Suppress documentation for include guards and additional

documentation fixes

Did this the long way. The documentation for Doxygen says
I should be able to hide those defines with a single knob.
However, I cannot make it work.  So each one is now filtered
out individually.

docs/conf.py

@@ -1,10 +1,11 @@
-import subprocess, os
+import os
+import subprocess
 
 from documenteer.sphinxconfig.utils import form_ltd_edition_name
 
-def configureDoxyfile(input_dir, output_dir):
 
-    with open('Doxyfile.in', 'r') as file :
+def configureDoxyfile(input_dir, output_dir):
+    with open('Doxyfile.in', 'r') as file:
         filedata = file.read()
 
     filedata = filedata.replace('@DOXYGEN_INPUT_DIR@', input_dir)
@@ -26,7 +27,7 @@ if read_the_docs_build:
 # -- Project information -----------------------------------------------------
 
 project = 'Kami'
-copyright = '2020-2021 The Johns Hopkins University Applied Physics Laboratory LLC'
+copyright = '2020-2022 The Johns Hopkins University Applied Physics Laboratory LLC'
 author = 'James P. Howard, II <james.howard@jhu.edu>'
 
 # -- General configuration ---------------------------------------------------
@@ -177,7 +178,7 @@ html_theme_options = {
 # (source start file, name, description, authors, manual section).
 man_pages = [
     (master_doc, 'kami', u'Kami: Agent-Based Modeling in Modern C++',
-     [author], 3)
+     [author], '3kami')
 ]
 
 # If true, show URL addresses after external links.

include/kami/agent.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_AGENT_H
+//! @cond SuppressGuard
 #define KAMI_AGENT_H
+//! @endcond
 
 #include <iostream>
 #include <memory>
@@ -36,15 +38,15 @@
 
 namespace kami {
 
-/**
- * @brief A unique identifier for each `Agent`.
- *
- * @details The unique identifier permits ordering to allow `AgentID`s to be used as keys
- * for `std::map`. The unique identifier is unique for the session, however,
- * `AgentID`s are not guaranteed to be unique from session-to-session.
- *
- * @see Agent
- */
+    /**
+     * @brief A unique identifier for each `Agent`.
+     *
+     * @details The unique identifier permits ordering to allow `AgentID`s to be used as keys
+     * for `std::map`. The unique identifier is unique for the session, however,
+     * `AgentID`s are not guaranteed to be unique from session-to-session.
+     *
+     * @see Agent
+     */
     class LIBKAMI_EXPORT AgentID {
     private:
         inline static long long _id_next = 1;
@@ -63,7 +65,7 @@ namespace kami {
         /**
          * @brief Constructs a new unique identifier.
          */
-        AgentID() : _id(_id_next++){};
+        AgentID() : _id(_id_next++) {};
 
         /**
          * @brief Convert the identifier to a human-readable string.
@@ -117,15 +119,15 @@ namespace kami {
         friend std::ostream &operator<<(std::ostream &lhs, const AgentID &rhs);
     };
 
-/**
- * @brief A superclass for all agents.
- *
- * @details All agents should subclass the `Agent` class. At a minimum, subclasses must
- * implement the `step()` function, to execute a single time step for each
- * agent.
- *
- * @see `StagedAgent`
- */
+    /**
+     * @brief A superclass for all agents.
+     *
+     * @details All agents should subclass the `Agent` class. At a minimum, subclasses must
+     * implement the `step()` function, to execute a single time step for each
+     * agent.
+     *
+     * @see `StagedAgent`
+     */
     class LIBKAMI_EXPORT Agent {
     private:
         const AgentID _agent_id;

include/kami/domain.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_DOMAIN_H
+//! @cond SuppressGuard
 #define KAMI_DOMAIN_H
+//! @endcond
 
 #include <string>
 

include/kami/grid.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_GRID_H
+//! @cond SuppressGuard
 #define KAMI_GRID_H
+//! @endcond
 
 #include <string>
 

include/kami/grid1d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_GRID1D_H
+//! @cond SuppressGuard
 #define KAMI_GRID1D_H
+//! @endcond
 
 #include <iostream>
 #include <map>

include/kami/grid2d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_GRID2D_H
+//! @cond SuppressGuard
 #define KAMI_GRID2D_H
+//! @endcond
 
 #include <iostream>
 #include <map>

include/kami/kami.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_KAMI_H
+//! @cond SuppressGuard
 #define KAMI_KAMI_H
+//! @endcond
 
 #include <semver.hpp>
 

include/kami/model.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_MODEL_H
+//! @cond SuppressGuard
 #define KAMI_MODEL_H
+//! @endcond
 
 #include <memory>
 #include <optional>

include/kami/multigrid1d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_MULTIGRID1D_H
+//! @cond SuppressGuard
 #define KAMI_MULTIGRID1D_H
+//! @endcond
 
 #include <kami/agent.h>
 #include <kami/domain.h>

include/kami/multigrid2d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_MULTIGRID2D_H
+//! @cond SuppressGuard
 #define KAMI_MULTIGRID2D_H
+//! @endcond
 
 #include <kami/agent.h>
 #include <kami/domain.h>

include/kami/population.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_POPULATION_H
+//! @cond SuppressGuard
 #define KAMI_POPULATION_H
+//! @endcond
 
 #include <map>
 #include <vector>

include/kami/random.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_RANDOM_H
+//! @cond SuppressGuard
 #define KAMI_RANDOM_H
+//! @endcond
 
 #include <memory>
 #include <optional>

include/kami/scheduler.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_SCHEDULER_H
+//! @cond SuppressGuard
 #define KAMI_SCHEDULER_H
+//! @endcond
 
 #include <memory>
 #include <optional>

include/kami/sequential.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_SEQUENTIAL_H
+//! @cond SuppressGuard
 #define KAMI_SEQUENTIAL_H
+//! @endcond
 
 #include <memory>
 #include <optional>

include/kami/sologrid1d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_SOLOGRID1D_H
+//! @cond SuppressGuard
 #define KAMI_SOLOGRID1D_H
+//! @endcond
 
 #include <kami/KAMI_EXPORT.h>
 #include <kami/agent.h>

include/kami/sologrid2d.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_SOLOGRID2D_H
+//! @cond SuppressGuard
 #define KAMI_SOLOGRID2D_H
+//! @endcond
 
 #include <kami/KAMI_EXPORT.h>
 #include <kami/agent.h>

include/kami/staged.h

@@ -25,7 +25,9 @@
 
 #pragma once
 #ifndef KAMI_STAGED_H
+//! @cond SuppressGuard
 #define KAMI_STAGED_H
+//! @endcond
 
 #include <memory>
 #include <optional>