Merge pull request #25 from EMOD-Hub/format-cleanup-1

Format cleanup 1

Author: JSchripsema-IDM

README.md

@@ -18,6 +18,10 @@ Community contributions are welcome, and trusted collaborators may review and
 merge pull requests, but no guarantees are made regarding support, pull request
 review, security response, maintenance, or release timelines.
 
+## Documentation
+
+Documentation available at https://emod.idmod.org/EMOD-Generic
+
 ## Community
 
 Have a question or a comment? Check out our

docs/md_dev/dev-regression-run.md

@@ -22,39 +22,36 @@ produce output that should not be considered scientifically accurate.
       sections for your cluster that contain the same variables as shown for IDM HPC
       clusters.
 
-1. Select the suite of regression tests you want to run. This is indicated by a JSON file in the
+2. Select the suite of regression tests you want to run. This is indicated by a JSON file in the
     following format:
 
-```json
-
         {
             "tests": [{
                 "path": "Relative path to test directory."
             }, {
                 "path": "Relative path to test directory."
             }]
         }
-```
 
     You can use one of the JSON files in the Regression directory or create your own. The sanity.json
     file is recommended for quickly testing a wide range of EMOD functionality.
 
-1. From the Regression directory, open a Command Prompt window and run the regression test script,
+3. From the Regression directory, open a Command Prompt window and run the regression test script,
     regression_test.py. It requires the name of the regression suite (without the .json extension)
     and the relative path to Eradication.exe. For example:
 
-```
-        regression_test.py sanity ..\Eradication\x64\Release\Eradication.exe
-```
+    ```
+            regression_test.py sanity ..\Eradication\x64\Release\Eradication.exe
+    ```
 
     In addition, you may need to include the following optional arguments depending on your
     testing environment or how Eradication.exe was built.
 
-| Argument | Default | Description |
-| --- | --- | --- |
-| `--perf` | False | Measure Eradication.exe performance.         `--hidegraphs` |
+    | Argument | Default | Description |
+    | --- | --- | --- |
+    | `--perf` | False | Measure Eradication.exe performance.         `--hidegraphs` |
 
-1. Review the output and examine any failures.
+4. Review the output and examine any failures.
 
     EMOD will output the standard error and logging files, StdErr.txt and StdOut.txt, produced from
     any simulation (see [software-error-logging](../md_software/software-error-logging.md)). In addition, regression_test.py will output time.txt
@@ -70,7 +67,6 @@ produce output that should not be considered scientifically accurate.
     adjusting the scale of the plots, zooming or panning, and so forth, through the icons at the
     bottom of the chart window.
 
-![Popup Chart](../figures/dev/matplotlibPopupChart.png)
+    ![Popup Chart](../figures/dev/matplotlibPopupChart.png)
 
-If any of the regression tests fail and you have *not* made any changes to the EMOD source code,
-email support@idmod.org.
+If any of the regression tests fail and you have *not* made any changes to the EMOD source code, visit <https://github.com/orgs/EMOD-Hub/discussions> or use the GitHub link at the top of the page to submit a new issue in the repo. Be sure to include any error information.

docs/md_dev/dev-trouble-build.md

@@ -3,9 +3,7 @@
 If you encounter any of the following warnings or errors when attempting to build the EMOD executable (Eradication.exe) or
 Eradication binary for Linux, see the information below to resolve the issue.
 
-If you need assistance, you can contact support for help with solving issues. You can contact
-Institute for Disease Modeling (IDM) support at support@idmod.org. When submitting the issue, please include any error
-information.
+If you encounter an issue, use the GitHub link at the top of the page to submit a new issue in the repo. Be sure to include any error information. For general discussion and questions, please visit https://github.com/orgs/EMOD-Hub/discussions.
 
 ## Unknown compiler version
 

docs/md_parameter/parameter-campaign-event-broadcastcoordinatorevent.md

@@ -2,21 +2,24 @@
 
 !!! note
 
-        This campaign class and associated parameters are currently in beta release and have not yet been fully tested.
+    This campaign class and associated parameters are currently in beta release and have not yet
+    been fully tested.
 
 The **BroadcastCoordinatorEvent** coordinator class broadcasts the event you specify. This can be used with the campaign class, [parameter-campaign-event-surveillanceeventcoordinator](parameter-campaign-event-surveillanceeventcoordinator.md), 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. For more information, see [dev-architecture-core](../md_dev/dev-architecture-core.md).
 
 !!! note
 
-        Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false.
-        Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
-        that parameter.
+    Parameters are case-sensitive. For Boolean parameters, set to 1 for true or 0 for false.
+    Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
+    that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+    EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+    parameter is required, you must supply a value for it. However, many of the tools used to work 
+    with EMOD will use the default values provided below.
 
-        JSON format does not permit comments, but you can add "dummy" parameters to add contextual
-        information to your files. Any keys that are not EMOD parameter names will be ignored by the
-        model.
+    JSON format does not permit comments, but you can add "dummy" parameters to add contextual
+    information to your files. Any keys that are not EMOD parameter names will be ignored by the
+    model.
 
 The table below describes all possible parameters with which this class can be configured. The JSON
 example that follows shows one potential configuration.

docs/md_parameter/parameter-campaign-event-calendareventcoordinator.md

@@ -10,7 +10,9 @@ for this event coordinator.
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the

docs/md_parameter/parameter-campaign-event-campaignevent.md

@@ -10,7 +10,9 @@ campaign event.
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the

docs/md_parameter/parameter-campaign-event-communityhealthworkereventcoordinator.md

@@ -12,7 +12,9 @@ of drugs  and node-level interventions could be spraying houses with insecticide
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the

docs/md_parameter/parameter-campaign-event-coveragebynodeeventcoordinator.md

@@ -17,7 +17,9 @@ parameters for this event coordinator.
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the

docs/md_parameter/parameter-campaign-event-delayeventcoordinator.md

@@ -13,7 +13,9 @@ event is typically used with [parameter-campaign-event-broadcastcoordinatorevent
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the

docs/md_parameter/parameter-campaign-event-incidenceeventcoordinator.md

@@ -8,7 +8,9 @@ The **IncidenceEventCoordinator** coordinator class distributes interventions ba
         Minimum, maximum, or default values of "NA" indicate that those values are not applicable for
         that parameter.
 
-        EMOD does not use true defaults; that is, if the dependency relationships indicate that a parameter is required, you must supply a value for it. However, many of the tools used to work with EMOD will use the default values provided below.
+        EMOD does not use true defaults; that is, if the dependency relationships indicate that a 
+        parameter is required, you must supply a value for it. However, many of the tools used to work 
+        with EMOD will use the default values provided below.
 
         JSON format does not permit comments, but you can add "dummy" parameters to add contextual
         information to your files. Any keys that are not EMOD parameter names will be ignored by the