Adding script for generating table of parameters

[matt-graham]

Work in progress but should resolve #1419

Script can be run from root of respository with

python docs/tlo_parameters.py resources parameters.md

with this generating a Markdown output parameters.md which can be converted to HTML with

pandoc -s parameters.md -o parameters.html --css pandoc.css --self-contained

using CSS from https://gist.github.com/killercup/5917178

I'll hopefully be able to get this to also output reStructuredText to allow running as part of the documentation build and including on the website.

[tbhallett]

I've made an edit to make the pagination more manageable (by excluding two parameters, which are really just datasets). Also, excluded the Wasting module that has no parameters.

Subject: [PATCH] exclude wasting and exclude certain parameters
---
Index: docs/tlo_parameters.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/docs/tlo_parameters.py b/docs/tlo_parameters.py
--- a/docs/tlo_parameters.py    (revision de44e443565ff02dfd836db4a40e101a792866e2)
+++ b/docs/tlo_parameters.py    (revision 8b315ded68f4bd4bcdaa8f1c6a152f1cfb696886)
@@ -73,6 +73,7 @@
     modules: Iterable[Module],
     overriden_parameters: dict[str, dict[str, ParameterValue]],
     excluded_modules: set[str],
+    excluded_parameters: dict[str, str],
     max_inline_parameter_length: int = 10,
 ) -> tuple[ModuleParameterTablesDict, ModuleStructuredParametersDict]:
     module_parameter_tables = {}
@@ -83,6 +84,8 @@
         parameter_records = []
         module_structured_parameters[module.name] = {}
         for parameter_name, parameter in module.PARAMETERS.items():
+            if parameter_name in excluded_parameters.get(module.name, set()):
+                continue
             if (
                 module.name in overriden_parameters
                 and parameter_name in overriden_parameters[module.name]
@@ -225,7 +228,9 @@
     status_quo_parameters = get_parameters_for_status_quo()
     simulation.register(*fullmodel.fullmodel(args.resource_file_path))
     module_parameter_tables, module_structured_parameters = get_parameter_tables(
-        simulation.modules.values(), status_quo_parameters, {"HealthBurden"}
+        simulation.modules.values(), status_quo_parameters, {"HealthBurden", "Wasting"},
+        {"Demography": "gbd_causes_of_death_data",
+         "Tb": "who_incidence_estimates"}
     )
     write_parameters_markdown_file(
         args.output_file_path, module_parameter_tables, module_structured_parameters

[matt-graham]

Thanks @tbhallett - I've applied the patch you suggested and also now updated to allow outputting a reStructuredText file as well as Markdown to allow inclusion in our docs, and updated the docs build to automatically generate this page.

[tbhallett]

Thanks @matt-graham -- that's brilliant and very timely. It will be great to have this on the website.

[matt-graham]

@tbhallett just to check are you happy for this to be merged in? Know that you already approved but as I made a few subsequent changes after that wanted to make sure!

[tbhallett]

Yes please do merge in. Thanks again. And, if you can, please could you also regenerate the website so that it appears there?