Reorganization of include files. Added missing license.

.idea/misc.xml

@@ -11,6 +11,7 @@
     <excludeRoots>
       <file path="$PROJECT_DIR$/PAG_XXV" />
       <file path="$PROJECT_DIR$/attic" />
+      <file path="$PROJECT_DIR$/attic/attic" />
       <file path="$PROJECT_DIR$/cmake-build-debug/CMakeFiles" />
       <file path="$PROJECT_DIR$/cmake-build-release/CMakeFiles" />
       <file path="$PROJECT_DIR$/data" />
@@ -18,7 +19,6 @@
       <file path="$PROJECT_DIR$/examples/F3-outbred-pleio/spell" />
       <file path="$PROJECT_DIR$/examples/small/S.cache" />
       <file path="$PROJECT_DIR$/examples/three_parents_F2/spell" />
-      <file path="$PROJECT_DIR$/include/attic" />
       <file path="$PROJECT_DIR$/sample-data" />
       <file path="$PROJECT_DIR$/sandbox" />
       <file path="$PROJECT_DIR$/simulation" />
@@ -38,8 +38,12 @@
       <file path="$PROJECT_DIR$/src/experiments" />
       <file path="$PROJECT_DIR$/src/include-graphs" />
       <file path="$PROJECT_DIR$/src/misc_outputs" />
+      <file path="$PROJECT_DIR$/src/r-glue/package" />
       <file path="$PROJECT_DIR$/test_ril_ril2" />
       <file path="$PROJECT_DIR$/tests/TestCodeCoverage" />
     </excludeRoots>
   </component>
+  <component name="JavaScriptSettings">
+    <option name="languageLevel" value="ES6" />
+  </component>
 </project>
\ No newline at end of file

3rd-party/ThreadPool/ThreadPool.h

@@ -14,7 +14,7 @@
 #include <future>
 #include <functional>
 #include <stdexcept>
-#include "error.h"
+#include "io/error.h"
 
 
 class ThreadPool {

CMakeLists.txt

@@ -108,18 +108,18 @@ set(SPELL_MAP_SRC
 
 set(SPELL_MARKER_SRC
         src/input/read_mark.cc src/input/read_map.cc
-        # src/input/design.cc src/input/xml/xml_design.cc src/input/xml/xml_format.cc
         src/static_data.cc
         src/bayes/main.cc src/bayes/dispatch.cc src/bayes/jobs.cc src/bayes/cli.cc
 )
+# src/input/design.cc src/input/xml/xml_design.cc src/input/xml/xml_format.cc
 
 set(SPELL_QTL_SRC
         src/input/read_map.cc src/input/read_trait.cc src/input/read_settings.cc src/input/ld_matrices.cc
-#         src/input/xml/xml_format.cc src/input/xml/xml_settings.cc
         src/static_data.cc src/main.cc src/beta_gamma.cc
         src/computations/basic_data.cc src/computations/probabilities.cc src/computations/model.cc src/computations/frontends.cc
         src/computations/report.cc
 )
+#         src/input/xml/xml_format.cc src/input/xml/xml_settings.cc
 
 MESSAGE(STATUS "spell-pedigree src = ${SPELL_PEDIGREE_SRC}")
 

include/cache/async.h → attic/async.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_CACHE_ASYNC_H_
+#ifdef _SPEL_CACHE_ASYNC_H_
+#error "_SPEL_CACHE_ASYNC_H_ already defined!"
+#else
 #define _SPEL_CACHE_ASYNC_H_
 
 #define DEFAULT_CACHE_DIR "tmp/"

include/model/block.h → attic/block.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_MODEL_BLOCK_H_
+#ifdef _SPEL_MODEL_BLOCK_H_
+#error "_SPEL_MODEL_BLOCK_H_ already defined!"
+#else
 #define _SPEL_MODEL_BLOCK_H_
 
 #include "labelled_matrix.h"

include/bracket.h → attic/bracket.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BRACKET_H_
+#ifdef _SPEL_BRACKET_H_
+#error "_SPEL_BRACKET_H_ already defined!"
+#else
 #define _SPEL_BRACKET_H_
 
 #include "eigen.h"

include/bracket2.h → attic/bracket2.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_BRACKET_H_
+#ifdef _SPEL_BRACKET_H_
+#error "_SPEL_BRACKET_H_ already defined!"
+#else
 #define _SPEL_BRACKET_H_
 
 #include "eigen.h"

include/cache/call_tuple.h → attic/call_tuple.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
+#ifdef _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
+#error "_SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_ already defined!"
+#else
 #define _SPEL_3RD_PARTY_TUPLE_CALL_CODE_H_
 
 /* from http://stackoverflow.com/a/10766422 */

include/cache/cartesian_product.h → attic/cartesian_product.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_CACHE_CARTESIAN_PRODUCT_H_
+#ifdef _SPEL_CACHE_CARTESIAN_PRODUCT_H_
+#error "_SPEL_CACHE_CARTESIAN_PRODUCT_H_ already defined!"
+#else
 #define _SPEL_CACHE_CARTESIAN_PRODUCT_H_
 
 namespace cache {

include/input/design.h → attic/design.h

@@ -15,7 +15,9 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#ifndef _SPEL_DESIGN_H_
+#ifdef _SPEL_DESIGN_H_
+#error "_SPEL_DESIGN_H_ already defined!"
+#else
 #define _SPEL_DESIGN_H_
 
 #include <map>