Fixing JSON Schema not Rendering Properly in the Documentation (#1594)

* Fixing JSON Schema not rendering in the documentation

* Restructuring the configurational abstract

* Moving the documentation part to relevant sections

docs/using/components/configuration/configuration.rst

@@ -50,29 +50,52 @@ file type where the information is stored or a number of other sections.
 
 .. jsonschema:: schemas/model.yml
 
+Abundances
+^^^^^^^^^^
+The ``abundance`` section has a possible ``file`` parameter with ``type`` (currently only ``artis`` is allowed)
+and a ``name`` parameter giving a path to a file containing the abundance information.
+
+.. warning::
+    In contrast to the ``structure`` section, the ``abundance`` section will not ignore abundances set in the rest of
+    the section but merely will overwrite the abundances given in the file section.
+
+The rest of the section can be used to configure uniform abundances for all shells, by giving the atom name and a
+relative abundance fraction. If it does not add up to 1., TARDIS will warn --- but normalize the numbers.
+
+
+.. jsonschema:: schemas/model_definitions.yml#/definitions/abundances/file
+
+.. jsonschema:: schemas/model_definitions.yml#/definitions/abundances/uniform
+
+Structure
+^^^^^^^^^
 All types of ``structure`` definitions have two keywords in common: ``v_inner_boundary`` and ``v_outer_boundary``.
+
 In the ``structure`` section, one can specify a ``file`` section containing a ``type`` parameter
 (currently only ``artis`` is supported``) and a ``name`` parameter giving a path top a file.
 
 If one doesn't specify a ``file`` section, the code requires two sections (``velocities`` and ``densities``) and a
 parameter ``no_of_shells``. ``no_of_shells`` is the requested number of shells for a model. The ``velocity`` section
 requires a ``type``. Currently, only ``linear`` is supported.
 
+.. jsonschema:: schemas/model_definitions.yml#/definitions/structure/file
+
+.. jsonschema:: schemas/model_definitions.yml#/definitions/structure/specific
+
+Densities
+"""""""""
 In the ``densities`` section the ``type`` parameter again decides on the parameters. The type ``uniform`` only needs a
- ``value`` parameter with a density compatible quantity. The type ``branch85_w7`` uses a seven-order polynomial fit to
- the W7 model and is parametrised by time since explosion. The parameters ``time_0`` and ``density_coefficient`` are set
- to sensible defaults and should not be changed.
+``value`` parameter with a density compatible quantity. The type ``branch85_w7`` uses a seven-order polynomial fit to
+the W7 model and is parametrised by time since explosion. The parameters ``time_0`` and ``density_coefficient`` are set
+to sensible defaults and should not be changed.
 
-The ``abundance`` section again has a possible ``file`` parameter with ``type`` (currently only ``artis`` is allowed)
-and a ``name`` parameter giving a path to a file containing the abundance information.
+.. jsonschema:: schemas/model_definitions.yml#/definitions/density/branch85_w7
 
-.. warning::
-    In contrast to the ``structure`` section, the ``abundance`` section will not ignore abundances set in the rest of
-    the section but merely will overwrite the abundances given in the file section.
+.. jsonschema:: schemas/model_definitions.yml#/definitions/density/exponential
 
-The rest of the section can be used to configure uniform abundances for all shells, by giving the atom name and a
-relative abundance fraction. If it does not add up to 1., TARDIS will warn --- but normalize the numbers.
+.. jsonschema:: schemas/model_definitions.yml#/definitions/density/power_law
 
+.. jsonschema:: schemas/model_definitions.yml#/definitions/density/uniform
 
 
 Plasma
@@ -127,6 +150,10 @@ The ``montecarlo`` section describes the parameters for the Monte Carlo radiatio
 
 .. jsonschema:: schemas/montecarlo.yml
 
+.. jsonschema:: schemas/montecarlo_definitions.yml#/definitions/convergence_strategy/damped
+
+.. jsonschema:: schemas/montecarlo_definitions.yml#/definitions/convergence_strategy/custom
+
 The ``seed`` parameter seeds the random number generator first for the creation of the packets
 (:math:`\nu` and :math:`\mu`) and then the interactions in the actual Monte Carlo process.
 The ``no_of_packets`` parameter can take a float number for input convenience and gives the number of packets normally
@@ -143,8 +170,8 @@ All convergence criteria can be specified separately for the three variables for
 override the defaults.
 
 
-#. ``damped`` only has one parameter ``damping-constant`` and does not check for convergence. This can be used to fix the
-    temperature of the inner boundary (by increasing the ``convergence_criteria`` and
+``damped`` only has one parameter ``damping-constant`` and does not check for convergence. This can be used to fix the
+temperature of the inner boundary (by increasing the ``convergence_criteria`` and
 
 
 
@@ -162,10 +189,9 @@ just an integer. Finally, the method option selects the final spectral synthesis
 * integrated: use the :doc:`formal integral method <../../../physics/montecarlo/sourceintegration>` of Lucy 1999
 
 .. warning::
-
-  Currently, the "integrated" mode only works with the downbranching line
-  interaction mode. Note also the limitations listed at the bottom of the
-  dedicated page.
+    Currently, the "integrated" mode only works with the downbranching line
+    interaction mode. Note also the limitations listed at the bottom of the
+    dedicated page.
 
 
 .. include:: ../../example_data.inc

tardis/io/schemas/model.yml

@@ -4,171 +4,9 @@ additionalProperties: false
 properties:
   structure:
     oneOf:
-    - $ref: '#/definitions/structure/file'
-    - $ref: '#/definitions/structure/specific'
+    - $ref: 'model_definitions.yml#/definitions/structure/specific'
+    - $ref: 'model_definitions.yml#/definitions/structure/file'
   abundances:
     oneOf:
-    - $ref: '#/definitions/abundances/file'
-    - $ref: '#/definitions/abundances/uniform'
-
-definitions:
-  density:
-    branch85_w7:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - branch85_w7
-        w7_time_0:
-          type: quantity
-          default: 0.000231481 day
-          description: This needs no change - DO NOT TOUCH
-        w7_rho_0:
-          type: quantity
-          default: 3e29 g/cm^3
-          description: This needs no change - DO NOT TOUCH
-        w7_v_0:
-          type: quantity
-          default: 1 km/s
-          description: This needs no change - DO NOT TOUCH
-    exponential:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - exponential
-        time_0:
-          type: quantity
-          description: Time at which the pure model densities are right
-        rho_0:
-          type: quantity
-          description: density at time_0
-        v_0:
-          type: quantity
-          description: at what velocity the density rho_0 applies
-      required:
-      - rho_0
-      - v_0
-    power_law:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - power_law
-        time_0:
-          type: quantity
-          description: Time at which the pure model densities are right
-        rho_0:
-          type: quantity
-          description: density at time_0
-        v_0:
-          type: quantity
-          description: at what velocity the density rho_0 applies
-        exponent:
-          type: number
-          description: exponent for exponential density profile
-      required:
-      - rho_0
-      - v_0
-      - exponent
-    uniform:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - uniform
-        time_0:
-          type: quantity
-          description: Time at which the pure model densities are right
-        value:
-          type: quantity
-          description: value for uniform density
-      required:
-      - value
-  structure:
-    file:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - file
-        filename:
-          type: string
-          description: file name (with path) to structure model
-        filetype:
-          type: string
-          enum:
-          - simple_ascii
-          - artis
-          - cmfgen_model
-          description: file type
-        v_inner_boundary:
-          type: quantity
-          default: -1 km/s
-          description: location of the inner boundary chosen from the model
-        v_outer_boundary:
-          type: quantity
-          default: -1 km/s
-          description: location of the inner boundary chosen from the model
-      required:
-      - filename
-      - filetype
-    specific:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - specific
-        velocity:
-          type: object
-          properties:
-            start:
-              type: quantity
-            stop:
-              type: quantity
-            num:
-              type: number
-              multipleOf: 1.0
-          description: description of the boundaries of the shells
-        density:
-          oneOf:
-          - $ref: '#/definitions/density/branch85_w7'
-          - $ref: '#/definitions/density/exponential'
-          - $ref: '#/definitions/density/power_law'
-          - $ref: '#/definitions/density/uniform'
-      required:
-      - velocity
-      - density
-  abundances:
-    file:
-      type: object
-      additionalProperties: false
-      properties:
-        type:
-          enum:
-          - file
-        filetype:
-          type: string
-          description: type of abundance file to read in
-        filename:
-          type: string
-          description: filename
-      required:
-      - filetype
-      - filename
-    uniform:
-      type: object
-      properties:
-        type:
-          enum:
-          - uniform
-      additionalProperties:
-        type: number
-        minimum: 0
-        maximum: 1
+    - $ref: 'model_definitions.yml#/definitions/abundances/file'
+    - $ref: 'model_definitions.yml#/definitions/abundances/uniform'