move sina to axom and add cmake files so it can be built

src/axom/CMakeLists.txt

@@ -28,6 +28,7 @@ endif()
 # Add components so that later ones depend on earlier ones
 # (i.e. quest depends on mint, so quest follows mint)
 axom_add_component(COMPONENT_NAME slic   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
+axom_add_component(COMPONENT_NAME sina   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME slam   DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME primal DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})
 axom_add_component(COMPONENT_NAME sidre  DEFAULT_STATE ${AXOM_ENABLE_ALL_COMPONENTS})

src/axom/config.hpp.in

@@ -111,6 +111,7 @@
 #cmakedefine AXOM_USE_SLAM
 #cmakedefine AXOM_USE_SLIC
 #cmakedefine AXOM_USE_SPIN
+#cmakedefine AXOM_USE_SINA
 
 /*
  * For gradual removal of types that have been deprecated in favor of

src/axom/core/utilities/About.cpp.in

@@ -102,6 +102,10 @@ void about(std::ostream &oss)
     comps.push_back("sidre");
 #endif
 
+#ifdef AXOM_USE_SINA
+    comps.push_back("sina");
+#endif
+
 #ifdef AXOM_USE_SLAM
     comps.push_back("slam");
 #endif

src/axom/sina/CMakeLists.txt

@@ -0,0 +1,109 @@
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
+# other Axom Project Developers. See the top-level LICENSE file for details.
+#
+# SPDX-License-Identifier: (BSD-3-Clause)
+#------------------------------------------------------------------------------
+# Sina -- API to write data to Sina's common file format
+#------------------------------------------------------------------------------
+
+#------------------------------------------------------------------------------
+# Specify necessary dependencies
+#
+# Note: Sina also optionally depends on Adiak when AXOM_SINA_USE_ADIAK=ON
+#------------------------------------------------------------------------------
+axom_component_requires(NAME       Sina
+                        TPLS       Conduit )
+
+#------------------------------------------------------------------------------
+# Add Sina options
+#------------------------------------------------------------------------------
+cmake_dependent_option( AXOM_SINA_USE_ADIAK "Enables Adiak support in Sina" ON
+                       "AXOM_USE_ADIAK" OFF)
+
+#------------------------------------------------------------------------------
+# Generate Sina config
+#------------------------------------------------------------------------------
+axom_configure_file ( config.hpp.in ${PROJECT_BINARY_DIR}/include/axom/sina/config.hpp )
+
+#------------------------------------------------------------------------------
+# Specify the sina headers/sources
+#------------------------------------------------------------------------------
+set(sina_headers
+    include/ConduitUtil.hpp
+    include/CppBridge.hpp
+    include/Curve.hpp
+    include/CurveSet.hpp
+    include/DataHolder.hpp
+    include/Datum.hpp
+    include/Document.hpp
+    include/File.hpp
+    include/ID.hpp
+    include/Record.hpp
+    include/Relationship.hpp
+    include/Run.hpp
+    )
+
+set(sina_sources
+    src/ConduitUtil.cpp
+    src/Curve.cpp
+    src/CurveSet.cpp
+    src/DataHolder.cpp
+    src/Datum.cpp
+    src/Document.cpp
+    src/File.cpp
+    src/ID.cpp
+    src/Record.cpp
+    src/Relationship.cpp
+    src/Run.cpp
+    )
+
+# Add Adiak header and source
+if (AXOM_SINA_USE_ADIAK)
+    list(APPEND sina_headers include/AdiakWriter.hpp)
+    list(APPEND sina_sources src/AdiakWriter.cpp)
+endif()
+
+blt_list_append( TO sina_headers ELEMENTS include/AdiakWriter.hpp IF AXOM_SINA_USE_ADIAK )
+blt_list_append( TO sina_sources ELEMENTS src/AdiakWriter.cpp IF AXOM_SINA_USE_ADIAK )
+
+#------------------------------------------------------------------------------
+# Build and install the library
+#------------------------------------------------------------------------------
+set(sina_depends
+    core
+    conduit::conduit
+    )
+
+blt_list_append( TO sina_depends ELEMENTS adiak::adiak IF AXOM_SINA_USE_ADIAK )
+
+axom_add_library(NAME       sina
+                 SOURCES    ${sina_sources}
+                 HEADERS    ${sina_headers}
+                 DEPENDS_ON ${sina_depends}
+                 FOLDER     axom/sina)
+
+axom_write_unified_header(NAME    sina
+                          HEADERS ${sina_headers})
+
+axom_install_component(NAME    sina
+                       HEADERS ${sina_headers})
+
+install(FILES           ${PROJECT_BINARY_DIR}/include/axom/sina/config.hpp
+        DESTINATION     include/axom/sina
+        )
+
+#------------------------------------------------------------------------------
+# Add tests and examples
+#------------------------------------------------------------------------------
+# if(AXOM_ENABLE_TESTS)
+#   add_subdirectory(tests)
+# endif()
+
+# if(AXOM_ENABLE_EXAMPLES)
+#   add_subdirectory(examples)
+# endif()
+
+#------------------------------------------------------------------------------
+# Add code checks
+#------------------------------------------------------------------------------
+axom_add_code_checks(PREFIX sina)

src/axom/sina/config.hpp.in

@@ -0,0 +1,9 @@
+#ifndef SINA_CONFIG_HPP_
+#define SINA_CONFIG_HPP_
+
+/// \file
+
+#cmakedefine AXOM_SINA_USE_ADIAK
+
+#endif // SINA_CONFIG_HPP_
+

src/axom/sina/include/AdiakWriter.hpp

@@ -0,0 +1,50 @@
+#ifndef SINA_ADIAK_HPP
+#define SINA_ADIAK_HPP
+
+/// @file
+
+#include "axom/sina/config.hpp"
+#ifdef AXOM_SINA_USE_ADIAK
+
+#include <string>
+#include <type_traits>
+
+#include "axom/sina/include/ConduitUtil.hpp"
+#include "axom/sina/include/Record.hpp"
+#include "axom/sina/include/Run.hpp"
+
+extern "C" {
+#include "adiak_tool.h"
+}
+
+namespace axom
+{
+namespace sina
+{
+
+/**
+ * The callback function to pass to Adiak in order to write collected data to a Sina Record.
+ *
+ * To register this with Adiak, you should call adiak_register_cb, passing in
+ * a pointer to the record as the last value. Your code should look something
+ * like this:
+ *
+ * \code
+ *     Record record{ID{"my_id", IDType::Local}, "my_record_type"};
+ *     adiak_register_cb(1, adiak_category_all, adiakSinaCallback, 0, &record);
+ * \endcode
+ *
+ * Note that not everything that Sina can capture an be captured through the
+ * Adiak API. For example, there is currently no support in Adiak to capture
+ * anything like a CurveSet. As a result, to do that, you must hold on to
+ * the Record object passed here as the opaque value and manipulate it directly.
+ **/
+void adiakSinaCallback(const char *name, adiak_category_t category, const char *subcategory, adiak_value_t *value, adiak_datatype_t *t, void *opaque_value);
+
+}  // end sina namespace
+}  // end axom namespace
+
+#endif // AXOM_SINA_USE_ADIAK
+
+#endif // SINA_ADIAK_HPP
+

src/axom/sina/include/ConduitUtil.hpp

@@ -0,0 +1,106 @@
+#ifndef SINA_JSONUTIL_HPP
+#define SINA_JSONUTIL_HPP
+
+#include <string>
+#include <vector>
+
+#include "conduit.hpp"
+
+namespace axom
+{
+namespace sina
+{
+
+/**
+ * Get a required field from a conduit Node.
+ *
+ * @param fieldName the name of the field to get
+ * @param parent the parent object from which to get the field
+ * @param parentType a user-friendly name of the type of the parent to use
+ * in an error message if the field doesn't exist.
+ * @return the requested field as a Node
+ * @throws std::invalid_argument if the field does not exist
+ */
+conduit::Node const &getRequiredField(std::string const &fieldName,
+        conduit::Node const &parent, std::string const &parentType);
+
+/**
+ * Get the value of a required field from a conduit Node. The field value
+ * must be a string.
+ *
+ * @param fieldName the name of the field to get
+ * @param parent the parent object from which to get the field
+ * @param parentType a user-friendly name of the type of the parent to use
+ * in an error message if the field doesn't exist.
+ * @return the value of the requested field
+ * @throws std::invalid_argument if the field does not exist or is not a string
+ */
+std::string getRequiredString(std::string const &fieldName,
+        conduit::Node const &parent, std::string const &parentType);
+
+/**
+ * Get the value of a required field from a conduit Node. The field value
+ * must be a double.
+ *
+ * @param fieldName the name of the field to get
+ * @param parent the parent object from which to get the field
+ * @param parentType a user-friendly name of the type of the parent to use
+ * in an error message if the field doesn't exist.
+ * @return the value of the requested field
+ * @throws std::invalid_argument if the field does not exist or is not a double
+ */
+double getRequiredDouble(std::string const &fieldName,
+        conduit::Node const &parent, std::string const &parentType);
+
+/**
+ * Get the value of an optional field from a conduit Node. The field value
+ * must be a string if it is present.
+ *
+ * @param fieldName the name of the field to get
+ * @param parent the parent object from which to get the field
+ * @param parentType a user-friendly name of the type of the parent to use
+ * in an error message if the field doesn't exist.
+ * @return the value of the requested field, or an empty string if it
+ * does not exist
+ * @throws std::invalid_argument if the field exists but is not a string
+ */
+std::string getOptionalString(std::string const &fieldName,
+        conduit::Node const &parent, std::string const &parentType);
+
+/**
+ * Convert the given node to a vector of doubles.
+ *
+ * @param node the node to convert
+ * @param name the name of the node, used in error reporting
+ * @return the node as a list of doubles
+ * @throws std::invalid_argument if the node is not a list of doubles
+ */
+std::vector<double> toDoubleVector(conduit::Node const &node,
+        std::string const &name);
+
+/**
+ * Convert the given node to a vector of strings.
+ *
+ * @param node the node to convert
+ * @param name the name of the node, used in error reporting
+ * @return the node as a list of strings
+ * @throws std::invalid_argument if the node is not a list of strings
+ */
+std::vector<std::string> toStringVector(conduit::Node const &node,
+        std::string const &name);
+
+/**
+ * Add a vector of strings to a Node. This operation's not natively
+ * part of Conduit.
+ *
+ * @param parent the node to add the strings to
+ * @param child_name the name of the child (aka the name of the field)
+ * @param string_values the data values for the field
+ */
+void addStringsToNode(conduit::Node &parent, const std::string &child_name,
+      std::vector<std::string> const &string_values);
+
+}  // end namespace sina
+}  // end namespace axom
+
+#endif //SINA_JSONUTIL_HPP

src/axom/sina/include/CppBridge.hpp

@@ -0,0 +1,40 @@
+#ifndef SINA_CPPBRIDGE_HPP
+#define SINA_CPPBRIDGE_HPP
+
+/**
+ * @file
+ *
+ * This file contains functions which can go away once this library is
+ * migrated to C++14 or later.
+ */
+
+#include <memory>
+#include <utility>
+
+namespace axom
+{
+namespace sina
+{
+namespace internal
+{
+
+/**
+ * Make a unique pointer pointing to a new object.
+ *
+ * Delete when switch to C++14 in favor of std::make_unique.
+ *
+ * @tparam T the type of the object
+ * @tparam ParamTypes the types of the parameters
+ * @param params the parameters to the constructor
+ * @return a unique_ptr to the newly-constructed object
+ */
+template<typename T, typename... ParamTypes>
+std::unique_ptr<T> make_unique(ParamTypes &&... params) {
+    return std::unique_ptr<T>(new T(std::forward<ParamTypes>(params)...));
+};
+
+}  // end internal namespace
+}  // end sina namespace
+}  // end axom namespace
+
+#endif //SINA_CPPBRIDGE_HPP