on Energy Packet Initialization and Model pages

* updating TOC trees on index pages with new file names

* went through all docs to update embedded links with new files names

docs/io/configuration/components/spectrum.rst

@@ -38,12 +38,12 @@ The following example shows how to edit variables for the different methods.
                         virtual_packet_logging: True
  
 
-One can also change these parameters as they wish by reading in the configuration file and editing them before running the simulation (see :doc:`Reading a Configuration <../read_configuration>`).
+One can also change these parameters as they wish by reading in the configuration file and editing them before running the simulation (see :doc:`Reading a Configuration <../tutorial_read_configuration>`).
 
 
 .. warning::
     As of now, the `method` argument serves no purpose other than adding 
     the integrated spectrum to the HDF output when "integrated" is used as the method
-    (see :doc:`Storing Simulations to HDF <../../output/to_hdf>`). 
+    (see :doc:`How to Store Simulations to HDF <../../output/how_to_to_hdf>`). 
 
 

docs/io/configuration/index.rst

@@ -16,4 +16,4 @@ file is valid, and demonstrates how a YAML configuration file is read in.
   components/index
   example
   config_validator
-  read_configuration
+  tutorial_read_configuration

docs/io/model/index.rst

@@ -7,5 +7,5 @@ TARDIS can read a variety of models. The following models are currently supporte
 .. toctree::
     :maxdepth: 1
 
-    read_stella_model.ipynb
-    read_cmfgen_model.ipynb
+    how_to_read_stella_model.ipynb
+    how_to_read_cmfgen_model.ipynb

docs/io/optional/index.rst

@@ -9,9 +9,9 @@ TARDIS also allows other inputs that are passed as keyword arguments into the ``
 .. toctree::
     :maxdepth: 1
 
-    custom_source
-    callback_example
-    logging_configuration
+    how_to_custom_source
+    tutorial_callback_example
+    tutorial_logging_configuration
 
 
 Additionally, ``run_tardis`` can take in a filepath for the atomic data and a boolean for virtual packet logging. For example:

docs/io/output/callback.rst

@@ -3,4 +3,4 @@ Callbacks
 *********
 
 Outputs can be customized using callbacks that are executed at the end of each Monte Carlo iteration. For more
-information, see :doc:`../optional/callback_example`.
+information, see :doc:`../optional/tutorial_callback_example`.

docs/io/output/index.rst

@@ -7,11 +7,11 @@ In addition to the widgets, TARDIS can output information in several other forms
 .. toctree::
     :maxdepth: 1
 
-    physical_quantities
+    how_to_physical_quantities
     access_iterations
-    to_hdf
+    how_to_to_hdf
     callback
     vpacket_logging
     progress_bars
-    rpacket_tracking
-    plasma_graph
+    how_to_rpacket_tracking
+    how_to_plasma_graph

docs/io/output/vpacket_logging.rst

@@ -38,22 +38,22 @@ After running the simulation, the following information can be retrieved:
     * - ``transport.virt_packet_last_interaction_type``
       - Numpy array
       - | Type of interaction that caused the virtual packets to be spawned
-        | (enum, see :doc:`physical_quantities`)
+        | (enum, see :doc:`how_to_physical_quantities`)
     * - ``transport.virt_packet_last_interaction_in_nu``
       - Numpy array
       - Frequencies of the r-packets which spawned the virtual packet
     * - ``transport.virt_packet_last_line_interaction_in_id``
       - Numpy array
       - | If the last interaction was a line interaction, the
         | line_interaction_in_id for that interaction 
-        | (see :doc:`physical_quantities`)
+        | (see :doc:`how_to_physical_quantities`)
     * - ``transport.virt_packet_last_line_interaction_out_id``
       - Numpy array
       - | If the last interaction was a line interaction, the
         | line_interaction_out_id for that interaction 
-        | (see :doc:`physical_quantities`)
+        | (see :doc:`how_to_physical_quantities`)
     * - ``transport.virt_packet_last_line_interaction_shell_id``
       - Numpy array
       - | If the last interaction was a line interaction, the
         | line_interaction_shell_id for that interaction 
-        | (see :doc:`physical_quantities`)
+        | (see :doc:`how_to_physical_quantities`)

docs/io/visualization/index.rst

@@ -12,9 +12,9 @@ diagnostic visualizations.
 .. toctree::
     :maxdepth: 2
 
-    sdec_plot
-    convergence_plot
-    montecarlo_packet_visualization
+    how_to_sdec_plot
+    tutorial_convergence_plot
+    tutorial_montecarlo_packet_visualization
 
 
 TARDIS Widgets (Graphical User Interfaces)
@@ -28,5 +28,5 @@ Jupyter Notebooks, making data exploration much easier.
     :maxdepth: 2
 
     using_widgets
-    Generating Custom Abundance Widget <abundance_widget>
-    Generating Data Exploration Widgets <generating_widgets>
+    Generating Custom Abundance Widget <how_to_abundance_widget>
+    Generating Data Exploration Widgets <how_to_generating_widgets>

docs/io/visualization/tutorial_montecarlo_packet_visualization.ipynb

@@ -14,7 +14,7 @@
    "metadata": {},
    "source": [
     "This visualization tool plots the `RPackets` that are generated by the [Montecarlo](https://tardis-sn.github.io/tardis/physics/montecarlo/index.html) method and creates an animated plot that contains the packet trajectories as they move away from the photosphere.\n",
-    "The properties of individual RPackets are taken from the [rpacket_tracker](https://tardis-sn.github.io/tardis/io/output/rpacket_tracking.html). "
+    "The properties of individual RPackets are taken from the [rpacket_tracker](https://tardis-sn.github.io/tardis/io/output/how_to_rpacket_tracking.html). "
    ]
   },
   {

docs/io/visualization/using_widgets.rst

@@ -4,8 +4,8 @@ Using TARDIS Widgets
 
 This page describes what each TARDIS Widget has to offer and how you can make
 the best use of it. If you're looking for the code to generate widgets, head
-over to `Generating Custom Abundance Widget <abundance_widget>`_ section or 
-`Generating Data Exploration Widgets <generating_widgets>`_ section to see the
+over to `Generating Custom Abundance Widget <how_to_abundance_widget>`_ section or 
+`Generating Data Exploration Widgets <how_to_generating_widgets>`_ section to see the
 notebook in action.
 
 Currently, TARDIS supports the following widgets:

docs/physics/intro/index.rst

@@ -9,7 +9,7 @@ How TARDIS Works
 
 The goal of TARDIS is, given input information about a supernova, to determine (i) properties of the plasma making up the supernova and (ii) the spectrum of light that is emitted from the supernova.
 
-The physics of TARDIS is in four major parts, which are summarized here and in the diagram below. First, the TARDIS simulation is set up (:doc:`../setup/index`) from a TARDIS configuration (see :doc:`here <../../io/configuration/read_configuration>` for how the configuration is created). This involves the creation of the supernova model and the initial conditions of the supernova's plasma, as well as initializing the Monte Carlo transport. Next is the Monte Carlo Iteration (:doc:`../montecarlo/index`) where the heart of TARDIS takes place; packets of light are sent through the supernova and tracked as they interact with matter. Next, TARDIS uses information from the Monte Carlo iteration to update properties of the plasma to eventually find the correct plasma state (:doc:`../update_and_conv/update_and_conv`). This process of doing a Monte Carlo iteration and then updating the plasma is repeated for a specified number of times or until certain aspects of the plasma state converge (as is also discussed in :doc:`../update_and_conv/update_and_conv`). After that, data generated in the Monte Carlo simulation is used to synthesize the output spectrum of the supernova (:doc:`../spectrum/index`).
+The physics of TARDIS is in four major parts, which are summarized here and in the diagram below. First, the TARDIS simulation is set up (:doc:`../setup/index`) from a TARDIS configuration (see :doc:`here <../../io/configuration/tutorial_read_configuration>` for how the configuration is created). This involves the creation of the supernova model and the initial conditions of the supernova's plasma, as well as initializing the Monte Carlo transport. Next is the Monte Carlo Iteration (:doc:`../montecarlo/index`) where the heart of TARDIS takes place; packets of light are sent through the supernova and tracked as they interact with matter. Next, TARDIS uses information from the Monte Carlo iteration to update properties of the plasma to eventually find the correct plasma state (:doc:`../update_and_conv/update_and_conv`). This process of doing a Monte Carlo iteration and then updating the plasma is repeated for a specified number of times or until certain aspects of the plasma state converge (as is also discussed in :doc:`../update_and_conv/update_and_conv`). After that, data generated in the Monte Carlo simulation is used to synthesize the output spectrum of the supernova (:doc:`../spectrum/index`).
 
 In the diagram, each physics step is shown in a box with the name of the step (bolded and underlined) along with the method that triggers the step (italicized) and the major components of the step. The reading of the configuration and the overall iterative process (comprising the Monte Carlo Iteration step and Updating Plasma and Convergence step) are also shown, again with the methods triggering these processes in italics.
 

docs/physics/montecarlo/initialization.ipynb

@@ -327,7 +327,7 @@
    "source": [
     "## Custom Packet Source\n",
     "\n",
-    "TARDIS allows for the user to input a custom function that generates energy packets instead of the basic blackbody source described here. See [Running TARDIS with a Custom Packet Source](../../io/optional/custom_source.ipynb) for more information.\n"
+    "TARDIS allows for the user to input a custom function that generates energy packets instead of the basic blackbody source described here. See [How to Run TARDIS with a Custom Packet Source](../../io/optional/how_to_custom_source.ipynb) for more information."
    ]
   }
  ],

docs/physics/setup/model.ipynb

@@ -9,9 +9,9 @@
     "\n",
     "As shown previously, when `Simulation.from_config()` is called, a `SimulationState` object is created. This is done via the class method `SimulationState.from_config()`. This model object contains important information about the shell structure, density, abundance, radiative temperature, and dilution factor throughout the supernova.\n",
     "\n",
-    "Throughout this notebook, we show various configuration inputs into the TARDIS model and the resulting model. In interactive mode, these parameters can be varied to explore how the model changes. Editing configuration parameters in the notebook is explained [here](../../io/configuration/read_configuration.ipynb).\n",
+    "Throughout this notebook, we show various configuration inputs into the TARDIS model and the resulting model. In interactive mode, these parameters can be varied to explore how the model changes. Editing configuration parameters in the notebook is explained [here](../../io/configuration/tutorial_read_configuration.ipynb).\n",
     "\n",
-    "This notebook is based on the [built-in TARDIS models](../../io/configuration/components/models/index.rst#built-in-structure-density-and-abundance), but these parameters can also be input via [custom model configurations](../../io/configuration/components/models/index.rst#custom-model-configurations), the [CSVY model](../../io/configuration/components/models/index.rst#csvy-model) or the [custom abundance widget](../../io/visualization/abundance_widget.ipynb).\n",
+    "This notebook is based on the [built-in TARDIS models](../../io/configuration/components/models/index.rst#built-in-structure-density-and-abundance), but these parameters can also be input via [custom model configurations](../../io/configuration/components/models/index.rst#custom-model-configurations), the [CSVY model](../../io/configuration/components/models/index.rst#csvy-model) or the [custom abundance widget](../../io/visualization/how_to_abundance_widget.ipynb).\n",
     "\n",
     "## Shell Structure\n",
     "\n",
@@ -131,7 +131,7 @@
     "    \n",
     "Note\n",
     "\n",
-    "Using the built-in shell structure, as shown here, the shells are all equally spaced. This is not necessarily the case if one uses the [file structure](../../io/configuration/components/models/index.rst#file-structure), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), or [custom abundance widget](../../io/visualization/abundance_widget.ipynb).\n",
+    "Using the built-in shell structure, as shown here, the shells are all equally spaced. This is not necessarily the case if one uses the [file structure](../../io/configuration/components/models/index.rst#file-structure), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), or [custom abundance widget](../../io/visualization/how_to_abundance_widget.ipynb).\n",
     "\n",
     "</div>"
    ]
@@ -143,7 +143,7 @@
    "source": [
     "## Density\n",
     "\n",
-    "We now look at how TARDIS models the density inside each shell. If you use the [built-in densities](../../io/configuration/components/models/index.rst#density), TARDIS allows you to choose between the four models discussed below. The [file structure](../../io/configuration/components/models/index.rst#file-structure), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), and [custom abundance widget](../../io/visualization/abundance_widget.ipynb) options allow more freedom in assigning densities to each shell.\n",
+    "We now look at how TARDIS models the density inside each shell. If you use the [built-in densities](../../io/configuration/components/models/index.rst#density), TARDIS allows you to choose between the four models discussed below. The [file structure](../../io/configuration/components/models/index.rst#file-structure), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), and [custom abundance widget](../../io/visualization/how_to_abundance_widget.ipynb) options allow more freedom in assigning densities to each shell.\n",
     "\n",
     "In general, the density in the supernova at a specific moment in time is a function of the radius or velocity of the ejecta (either can be used, since the radius and velocity are linearly related at any moment of time). Since the shell velocities do not change over time, it is more simple to write the densities as a function of ejecta velocity. If we do this, the time-dependence of the density is simple. We know the total mass of the ejecta is constant in each shell due to the nature of homologous expansion. The inner and outer radii of each shell increase linearly over time, meaning the volume increases as time cubed. Since density is mass divided by volume, the density is inverse-cubic in time. Mathematically, if $\\rho(v,t_\\mathrm{explosion})$ is the density at a velocity $v$ after a time $t_\\mathrm{explosion}$, given some characteristic time $t_0$, we have\n",
     "\n",
@@ -398,7 +398,7 @@
     "\n",
     "The `SimulationState` also carries important information about elemental abundances in each shell. These are mass abundances -- that is, the abundance of oxygen is the fraction of the shell's mass that is made up of oxygen.\n",
     "\n",
-    "The only built-in abundance model that TARDIS offers is a uniform abundance, meaning each shell has identical abundances. Like density, however, the [file abundance](../../io/configuration/components/models/index.rst#file-abundance), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), and [custom abundance widget](../../io/visualization/abundance_widget.ipynb) methods allow users more freedom with assigning different abundances in each shell.\n",
+    "The only built-in abundance model that TARDIS offers is a uniform abundance, meaning each shell has identical abundances. Like density, however, the [file abundance](../../io/configuration/components/models/index.rst#file-abundance), [CSVY model](../../io/configuration/components/models/index.rst#csvy-model), and [custom abundance widget](../../io/visualization/how_to_abundance_widget.ipynb) methods allow users more freedom with assigning different abundances in each shell.\n",
     "\n",
     "A table of abundances in each shell is stored in the `abundance` attribute of the `SimulationState` object.\n",
     "\n",

docs/physics/setup/setup_example.ipynb

@@ -33,7 +33,7 @@
    "id": "97737e54",
    "metadata": {},
    "source": [
-    "We read a configuration as shown [here](../../io/configuration/read_configuration.ipynb):"
+    "We read a configuration as shown [here](../../io/configuration/tutorial_read_configuration.ipynb):"
    ]
   },
   {

docs/physics/update_and_conv/update_and_conv.ipynb

@@ -111,9 +111,9 @@
    "source": [
     "## Convergence Information\n",
     "\n",
-    "During the simulation, information about the how $T_\\mathrm{rad}$, $W$, and $T_\\mathrm{inner}$ are updated as well as a comparison of the total output luminosity and the requested luminosity are logged at the INFO level (see [Configuring the Logging Output for TARDIS](../../io/optional/logging_configuration.ipynb)) as shown in the code below, to give users a better idea of how the convergence process is working.\n",
+    "During the simulation, information about the how $T_\\mathrm{rad}$, $W$, and $T_\\mathrm{inner}$ are updated as well as a comparison of the total output luminosity and the requested luminosity are logged at the INFO level (see [Configuring the Logging Output for TARDIS](../../io/optional/tutorial_logging_configuration.ipynb)) as shown in the code below, to give users a better idea of how the convergence process is working.\n",
     "\n",
-    "In addition, TARDIS allows for the displaying of convergence plots, which allows users to visualize the convergence process for $T_\\mathrm{rad}$, $W$, $T_\\mathrm{inner}$, and the total luminosity of the supernova being modeled. For more information, see [Convergence Plots](../../io/visualization/convergence_plot.ipynb)."
+    "In addition, TARDIS allows for the displaying of convergence plots, which allows users to visualize the convergence process for $T_\\mathrm{rad}$, $W$, $T_\\mathrm{inner}$, and the total luminosity of the supernova being modeled. For more information, see [Convergence Plots](../../io/visualization/tutorial_convergence_plot.ipynb)."
    ]
   },
   {

docs/quickstart.ipynb

@@ -102,7 +102,7 @@
     "\n",
     "**Note:**\n",
     "\n",
-    "Get more information about the [progress bars](io/output/progress_bars.rst), [logging configuration](io/optional/logging_configuration.ipynb), and [convergence plots](io/visualization/convergence_plot.ipynb). \n",
+    "Get more information about the [progress bars](io/output/progress_bars.rst), [logging configuration](io/optional/tutorial_logging_configuration.ipynb), and [convergence plots](io/visualization/tutorial_convergence_plot.ipynb). \n",
     "    \n",
     "</div>"
    ]