Merge pull request #9 from MeteoSwiss-APN/master

Merging the changes of the last few weeks for release `0.1`.

.gitignore

@@ -0,0 +1 @@
+build

CMakeLists.txt

@@ -8,7 +8,6 @@ SET(CMAKE_INSTALL_PREFIX "${CMAKE_SOURCE_DIR}/install/" CACHE PATH "installation
 project( SerialBox )
 enable_language (Fortran)
 find_package( Boost )
-include_directories( SYSTEM ${Boost_INCLUDE_DIRS} )
 
 set(ENABLE_DOC "OFF" CACHE BOOL "enable building doc" )
 if(ENABLE_DOC)
@@ -45,13 +44,6 @@ if( CMAKE_HOST_UNIX )
     set ( CMAKE_EXE_LINKER_FLAGS "${CMAKE_LINK_FLAGS} ${CMAKE_THREAD_LIBS_INIT}")
 endif()
 
-# Single precision
-set( SINGLEPRECISION "OFF" CACHE BOOL "Single precision" )
-if( SINGLEPRECISION )
-    add_definitions( -DSINGLEPRECISION )
-endif( SINGLEPRECISION )
-
-
 # OSX specific configuration
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
 
@@ -64,13 +56,6 @@ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     set(CMAKE_MACOSX_RPATH "${CMAKE_INSTALL_RPATH}")
 endif ()
 
-# Serialization
-include_directories( SYSTEM libs/libjson )
-include_directories( libs/sha256 )
-include_directories( libs/gmock-gtest)
-include_directories( src)
-
-
 # Python installation path 
 set (PYTHON_PATH "python")
 

ChangeLog

@@ -0,0 +1,8 @@
+# Release 0.1
+
+ * Seamlessly support single precision and double precision floating point values
+ * Fix issue with files larger than 2 GiB
+ * Support variable declaration in multiple lines in pp_ser
+ * Correctly install utils_ppser fortran module
+ * Python can access global metainformation of serializers, register fields
+   with nontrivial halo and use handle single precision numpy fields

fortran/CMakeLists.txt

@@ -1,10 +1,11 @@
+
+SET(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -cpp ")
 set(
     SOURCES
     "m_serialize.f90"
+    "utils_ppser.f90"
 )
 
-add_library(fortranser_files OBJECT ${SOURCES})
-
 add_library(
     FortranSer STATIC ${SOURCES}
 )

libs/libjson/_internal/Source/JSONNode.h

@@ -161,7 +161,7 @@ class JSONNode {
 
 
     json_string as_string(void) const json_nothrow json_read_priority;
-    int as_int(void) const json_nothrow json_read_priority;
+    json_int_t as_int(void) const json_nothrow json_read_priority;
     json_number as_float(void) const json_nothrow json_read_priority;
     bool as_bool(void) const json_nothrow json_read_priority;
 
@@ -666,9 +666,9 @@ inline void JSONNode::set_name(const json_string & newname) json_nothrow{
 	   return static_cast<json_string>(*internal);
     }
 
-    inline int JSONNode::as_int(void) const json_nothrow {
+    inline json_int_t JSONNode::as_int(void) const json_nothrow {
 	   JSON_CHECK_INTERNAL();
-	   return static_cast<int>(*internal);
+	   return static_cast<json_int_t>(*internal);
     }
 
     inline json_number JSONNode::as_float(void) const json_nothrow {

libs/libjson/_internal/Source/internalJSONNode.h

@@ -156,8 +156,8 @@ class internalJSONNode {
 	   DECL_CAST_OP(short)
 	   DECL_CAST_OP(int)
 	   DECL_CAST_OP(long)
+	   DECL_CAST_OP(long long)
 	   #ifndef JSON_ISO_STRICT
-		  DECL_CAST_OP(long long)
 		  operator long double() const json_nothrow;
 	   #endif
 	   operator float() const json_nothrow;
@@ -466,11 +466,9 @@ inline JSONNode * internalJSONNode::at(json_index_t pos) json_nothrow {
     IMP_SMALLER_INT_CAST_OP(unsigned short, USHRT_MAX, 0)
     IMP_SMALLER_INT_CAST_OP(int, INT_MAX, INT_MIN)
     IMP_SMALLER_INT_CAST_OP(unsigned int, UINT_MAX, 0)
+    IMP_SMALLER_INT_CAST_OP(long long, LLONG_MAX, LLONG_MIN)
+    IMP_SMALLER_INT_CAST_OP(unsigned long long, ULLONG_MAX, 0)
 
-    #ifndef JSON_ISO_STRICT
-	   IMP_SMALLER_INT_CAST_OP(long, LONG_MAX, LONG_MIN)
-	   IMP_SMALLER_INT_CAST_OP(unsigned long, ULONG_MAX, 0)
-    #endif
 #endif
 
 inline internalJSONNode::operator json_string() const json_nothrow {

libs/libjson/longint.patch

@@ -0,0 +1,53 @@
+diff --git a/libs/libjson/_internal/Source/JSONNode.h b/libs/libjson/_internal/Source/JSONNode.h
+index 7812753..4ced605 100644
+--- a/libs/libjson/_internal/Source/JSONNode.h
++++ b/libs/libjson/_internal/Source/JSONNode.h
+@@ -161,7 +161,7 @@ public:
+
+
+     json_string as_string(void) const json_nothrow json_read_priority;
+-    int as_int(void) const json_nothrow json_read_priority;
++    json_int_t as_int(void) const json_nothrow json_read_priority;
+     json_number as_float(void) const json_nothrow json_read_priority;
+     bool as_bool(void) const json_nothrow json_read_priority;
+
+@@ -666,9 +666,9 @@ inline void JSONNode::set_name(const json_string & newname) json_nothrow{
+ 	   return static_cast<json_string>(*internal);
+     }
+
+-    inline int JSONNode::as_int(void) const json_nothrow {
++    inline json_int_t JSONNode::as_int(void) const json_nothrow {
+ 	   JSON_CHECK_INTERNAL();
+-	   return static_cast<int>(*internal);
++	   return static_cast<json_int_t>(*internal);
+     }
+
+     inline json_number JSONNode::as_float(void) const json_nothrow {
+diff --git a/libs/libjson/_internal/Source/internalJSONNode.h b/libs/libjson/_internal/Source/internalJSONNode.h
+index 2dd3a1e..8372a13 100644
+--- a/libs/libjson/_internal/Source/internalJSONNode.h
++++ b/libs/libjson/_internal/Source/internalJSONNode.h
+@@ -156,8 +156,8 @@ public:
+ 	   DECL_CAST_OP(short)
+ 	   DECL_CAST_OP(int)
+ 	   DECL_CAST_OP(long)
++	   DECL_CAST_OP(long long)
+ 	   #ifndef JSON_ISO_STRICT
+-		  DECL_CAST_OP(long long)
+ 		  operator long double() const json_nothrow;
+ 	   #endif
+ 	   operator float() const json_nothrow;
+@@ -466,11 +466,9 @@ inline JSONNode * internalJSONNode::at(json_index_t pos) json_nothrow {
+     IMP_SMALLER_INT_CAST_OP(unsigned short, USHRT_MAX, 0)
+     IMP_SMALLER_INT_CAST_OP(int, INT_MAX, INT_MIN)
+     IMP_SMALLER_INT_CAST_OP(unsigned int, UINT_MAX, 0)
++    IMP_SMALLER_INT_CAST_OP(long long, LLONG_MAX, LLONG_MIN)
++    IMP_SMALLER_INT_CAST_OP(unsigned long long, ULLONG_MAX, 0)
+
+-    #ifndef JSON_ISO_STRICT
+-	   IMP_SMALLER_INT_CAST_OP(long, LONG_MAX, LONG_MIN)
+-	   IMP_SMALLER_INT_CAST_OP(unsigned long, ULONG_MAX, 0)
+-    #endif
+ #endif
+
+ inline internalJSONNode::operator json_string() const json_nothrow {

python/pp_ser.py

@@ -3,6 +3,8 @@
 #See LICENSE.txt for more information
 
 from __future__ import print_function
+import linecache
+
 
 """
 pp_ser.py
@@ -438,6 +440,7 @@ def __ser_data(self, args, isacc = False):
         self.__calls.add(self.methods['dataread'])
         self.__calls.add(self.methods['getmode'])
         l = ''
+        l = '! file: ' + self.infile + ' lineno: #' + str(self.__linenum) + '\n'
         tab = ''
         if if_statement:
             l += 'IF (' + if_statement + ') THEN\n'
@@ -643,25 +646,52 @@ def __re_endmodule(self):
             self.__module = ''
         return m
 
+    def __check_intent_in(self, line):
+        lhs = re.sub(r'!.*', '', line) # Remove comments at end of the line
+        var_with_dim = [x.strip().replace(' ', '') for x in re.split(r',(?![^(]*\))', lhs)]
+        var = [re.sub(r'\(.*?\)', '', x) for x in var_with_dim]
+        fields_in_this_line = [x for x in self.intentin_to_remove if x in var]
+        self.intentin_removed.extend([x for x in fields_in_this_line if x not in self.intentin_removed])
+
+        if fields_in_this_line:
+            l =  '#ifdef ' + self.ifdef + '\n'
+            r = re.compile(r', *intent *\(in\)', re.IGNORECASE)
+            l += r.sub('', self.__line)
+            l += '#else\n' + self.__line + '#endif\n'
+            self.__line = l
+        return fields_in_this_line
+
+
     def __re_def(self):
         r = re.compile(r'.*intent *\(in\)[^:]*::\s*([^!]*)\s*.*', re.IGNORECASE)
+        r_cont = re.compile(r'.*intent *\(in\)[^:]*::\s*([^!]*)\s*.*&', re.IGNORECASE)
+
+        # Line contains intent with continuation
+        m_cont = r_cont.search(self.__line)
         m = r.search(self.__line)
-        if m:
+        if m_cont:
+            splitted = self.__line.split('::')
+            splitted[1] = re.sub(r'!.*', '', splitted[1]) # Remove comments at end of the line
+            if not self.__check_intent_in(splitted[1]):
+                # look ahead to find the variable
+                lookahead_index = self.__linenum
+                # set to line after the intent declaration
+                lookahead_index += 1
+                # look ahead
+                nextline = linecache.getline(os.path.join(self.infile), lookahead_index)
+                while nextline:
+                    self.__check_intent_in(nextline)
+                    if(nextline.find('&')!=-1):
+                        lookahead_index += 1
+                        nextline = linecache.getline(os.path.join(self.infile), lookahead_index)
+                    else:
+                        nextline = None
+
+        # Match a standard declaration with variable and intent on the same line
+        elif m:
             splitted = self.__line.split('::')
             splitted[1] = re.sub(r'!.*', '', splitted[1]) # Remove comments at end of the line
-            var_with_dim = [x.strip().replace(' ', '') for x in re.split(r',(?![^(]*\))', splitted[1])]
-            var = [re.sub(r'\(.*?\)', '', x) for x in var_with_dim]
-            fields_in_this_line = [x for x in self.intentin_to_remove if x in var]
-            self.intentin_removed.extend([x for x in fields_in_this_line if x not in self.intentin_removed])
-
-            if fields_in_this_line:
-                l =  '#ifdef ' + self.ifdef + '\n'
-                r = re.compile(r', *intent *\(in\)', re.IGNORECASE)
-                l += r.sub('', self.__line)
-                l += '#else\n' + self.__line + '#endif\n'
-
-                self.__line = l
-            return fields_in_this_line
+            self.__check_intent_in(splitted[1])
         return m
 
     # evaluate one line