core/*.{h,cpp}: speed up build time

Use lib/json.hpp only when needed, and use lib/json_fwd.h elsewhere.
Yield a 40% speedup in build time on at least one platform.

See #3307.

algo/core/cluster-junctions.cpp

@@ -22,6 +22,7 @@
 */
 
 #include "cluster-junctions.h"
+#include "../lib/json.hpp"
 #include<cstdlib>
 
   bool MySort(const pair<int, string>& lh, const pair<int, string>& rh){

algo/core/cluster-junctions.h

@@ -9,7 +9,7 @@
 #include <ctime>
 #include "dynprog.h"
 #include "windows.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 
 using namespace std ;
 using json = nlohmann::json;

algo/core/germline.cpp

 #include "filter.h"
 #include "germline.h"
 #include "automaton.hpp"
+#include "../lib/json.hpp"
 #include <fstream>
 #include <ctype.h>
 

algo/core/germline.h

@@ -9,7 +9,7 @@
 #include "automaton.hpp"
 #include "stats.h"
 #include "tools.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 #include "kmerstorefactory.hpp"
 #include "bioreader.hpp"
 #include "filter.h"

algo/core/segment.cpp

@@ -24,6 +24,7 @@
 #include <cassert>
 #include "segment.h"
 #include "tools.h"
+#include "../lib/json.hpp"
 #include "affectanalyser.h"
 #include <sstream>
 #include <cstring>

algo/core/segment.h

@@ -11,7 +11,7 @@
 #include "kmerstore.h"
 #include "kmeraffect.h"
 #include "affectanalyser.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 #include "filter.h"
 
 // #define DEBUG_EVALUE

algo/core/similarityMatrix.cpp

@@ -22,6 +22,7 @@
 */
 
 #include "similarityMatrix.h"
+#include "../lib/json.hpp"
 #include <cassert>
 #include <limits>
 #include <math.h>

algo/core/similarityMatrix.h

@@ -6,7 +6,7 @@
 #include <iostream>
 #include <iomanip>
 #include "json.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 
 using namespace std;
 using json = nlohmann::json;

algo/core/tools.cpp

@@ -3,6 +3,7 @@
 #include <iomanip>
 #include <algorithm>
 #include "tools.h"
+#include "../lib/json.hpp"
 
 string seed_contiguous(int k)
 {

algo/core/tools.h

@@ -37,7 +37,7 @@
 #include <vector>
 #include "bioreader.hpp"
 #include "kmeraffect.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 using json = nlohmann::json;
 using namespace std;
 

algo/core/windows.cpp

 #include <iostream>
 #include <string>
 #include "tools.h"
+#include "../lib/json.hpp"
 #include "windows.h"
 #include "representative.h"
 #include "segment.h"

algo/core/windows.h

@@ -19,7 +19,7 @@
 #include "read_score.h"
 #include "representative.h"
 #include "stats.h"
-#include "../lib/json.hpp"
+#include "../lib/json_fwd.hpp"
 
 #define NB_BINS 30
 #define MAX_VALUE_BINS 500