From cd2d75c45ba428d2eb247fb76708d135f92cab28 Mon Sep 17 00:00:00 2001
From: "w.klijn" <w.klijn@fz-juelich.de>
Date: Thu, 9 Jun 2016 11:19:16 +0200
Subject: [PATCH] Reintroduce all indirect includes and clean up CMakeLists.txt

---
 CMakeLists.txt                    | 3 ---
 src/cell_tree.hpp                 | 2 +-
 src/fvm.hpp                       | 2 +-
 src/indexed_view.hpp              | 2 +-
 src/ion.hpp                       | 2 +-
 src/matrix.hpp                    | 2 +-
 src/mechanism_interface.cpp       | 4 ++--
 src/tree.hpp                      | 2 +-
 src/util.hpp                      | 2 +-
 tests/test_tree.cpp               | 2 +-
 tests/util.hpp                    | 2 +-
 tests/validate_ball_and_stick.cpp | 2 +-
 tests/validate_soma.cpp           | 2 +-
 13 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9764e339..d49802d7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -15,10 +15,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 
 include_directories(${CMAKE_SOURCE_DIR}/external)
-include_directories(${CMAKE_SOURCE_DIR}/external/vector/include)
-include_directories(${CMAKE_SOURCE_DIR}/external/json/src)
 include_directories(${CMAKE_SOURCE_DIR}/include)
-include_directories(${CMAKE_SOURCE_DIR}/include/mechanisms)
 include_directories(${CMAKE_SOURCE_DIR}/src)
 include_directories(${CMAKE_SOURCE_DIR})
 
diff --git a/src/cell_tree.hpp b/src/cell_tree.hpp
index 8827bb01..fab1163b 100644
--- a/src/cell_tree.hpp
+++ b/src/cell_tree.hpp
@@ -9,7 +9,7 @@
 #include <ostream>
 #include <vector>
 
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 #include "tree.hpp"
 #include "util.hpp"
 
diff --git a/src/fvm.hpp b/src/fvm.hpp
index 1dbbdfde..d0c6f902 100644
--- a/src/fvm.hpp
+++ b/src/fvm.hpp
@@ -4,7 +4,7 @@
 #include <map>
 #include <string>
 #include <vector>
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 #include "algorithms.hpp"
 #include "cell.hpp"
diff --git a/src/indexed_view.hpp b/src/indexed_view.hpp
index 01df7e99..0cbc22a9 100644
--- a/src/indexed_view.hpp
+++ b/src/indexed_view.hpp
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 namespace nest {
 namespace mc {
diff --git a/src/ion.hpp b/src/ion.hpp
index 883658b4..8f526ade 100644
--- a/src/ion.hpp
+++ b/src/ion.hpp
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 #include "indexed_view.hpp"
 
diff --git a/src/matrix.hpp b/src/matrix.hpp
index 889a3e51..e86c9b89 100644
--- a/src/matrix.hpp
+++ b/src/matrix.hpp
@@ -1,7 +1,7 @@
 #pragma once
 
 #include <type_traits>
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 #include "util.hpp"
 
diff --git a/src/mechanism_interface.cpp b/src/mechanism_interface.cpp
index b02d7035..f44d1f56 100644
--- a/src/mechanism_interface.cpp
+++ b/src/mechanism_interface.cpp
@@ -4,8 +4,8 @@
 //  include the mechanisms
 //
 
-#include <hh.hpp>
-#include <pas.hpp>
+#include <mechanisms/hh.hpp>
+#include <mechanisms/pas.hpp>
 
 
 namespace nest {
diff --git a/src/tree.hpp b/src/tree.hpp
index 7d702cc2..be96e361 100644
--- a/src/tree.hpp
+++ b/src/tree.hpp
@@ -4,7 +4,7 @@
 #include <cassert>
 #include <numeric>
 #include <vector>
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 #include "algorithms.hpp"
 #include "util.hpp"
diff --git a/src/util.hpp b/src/util.hpp
index 25beee5b..c4362b25 100644
--- a/src/util.hpp
+++ b/src/util.hpp
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <Vector.hpp>
+#include <vector/include/Vector.hpp>
 
 #ifdef DEBUG
 #define EXPECTS(expression) assert(expression)
diff --git a/tests/test_tree.cpp b/tests/test_tree.cpp
index 3db9adbb..c27c1674 100644
--- a/tests/test_tree.cpp
+++ b/tests/test_tree.cpp
@@ -1,6 +1,6 @@
 #include <fstream>
 #include <iostream>
-#include <json.hpp>
+#include <json/src/json.hpp>
 #include <numeric>
 #include <vector>
 
diff --git a/tests/util.hpp b/tests/util.hpp
index 92a9bcb5..6252c7e4 100644
--- a/tests/util.hpp
+++ b/tests/util.hpp
@@ -6,7 +6,7 @@
 #include <string>
 #include <vector>
 
-#include <json.hpp>
+#include <json/src/json.hpp>
 #include <util.hpp>
 
 // helpful code for running tests
diff --git a/tests/validate_ball_and_stick.cpp b/tests/validate_ball_and_stick.cpp
index f871610c..1a9bddb7 100644
--- a/tests/validate_ball_and_stick.cpp
+++ b/tests/validate_ball_and_stick.cpp
@@ -1,5 +1,5 @@
 #include <fstream>
-#include <json.hpp>
+#include <json/src/json.hpp>
 
 #include "gtest.h"
 #include "util.hpp"
diff --git a/tests/validate_soma.cpp b/tests/validate_soma.cpp
index df9ac7bd..44d8235a 100644
--- a/tests/validate_soma.cpp
+++ b/tests/validate_soma.cpp
@@ -1,5 +1,5 @@
 #include <fstream>
-#include <json.hpp>
+#include <json/src/json.hpp>
 
 #include "gtest.h"
 #include "util.hpp"
-- 
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