InstituteforDiseaseModeling · jonathanhhb · Oct 2, 2023 · Sep 14, 2023 · Sep 14, 2023 · Sep 14, 2023
diff --git a/.gitignore b/.gitignore
@@ -70,7 +70,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/emodpy-typhoid*.rst
+docs/emodpy_typhoid*.rst
 docs/modules.rst
 
 # PyBuilder

diff --git a/docs/_templates/breadcrumbs.html b/docs/_templates/breadcrumbs.html
@@ -1,9 +1,9 @@
 {% extends '!breadcrumbs.html' %}
 {% block breadcrumbs %}
     <li><a href="https://idmod.org/documentation">IDM docs</a> &raquo;</li>
-    <li><a href="{{ pathto(master_doc) }}">emodpy-malaria</a> &raquo;</li>
+    <li><a href="{{ pathto(master_doc) }}">emodpy-typhoid</a> &raquo;</li>
     {% for doc in parents %}
         <li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
     {% endfor %}
     <li>{{ title }}</li>
-{% endblock %}
+{% endblock %}
diff --git a/docs/_templates/footer.html b/docs/_templates/footer.html
@@ -1,8 +1,8 @@
 {% extends '!footer.html' %}
 {% block extrafooter %}
-<p>emodpy-malaria is licensed under the <a href="https://creativecommons.org/licenses/by-sa/4.0/legalcode">Creative Commons
+<p>emodpy-typhoid is licensed under the <a href="https://creativecommons.org/licenses/by-sa/4.0/legalcode">Creative Commons
     Attribution-ShareAlike 4.0 International License</a>.</p>
 <p>Send documentation feedback to <a href="mailto:[email protected]" target="_top">[email protected]</a></p>
 <p><a href="https://www.gatesfoundation.org/Privacy-and-Cookies-Notice">Privacy and Cookies Notice</a>&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;
 <a href="https://www.gatesfoundation.org/Terms-of-Use">Terms of Use</a></p>
-{% endblock %}
+{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
@@ -29,7 +29,7 @@
 else:
     subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__)))
 
-# Rename "emodpy-malaria" to "API reference"
+# Rename "emodpy-typhoid" to "API reference"
 filename = 'modules.rst' # This must match the Makefile
 with open(filename) as f: # Read existing file
     lines = f.readlines()
@@ -59,10 +59,27 @@
     'sphinx_copybutton',
     'sphinx.ext.intersphinx',
     'sphinxext.remoteliteralinclude',
-    'myst_parser',
-    'sphinx_search.extension'
+    'myst_parser', # source files written in MD or RST
+    'sphinx_search.extension', # search across entire IDM docs domain
+    'sphinx.ext.viewcode' # link to view source code
 ]
 
+myst_enable_extensions = [
+    "amsmath",
+    "attrs_inline",
+    "colon_fence",
+    "deflist",
+    "dollarmath",
+    "fieldlist",
+    "html_admonition",
+    "html_image",
+    "linkify",
+    "replacements",
+    "smartquotes",
+    "strikethrough",
+    "substitution",
+    "tasklist",
+]
 plantuml = 'plantweb'
 
 autodoc_default_options = {
@@ -208,15 +225,14 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
+
 html_static_path = ['_static']
 
-html_context = {
-    'css_files': [
-        '_static/theme_overrides.css',
-        '_static/copy_button.css'
-        ]
-}
-html_js_files = ['show_block_by_os.js']
+html_css_files = ['theme_overrides.css']
+
+html_js_files = ['show_block_by_os.js'] 
+
+
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the docs.
@@ -310,7 +326,7 @@
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'emodpy-malaria'
+htmlhelp_basename = 'emodpy-typhoid'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -336,7 +352,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'emodpy-malaria-docs.tex', u'emodpy-malaria',
+    (master_doc, 'emodpy-typhoid-docs.tex', u'emodpy-typhoid',
      u'Institute for Disease Modeling', 'manual'),
 ]
 
@@ -378,7 +394,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria',
+    (master_doc, 'emodpy-typhoid-docs', u'emodpy-typhoid',
      [author], 1)
 ]
 
@@ -392,8 +408,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria',
-     author, 'Institute for Disease Modeling', 'How to use emodpy for malaria simulations.',
+    (master_doc, 'emodpy-typhoid-docs', u'emodpy-typhoid',
+     author, 'Institute for Disease Modeling', 'How to use emodpy for typhoid simulations.',
      'Miscellaneous'),
 ]
 
@@ -420,6 +436,6 @@
                        'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None),
                        'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None),
                        'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None),
-                       'emod-malaria': ('https://docs.idmod.org/projects/emod-malaria/en/latest/', None),
+                       'emod-typhoid': ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', None),
                        'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None)
-                       }
+                       }
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,13 +3,13 @@
 ==============================
 
 |EMODPY_typhoid| is a collection of Python scripts and utilities created to
-streamline user interactions with |EMOD_s| and |IT_s| for modeling malaria.
+streamline user interactions with |EMOD_s| and |IT_s| for modeling typhoid.
 Much of  the functionality is inherited from the
 :doc:`emod_api:emod_api` and :doc:`emodpy:emodpy`.
 
 Additional information about how to use |IT_s| can be found in
-:doc:`idmtools:index`.  Additional information about |EMOD_s| malaria
-parameters can be found in :doc:`emod-malaria:parameter-overview`.
+:doc:`idmtools:index`.  Additional information about |EMOD_s| typhoid
+parameters can be found in :doc:`emod-typhoid:parameter-overview`.
 
 See :doc:`idmtools:index` for a diagram showing how |IT_s| and each of the
 related packages are used in an end-to-end workflow using |EMOD_s| as the

diff --git a/docs/variables.txt b/docs/variables.txt
@@ -16,7 +16,7 @@
 
 .. |IDM_l| replace:: Institute for Disease Modeling (IDM)
 .. |EMODPY_s| replace:: emodpy
-.. |EMODPY_typhoid| replace:: typhoid
+.. |EMODPY_typhoid| replace:: emodpy-typhoid
 .. |emod_api| replace:: emod-api
 .. |IDM_s| replace:: IDM
 .. |EMOD_l| replace:: Epidemiological MODeling software (EMOD)

diff --git a/emodpy_typhoid/config.py b/emodpy_typhoid/config.py
@@ -0,0 +1,12 @@
+def cleanup_for_2018_mode( config ):
+    # when using 2018 binary
+    config.parameters.pop( "Serialized_Population_Filenames" )
+    config.parameters.pop( "Serialization_Time_Steps" )
+    config.parameters.pop( "Demographics_Filename" )
+
+    config.parameters.Incubation_Period_Distribution = "FIXED_DURATION" # hack
+    config.parameters.Infectious_Period_Distribution = "FIXED_DURATION" # hack
+    config.parameters.Base_Incubation_Period = 1
+    config.parameters.Base_Infectious_Period = 1
+    config.parameters["Listed_Events"] = []
+
diff --git a/emodpy_typhoid/demographics/TyphoidDemographics.py b/emodpy_typhoid/demographics/TyphoidDemographics.py
@@ -9,6 +9,10 @@ class TyphoidDemographics(Demographics):
     """
     def __init__(self, nodes, idref="Gridded world grump2.5arcmin", base_file=None):
         super().__init__( nodes, idref, base_file )
+        # The following is for back-compat with older versions of the model which looked for these keys unconditionally.
+        self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistributionFlag"] = 0
+        self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution1"] = 0
+        self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution2"] = 0
         #super().SetDefaultProperties()
 
 def fromBasicNode(lat=0, lon=0, pop=1e6, name=1, forced_id=1):
@@ -77,7 +81,7 @@ def from_csv( pop_filename_in, site="No_Site", min_node_pop = 0 ):
         site: A string to identify the country, village, or trial site.
 
     Returns:
-        A :py:class:`~emodpy_malaria.demographics.MalariaDemographics` instance.
+        A :py:class:`~emodpy_typhoid.demographics.MalariaDemographics` instance.
     """
     typhoid_demog = Demog.from_csv( pop_filename_in )
     nodes = []

diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py
@@ -3,18 +3,36 @@
 from emod_api.interventions import common
 import json
 
-def new_intervention( camp, efficacy=1.0, mode="Shedding" ):
-    """
-    TyphoidVaccine intervention wrapper. Just the intervention. No configuration yet.
+def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, decay_constant=6935.0 ):
     """
+     Create a new TyphoidVaccine intervention with specified parameters. If you use this function directly, you'll need to distribute the intervention with a function like ScheduledCampaignEvent or TriggeredCampaignEvent from emod_api.interventions.common.
+
+     Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Shedding".
+         constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
+         decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
+
+     Returns:
+         TyphoidVaccine: A fully configured instance of the TyphoidVaccine intervention with the specified parameters.
+     """
+
     intervention = s2c.get_class_with_defaults( "TyphoidVaccine", camp.schema_path )
     intervention.Effect = efficacy
     intervention.Mode = mode
-    # WaningEffect is TBD.
+    intervention.Changing_Effect = s2c.get_class_with_defaults( "WaningEffectBoxExponential" )
+    intervention.Changing_Effect.Initial_Effect = efficacy
+    intervention.Changing_Effect.Box_Duration = constant_period
+    intervention.Changing_Effect.Decay_Time_Constant = decay_constant
     return intervention
 
 def new_triggered_intervention( 
         camp, 
+        efficacy=0.82,
+        mode="Shedding",
+        constant_period=0,
+        decay_constant=6935.0,
         start_day=1, 
         triggers=[ "Births" ],
         coverage=1.0, 
@@ -23,29 +41,62 @@ def new_triggered_intervention(
         co_event=None # expansion slot
     ):
     """
-    Distribute TyphoidVaccine when something happens as determined by a signal published from the
-    model or another campaign event.
+    Create a new triggered TyphoidVaccine intervention based on specified parameters.
+
+    Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Shedding".
+         constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
+         decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
+         start_day (int, optional): The day on which the intervention starts. Default is 1.
+         triggers (list, optional): List of triggers for the intervention. Default is ["Births"].
+         coverage (float, optional): Demographic coverage of the intervention. Default is 1.0.
+         node_ids (list, optional): List of node IDs where the intervention is applied. Default is None.
+         property_restrictions_list (list, optional): List of property restrictions for the intervention. Default is an empty list.
+         co_event (None, optional): Expansion slot for future use.
+
+     Returns:
+         TriggeredCampaignEvent: An instance of a triggered campaign event with the TyphoidVaccine intervention.
     """
-    iv = new_intervention( camp )
+    iv = new_intervention( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
 
-    #event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=[ act_intervention, bcast_intervention ], Node_Ids=nodeIDs, Property_Restrictions=property_restrictions_list )
     event = common.TriggeredCampaignEvent( camp, Start_Day=start_day, Triggers=triggers, Demographic_Coverage=coverage, Intervention_List=[ iv ], Node_Ids=node_ids, Property_Restrictions=property_restrictions_list, Event_Name="Triggered Typhoid Vax" )
 
     return event
 
 def new_scheduled_intervention( 
         camp, 
+        efficacy=0.82,
+        mode="Shedding",
+        constant_period=0,
+        decay_constant=6935.0,
         start_day=1, 
         coverage=1.0, 
         node_ids=None,
         property_restrictions_list=[],
         co_event=None # expansion slot
     ):
     """
-    Distribute TyphoidVaccine when something happens as determined by a signal published from the
-    model or another campaign event.
+    Create a new scheduled TyphoidVaccine intervention based on specified parameters.
+
+    Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Shedding".
+         constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
+         decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
+         start_day (int, optional): The day on which the intervention starts. Default is 1.
+         coverage (float, optional): Demographic coverage of the intervention. Default is 1.0.
+         node_ids (list, optional): List of node IDs where the intervention is applied. Default is None.
+         property_restrictions_list (list, optional): List of property restrictions for the intervention. Default is an empty list.
+         co_event (None, optional): Expansion slot for future use.
+
+     Returns:
+         ScheduledCampaignEvent: An instance of a scheduled campaign event with the TyphoidVaccine intervention.
+
     """
-    iv = new_intervention( camp )
+    iv = new_intervention( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
 
     #event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=[ act_intervention, bcast_intervention ], Node_Ids=nodeIDs, Property_Restrictions=property_restrictions_list )
     event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=[ iv ], Node_Ids=node_ids, Property_Restrictions=property_restrictions_list )
@@ -54,7 +105,7 @@ def new_scheduled_intervention(
 
 def new_intervention_as_file( camp, start_day, filename=None ):
     import emod_api.campaign as camp
-    camp.add( new_triggered_intervention( camp, start_day ), first=True )
+    camp.add( new_triggered_intervention( camp, start_day=start_day ), first=True )
     if filename is None:
         filename = "TyphoidVaccine.json"
     camp.save( filename )