added back all links to EMOD dev docs and fixed broken links to origi…

…nal emod-malaria doc URLs
InstituteforDiseaseModeling · Sep 25, 2024 · 85e5a56 · 85e5a56
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diff --git a/docs/conf.py b/docs/conf.py
@@ -473,9 +473,8 @@ def setup(app):
  '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),
  'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None),
  'emod-generic': ('https://docs.idmod.org/projects/emod-generic/en/latest/', None),
- 'emod-hiv': ('https://docs.idmod.org/projects/emod-hiv/en/latest/', None)
+ 'emod': ('https://docs.idmod.org/projects/emod/en/latest/', None)
  }
 
diff --git a/docs/emod/install-linux.rst b/docs/emod/install-linux.rst
@@ -10,9 +10,8 @@ install Python virtual environments, software to plot the output of simulations,
 .. include:: ../reuse/testing-linux.txt
 
 
-.. If you want to download and modify the |EMOD_s| source code and build the |linux_binary|
- yourself, see :doc:`dev-install-overview`.
-.. TODO add link back
+If you want to download and modify the |EMOD_s| source code and build the |linux_binary|
+yourself, see :doc:`emod:dev-install-overview`.
 
 .. contents::
  :local:
@@ -33,8 +32,7 @@ The script provides the option to install input files that describe the demograp
 climate of many different locations across the world. While the script installs a pre-built version
 of the |linux_binary|, it also provides the option of installing the |EMOD_s| source code. 
 
-.. For information on building the |linux_binary| from source code, see :doc:`dev-install-overview`.
-.. TODO: add link to dev docset when set up
+For information on building the |linux_binary| from source code, see :doc:`emod:dev-install-overview`.
 
 .. include:: ../reuse/centos-install-to-run.txt
 

diff --git a/docs/emod/install-overview.rst b/docs/emod/install-overview.rst
@@ -7,12 +7,9 @@ Install |EMOD_s|
 system, there are relatively few prerequisites required and the |exe_l| or |linux_binary| is 
 pre-built from the latest |EMOD_s| source code release. After completing installation, you can run
 simulations locally or on an HPC cluster using real-world data.
-
-
-
-.. TODO add link once dev docs set up 
-.. If you want to download and modify the |EMOD_s| source code and build the |exe_s| or |linux_binary|
- yourself, see :doc:`dev-install-overview`.
+
+If you want to download and modify the |EMOD_s| source code and build the |exe_s| or |linux_binary|
+yourself, see :doc:`emod:dev-install-overview`.
 
 
 .. toctree::

diff --git a/docs/emod/install-windows.rst b/docs/emod/install-windows.rst
@@ -9,10 +9,8 @@ install Python virtual environments, software to plot the output of simulations,
 
 .. include:: ../reuse/testing-windows.txt
 
-.. If you want to download and modify the |EMOD_s| source code and build the |exe_s|
- yourself, see :doc:`dev-install-overview`.
-
-.. TODO: add link to dev content when set up
+If you want to download and modify the |EMOD_s| source code and build the |exe_s|
+yourself, see :doc:`emod:dev-install-overview`.
 
 .. contents::
  :local:

diff --git a/docs/emod/parameter-campaign-event-broadcastcoordinatorevent.rst b/docs/emod/parameter-campaign-event-broadcastcoordinatorevent.rst
@@ -4,7 +4,7 @@ BroadcastCoordinatorEvent
 
 The **BroadcastCoordinatorEvent** coordinator class broadcasts the event you specify. This can be used with the campaign class, :doc:`parameter-campaign-event-surveillanceeventcoordinator`, that can monitor and listen for events received from **BroadcastCoordinatorEvent** and then perform an action based on the broadcasted event. You can also use this for the reporting of the broadcasted events by setting the configuraton parameters, **Report_Node_Event_Recorder** and **Report_Surveillance_Event_Recorder**, which listen to events to be recorded. You must use this coordinator class with listeners that are operating on the same core. 
 
-.. TODO add link once dev docs set up. For more information, see :doc:`dev-architecture-core`.
+For more information, see :doc:`emod:dev-architecture-core`.
 
 .. include:: ../reuse/warning-case.txt
 

diff --git a/docs/emod/parameter-campaign-individual-outbreakindividual.rst b/docs/emod/parameter-campaign-individual-outbreakindividual.rst
@@ -7,7 +7,7 @@ with the simulation type to existing individuals using the individual targeted f
 in the appropriate event coordinator. To instead add new infection individuals, use :doc:`parameter-campaign-node-outbreak`.
 
 Note, when using **Malaria_Model**: MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS, do not use
-this intervention class. Instead, use :doc:`emod-malaria:parameter-campaign-individual-outbreakindividualmalariagenetics`.
+this intervention class. Instead, use :doc:`parameter-campaign-individual-outbreakindividualmalariagenetics`.
 
 .. include:: ../reuse/warning-case.txt
 

diff --git a/docs/emod/parameter-campaign-node-broadcastcoordinatoreventfromnode.rst b/docs/emod/parameter-campaign-node-broadcastcoordinatoreventfromnode.rst
@@ -12,7 +12,7 @@ that a **TriggeredEventCoordinator** is listening for. One can use the
 **Report_Coordinator_Event_Recorder** to report on the events broadcasted by this intervention. 
 Note, this coordinator class must be used with listeners that are operating on the same core. 
 
-.. TODO add link once dev docs set up. For more information, see :doc:`dev-architecture-core`.
+For more information, see :doc:`emod:dev-architecture-core`.
 
 .. include:: ../reuse/warning-case.txt
 

diff --git a/docs/emod/parameter-campaign-node-broadcastnodeevent.rst b/docs/emod/parameter-campaign-node-broadcastnodeevent.rst
@@ -11,7 +11,7 @@ configuraton parameters, **Report_Node_Event_Recorder** and **Report_Surveillanc
 which listen to events to be recorded. You must use this coordinator class with listeners that are
 operating on the same core. You can also use :doc:`parameter-campaign-node-nlhtivnode`.
 
-.. TODO add link once dev docs set up. For more information, see :doc:`dev-architecture-core`.
+For more information, see :doc:`emod:dev-architecture-core`.
 
 .. include:: ../reuse/warning-case.txt
 

diff --git a/docs/emod/parameter-campaign-waningeffects.rst b/docs/emod/parameter-campaign-waningeffects.rst
@@ -97,7 +97,7 @@ WaningEffectMapCount
 ====================
 
 The **WaningEffectMapCount** class assigns a probability to a particular update of the effect. This
-typically used with :doc:`emod-malaria:parameter-campaign-individual-adherentdrug` so one can assign a
+typically used with :doc:`parameter-campaign-individual-adherentdrug` so one can assign a
 probability that a person takes a particular dose. The **Times** value should be integers starting
 from 1 and increasing.
 

diff --git a/docs/emod/software-error-logging.rst b/docs/emod/software-error-logging.rst
@@ -81,10 +81,7 @@ the files in use, as well as other initialization information, including the def
 and the logging levels set for particular modules. The file follows that information
 with log output using the following format: <timestep><HPC rank><log level><module><message>.
 
-By default, the logging level is set to "INFO". 
-
-.. TODO add a link once the dev docs are set up
-.. If you want to change the logging level, see :doc:`dev-logging`.
+By default, the logging level is set to "INFO". If you want to change the logging level, see :doc:`emod:dev-logging`.
 
 For example::
 

diff --git a/docs/emod/software-run-simulation.rst b/docs/emod/software-run-simulation.rst
@@ -43,8 +43,12 @@ You can run a simulation locally from Visual Studio using the built-in debugger.
 to put in breakpoints and step through the code while inspecting the values of different state
 variables throughout the simulation.
 
-.. TODO add link to dev docs when set up
-.. You can use regression_test.py in the GitHub Regression_ directory to run multiple simulations on a cluster, including running the suite of regression tests run by the |IDM_s| testing team. For more information, see :doc:`dev-regression`. _Regression: https://github.com/InstituteforDiseaseModeling/EMOD/tree/master/Regression
+You can use regression_test.py in the GitHub Regression_ directory to run
+multiple simulations on a cluster, including running the suite of regression
+tests run by the |IDM_s| testing team. For more information,
+see :doc:`emod:dev-regression`. 
+
+.. _Regression: https://github.com/InstituteforDiseaseModeling/EMOD/tree/master/Regression
 
 
 Directory structure

diff --git a/docs/emod/software-simulation-mpiexec.rst b/docs/emod/software-simulation-mpiexec.rst
@@ -14,7 +14,7 @@ often used to run complex simulations in parallel on an HPC cluster or several l
 Mpiexec is part of the |HPC_SDK_supp| installed as a prerequisite for building |exe_s| from the
 |EMOD_s| source code. 
 
-.. TODO add link to dev docs. Also see if this topic is relevant anymore. See :doc:`dev-install-overview` for more information.
+See :doc:`emod:dev-install-overview` for more information.
 
 .. note::
 

diff --git a/docs/emod/troubleshooting.rst b/docs/emod/troubleshooting.rst
@@ -9,7 +9,7 @@ If you need assistance, you can contact support for help with solving issues. Yo
 |IDM_l| support at [email protected]. When submitting the issue, please include any error
 information. 
 
-.. TODO add link to dev docs when set up. See :doc:`dev-debugging-overview` for troubleshooting issues when attempting to build |exe_s| or |linux_binary|.
+See :doc:`emod:dev-debugging-overview` for troubleshooting issues when attempting to build |exe_s| or |linux_binary|.
 
 .. contents:: Contents
  :local:

diff --git a/docs/faq.rst b/docs/faq.rst
@@ -299,10 +299,10 @@ dynamics, behavior, or treatment based on the assigned values. For example, you
 properties to represent vitamin deficiencies, comorbidities, and more. For more information, see
 :doc:`emod/model-properties`.
 
-.. If individual and node properties cannot incorporate the functionality you need, |EMOD_s| is
- open-source software that can be extended to meet your needs. For more information, see 
- :doc:`dev-install-overview`.
-.. TODO: add links to developer docs when set up
+If individual and node properties cannot incorporate the functionality you need, |EMOD_s| is
+open-source software that can be extended to meet your needs. For more information, see 
+:doc:`emod:dev-install-overview`.
+
 
 Can I model regions, countries, provinces, or cities? 
 =====================================================

diff --git a/docs/index.rst b/docs/index.rst
@@ -45,7 +45,7 @@ Much of the functionality is inherited from the
 
 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`.
+parameters can be found in :doc:`emod/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/emodpy_malaria/demographics/MalariaDemographics.py b/emodpy_malaria/demographics/MalariaDemographics.py
@@ -1,7 +1,7 @@
 """
 This module contains the classes and functions for creating demographics files
 for malaria simulations. For more information on |EMOD_s| demographics files,
-see :doc:`emod-malaria:software-demographics`. 
+see :doc:`emod/software-demographics`. 
 """
 import os
 import emod_api.demographics.Demographics as Demog
@@ -20,7 +20,7 @@ class MalariaDemographics(Demog.Demographics):
  for each of the nodes in a simulation. "Gridded world" values use a grid 
  overlaid across the globe at some arcsec resolution. You may also generate 
  the grid using another tool or coordinate system. For more information,
- see :ref:`emod-malaria:demo-metadata`.
+ see :ref:`demo-metadata`.
  base_file: A basic demographics file used as a starting point for
  creating more complicated demographics files. For example,
  using a single node file to create a multi-node file for spatial
@@ -231,7 +231,7 @@ def from_params(tot_pop=1e6, num_nodes=100, frac_rural=0.3, id_ref="from_params"
  for each of the nodes in a simulation. "Gridded world" values use a grid 
  overlaid across the globe at some arcsec resolution. You may also generate 
  the grid using another tool or coordinate system. For more information,
- see :ref:`emod-malaria:demo-metadata`.
+ see :ref:`demo-metadata`.
 
  Returns:
  A :py:class:`~emodpy_malaria.demographics.MalariaDemographics` instance.

diff --git a/emodpy_malaria/interventions/common.py b/emodpy_malaria/interventions/common.py
@@ -16,15 +16,15 @@ def _malaria_diagnostic(
  campaign: The :py:obj:`emod_api:emod_api.campaign` object to which the intervention
  will be added.
  diagnostic_type: The setting for **Diagnostic_Type** in
- :doc:`emod-malaria:parameter-campaign-individual-malariadiagnostic`.
+ :doc:`emod/parameter-campaign-individual-malariadiagnostic`.
  In addition to the accepted values listed there, you may also set
  TRUE_INFECTION_STATUS, which calls
- :doc:`emod-malaria:parameter-campaign-individual-standarddiagnostic`
+ :doc:`emod/parameter-campaign-individual-standarddiagnostic`
  instead.
  measurement_sensitivity: The setting for **Measurement_Sensitivity**
- in :doc:`emod-malaria:parameter-campaign-individual-malariadiagnostic`.
+ in :doc:`emod/parameter-campaign-individual-malariadiagnostic`.
  detection_threshold: The setting for **Detection_Threshold** in
- :doc:`emod-malaria:parameter-campaign-individual-malariadiagnostic`.
+ :doc:`emod/parameter-campaign-individual-malariadiagnostic`.
 
  Returns:
  Configured individual-targeted MalariaDiagnostic intervention

diff --git a/emodpy_malaria/interventions/drug.py b/emodpy_malaria/interventions/drug.py
@@ -20,7 +20,7 @@ def add_scheduled_antimalarial_drug(
 ):
  """
  Add an antimalarial drug intervention to your campaign. This is equivalent to 
- :doc:`emod-malaria:parameter-campaign-individual-antimalarialdrug`.
+ :doc:`emod/parameter-campaign-individual-antimalarialdrug`.
 
  Args:
  campaign: The :py:obj:`emod_api:emod_api.campaign` object to which the intervention will be added.
@@ -42,7 +42,7 @@ def add_scheduled_antimalarial_drug(
  target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
  target_gender: The gender targeted for an intervention: All, Male, or Female.
  drug_type: The name of the drug to distribute in a drug intervention. Possible values are
- contained in **Malaria_Drug_Params** in :doc:`emod-malaria:parameter-configuration-drugs`.
+ contained in **Malaria_Drug_Params** in :doc:`emod/parameter-configuration-drugs`.
  Use :py:meth:`~emodpy_malaria.config.set_team_drug_params` to set those values
  cost_to_consumer: Per-unit cost when drug is distributed
  intervention_name: The optional name used to refer to this intervention as a means to differentiate it from
@@ -73,7 +73,7 @@ def _antimalarial_drug(campaign,
  Args:
  campaign: campaign object to which the intervention will be added, and schema_path container
  drug_type: The name of the drug to distribute in a drug intervention. Possible values are
- contained in **Malaria_Drug_Params** in :doc:`emod-malaria:parameter-configuration-drugs`.
+ contained in **Malaria_Drug_Params** in :doc:`emod/parameter-configuration-drugs`.
  Use :py:meth:`~emodpy_malaria.config.set_team_drug_params` to set those values
  cost_to_consumer: Per-unit cost when drug is distributed
  intervention_name: The optional name used to refer to this intervention as a means to differentiate it from
@@ -93,15 +93,15 @@ def _antimalarial_drug(campaign,
 
 def new_intervention_as_file(campaign, start_day, drug_type="Chloroquine", filename="AntimalarialDrug.json"):
  """
- Take an :doc:`emod-malaria:parameter-campaign-individual-antimalarialdrug`
+ Take an :doc:`emod/parameter-campaign-individual-antimalarialdrug`
  intervention from a JSON file and add it to your campaign.
 
  Args:
  campaign: The :py:obj:`emod_api:emod_api.campaign` object to which the intervention will be added.
  start_day: The day of the simulation on which the drug is distributed. We recommend 
  aligning this with the start of the simulation.
  drug_type: The name of the drug to distribute in a drug intervention. Possible values are
- contained in **Malaria_Drug_Params** in :doc:`emod-malaria:parameter-configuration-drugs`.
+ contained in **Malaria_Drug_Params** in :doc:`emod/parameter-configuration-drugs`.
  Use :py:meth:`~emodpy_malaria.config.set_team_drug_params` to set those values
  filename: The JSON file that contains the intervention.