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/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/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/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/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>"
    ]