get doxygen docs up and running

src/axom/doxygen_mainpage.md

@@ -14,6 +14,7 @@ Axom provides libraries that address common computer science needs.  It grew fro
 * @subpage primaltop provides an API for geometric primitives and computational geometry tests.
 * @subpage questtop provides an API to query point distance and position relative to meshes.
 * @subpage sidretop provides a data store with hierarchical structure.
+* @subpage sinatop provides an API to convert data to a common file format.
 * @subpage slamtop provides an API to construct and process meshes.
 * @subpage slictop provides infrastructure for logging application messages.
 * @subpage spintop provides spatial acceleration data structures, also known as spatial indexes.
@@ -29,6 +30,7 @@ Dependencies between components are as follows:
   - Quest depends on Slam, Primal, Spin, and Mint
   - Klee depends on Sidre, Inlet and Primal
   - Multimat depends on Slic, and Slam
+- Sina only depends on Core
 
 The figure below summarizes the dependencies between the modules.  Solid links
 indicate hard dependencies; dashed links indicate optional dependencies.

src/axom/sina/doxygen_mainpage.md

@@ -1,7 +1,7 @@
 Sina {#sinatop}
 =========
 
-[Sina](@ref axom::sina) provides an easy way to collect data directly within codes and output them to a common file format designed. This is accomplished in an object oriented manner through the following classes:
+[Sina](@ref axom::sina) provides an easy way to collect data directly within codes and output them to a common file format. This is accomplished in an object oriented manner through the following classes:
 
 - [Curve](@ref axom::sina::Curve): represents a 1D curve
 - [CurveSet](@ref axom::sina::CurveSet): represents an entry in a record's "curve_set"

src/axom/sina/include/Curve.hpp

@@ -18,7 +18,7 @@ namespace sina
 {
 
 /**
- * A Curve represents a 1-dimensional curve inside a \see CurveSet.
+ * A Curve represents a 1-dimensional curve inside a CurveSet.
  */
 class Curve {
 public:

src/axom/sina/include/CurveSet.hpp

@@ -30,6 +30,9 @@ namespace sina
  */
 class CurveSet {
 public:
+    /**
+     * An unordered map of Curve objects.
+     */
     using CurveMap = std::unordered_map<std::string, Curve>;
 
     /**

src/axom/sina/include/DataHolder.hpp

@@ -24,28 +24,48 @@ namespace sina
 /**
  * A DataHolder is a basic container for certain types of information.
  *
- * DataHolders contain curves, libraries, and data (\see Datum), and represent
+ * DataHolders contain curves, libraries, and data (Datum), and represent
  * all the information a library can have associated with it. Records expand
  * on DataHolders to contain additional info.
  *
  * \see Record
- * \see LibraryData
+ * \see LibraryDataMap
  */
 class DataHolder {
 public:
+    /**
+     * An unordered map of Datum objects.
+     */
     using DatumMap = std::unordered_map<std::string, Datum>;
+
+    /**
+     * An unordered map of CurveSet objects.
+     */
     using CurveSetMap = std::unordered_map<std::string, CurveSet>;
+
+    /**
+     * An unordered map of shared pointers to DataHolder objects.
+     */
     using LibraryDataMap = std::unordered_map<std::string, std::shared_ptr<DataHolder>>;
 
     /**
      * Construct an empty DataHolder.
      */
     DataHolder() = default;
 
+    /**
+     * Virtual destructor to automatically clean up resources held by an instance of the DataHolder class.
+     */
     virtual ~DataHolder() = default;
 
+    /**
+     * Copy constructor that disallows this constructor type.
+     */
     DataHolder(DataHolder const &) = delete;
 
+    /**
+     * Disable copy assignment.
+     */
     DataHolder &operator=(DataHolder const &) = delete;
 
     /**
@@ -99,6 +119,11 @@ class DataHolder {
      */
     std::shared_ptr<DataHolder> addLibraryData(std::string const &name);
 
+    /**
+     * Add a new library to this DataHolder with existing library data.
+     *
+     * @return a pointer to a new DataHolder for a library of the given name.
+     */
     std::shared_ptr<DataHolder> addLibraryData(std::string const &name, conduit::Node existingLibraryData);
 
     /**
@@ -118,6 +143,13 @@ class DataHolder {
     std::shared_ptr<DataHolder> getLibraryData(std::string const &libraryName) {
       return libraryData.at(libraryName);
     }
+
+    /**
+     * Get a specific library associated with this DataHolder.
+     * Used when the object on which this function is called is a const.
+     *
+     * @return the dataholder's library data
+     */
     std::shared_ptr<DataHolder> const getLibraryData(std::string const &libraryName) const {
       return libraryData.at(libraryName);
     }

src/axom/sina/include/Datum.hpp

@@ -42,12 +42,16 @@ enum class ValueType {
  * sina::Datum myOtherDatum{value};
  * std::vector<double> scalars = {1, 2, 20.0};
  * sina::Datum myArrayDatum{scalars};
+ *
  * //prints 1, corresponding to Scalar
  * std::cout << static_cast<std::underlying_type<sina::ValueType>::type>(myDatum.getType()) << std::endl;
+ *
  * //prints 0, corresponding to String
  * std::cout << static_cast<std::underlying_type<sina::ValueType>::type>(myOtherDatum.getType()) << std::endl;
+ *
  * //prints 3, corresponding to ScalarArray
  * std::cout << static_cast<std::underlying_type<sina::ValueType>::type>(myArrayDatum.getType()) << std::endl;
+ *
  * myRecord->add(myDatum);
  * myOtherDatum.setUnits("km/s");
  * myRecord->add(myOtherDatum);

src/axom/sina/include/Document.hpp

@@ -61,19 +61,40 @@ namespace sina
  */
 class Document {
 public:
+    /**
+     * A vector of pointers to Record objects.
+     */
     using RecordList = std::vector<std::unique_ptr<Record>>;
+
+    /**
+     * A vector of Relationship objects.
+     */
     using RelationshipList = std::vector<Relationship>;
 
+    /**
+     * Construct an empty Document.
+     */
     Document() = default;
 
-    // Since we hold pointers to polymorphic objects, we can't support
-    // copying or assignment
+    /**
+     * Disable copying Document objects. We must do this since we hold
+     * pointers to polymorphic objects.
+     */
     Document(Document const &) = delete;
 
+    /**
+     * Disabling copy assignment.
+     */
     Document &operator=(Document const &) = delete;
 
+    /**
+     * Move constructor which should be handled by the compiler.
+     */
     Document(Document &&) = default;
 
+    /**
+     * Move assignment which should be handled by the compiler.
+     */
     Document &operator=(Document &&) = default;
 
     /**

src/axom/sina/include/ID.hpp

@@ -28,7 +28,7 @@ enum class IDType {
 };
 
 /**
- * An ID is used to represent the ID of an record. This class holds both the
+ * An ID is used to represent the ID of a Record. This class holds both the
  * actual ID and whether it is a local or global ID.
  */
 class ID {

src/axom/sina/include/Record.hpp

@@ -67,6 +67,9 @@ struct FileHashByURI {
  */
 class Record : public DataHolder {
 public:
+    /**
+     * An unordered set of File objects.
+     */
     using FileSet = std::unordered_set<File, FileHashByURI, FileEqualByURI>;
 
     /**
@@ -84,8 +87,14 @@ class Record : public DataHolder {
      */
     explicit Record(conduit::Node const &asNode);
 
+    /**
+     * Disable the copy constructor.
+     */
     Record(Record const &) = delete;
 
+    /**
+     * Disable copy assignment.
+     */
     Record &operator=(Record const &) = delete;
 
     /**

src/docs/dependencies.dot

@@ -7,6 +7,7 @@ digraph dependencies {
   multimat -> {slic slam};
   spin -> {slam primal};
   sidre -> {slic core};
+  sina -> {core};
   slic -> core;
   slic -> lumberjack [style="dashed"];
   lumberjack -> core;

src/docs/doxygen/Doxyfile.in

@@ -797,6 +797,10 @@ INPUT                  = @PROJECT_SOURCE_DIR@/axom/doxygen_mainpage.md \
                          @PROJECT_SOURCE_DIR@/axom/sidre/doxygen_mainpage.md \
                          @PROJECT_SOURCE_DIR@/axom/sidre/core \
                          @PROJECT_SOURCE_DIR@/axom/sidre/spio \
+                         @PROJECT_SOURCE_DIR@/axom/sina \
+                         @PROJECT_SOURCE_DIR@/axom/sina/doxygen_mainpage.md \
+                         @PROJECT_SOURCE_DIR@/axom/sina/src \
+                         @PROJECT_SOURCE_DIR@/axom/sina/include \
                          @PROJECT_SOURCE_DIR@/axom/slam \
                          @PROJECT_SOURCE_DIR@/axom/slam/doxygen_mainpage.md \
                          @PROJECT_SOURCE_DIR@/axom/slam/policies \