Update all files to point at include subdir

src/SimpleDiffractionPatternPrediction.cpp

-#include "SimpleDiffractionPatternPrediction.h"
+#include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
 
-#include "eigenSTLContainers.h"
+#include <pinkIndexer/eigenSTLContainers.h>
 #include <cmath>
 
 
@@ -103,4 +103,4 @@ namespace pinkIndexer
         peaksOnEwaldSphere = Map<Matrix3Xf>((float*)peaks.data(), 3, peaks.size());
         millerIndices = Map<Matrix3Xi>((int*)millers.data(), 3, millers.size());
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/SimpleProjection.cpp

-#include "SimpleProjection.h"
+#include <pinkIndexer/SimpleProjection.h>
 
 using namespace std;
 using namespace Eigen;
@@ -19,4 +19,4 @@ namespace pinkIndexer
         projectedPeaks =
             reciprocalPeaks.bottomRows(2).array().rowwise() / (reciprocalPeaks.row(0) - rayOriginsX).array() * experimentSettings.getDetectorDistance_m();
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/Sinogram.cpp

 #define _USE_MATH_DEFINES
 #include <cmath>
 
-#include "Sinogram.h"
+#include <pinkIndexer/Sinogram.h>
 
 #include <algorithm>
 #include <fstream>
@@ -373,4 +373,4 @@ namespace pinkIndexer
         myfile.write((const char*)sinogram.data(), sinogram.size());
         myfile.close();
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/ExperimentSettings.cpp

-#include "adaptions/crystfel/ExperimentSettings.h"
-#include "ExperimentSettings.h"
+#include <pinkIndexer/adaptions/crystfel/ExperimentSettings.h>
+#include <pinkIndexer/ExperimentSettings.h>
 
 #include <Eigen/Dense>
 
@@ -30,4 +30,4 @@ namespace pinkIndexer
     {
         delete experimentSettings;
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/PinkIndexer.cpp

-#include "PinkIndexer.h"
-#include "adaptions/crystfel/PinkIndexer.h"
+#include <pinkIndexer/PinkIndexer.h>
+#include <pinkIndexer/adaptions/crystfel/PinkIndexer.h>
 
 namespace pinkIndexer
 {
@@ -213,4 +213,4 @@ namespace pinkIndexer
         float disbalance = 1.0f - std::abs(fittedMeanDist / totalMeanDist);
         return disbalance;
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/SimpleDiffractionPatternPrediction.cpp

-#include "adaptions/crystfel/SimpleDiffractionPatternPrediction.h"
-#include "SimpleDiffractionPatternPrediction.h"
+#include <pinkIndexer/adaptions/crystfel/SimpleDiffractionPatternPrediction.h>
+#include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
 
 namespace pinkIndexer
 {
@@ -64,4 +64,4 @@ namespace pinkIndexer
             projectionDirections->coordinates_z[i] = projectionDirections_matrix(2, i);
         }
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/SimpleProjection.cpp

-#include "adaptions/crystfel/SimpleProjection.h"
-#include "SimpleProjection.h"
+#include <pinkIndexer/adaptions/crystfel/SimpleProjection.h>
+#include <pinkIndexer/SimpleProjection.h>
 
 namespace pinkIndexer
 {
@@ -34,4 +34,4 @@ namespace pinkIndexer
             projectedPeaks_m->coordinates_y[i] = projectedPeaks_m_matrix(1, i);
         }
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/indexerData.cpp

-#include "adaptions/crystfel/indexerData.h"
+#include <pinkIndexer/adaptions/crystfel/indexerData.h>
 
 void allocReciprocalPeaks(reciprocalPeaks_1_per_A_t* reciprocalPeaks_1_per_A)
 {
@@ -12,4 +12,4 @@ void freeReciprocalPeaks(reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A)
     delete[] reciprocalPeaks_1_per_A.coordinates_x;
     delete[] reciprocalPeaks_1_per_A.coordinates_y;
     delete[] reciprocalPeaks_1_per_A.coordinates_z;
-}
\ No newline at end of file
+}

src/adaptions/crystfel/lattice.cpp

-#include "adaptions/crystfel/Lattice.h"
+#include <pinkIndexer/adaptions/crystfel/Lattice.h>
 
-#include "Lattice.h"
+#include <pinkIndexer/Lattice.h>
 #include <Eigen/Dense>
 
 namespace pinkIndexer
@@ -91,4 +91,4 @@ namespace pinkIndexer
         lattice->cz = basis(2, 2);
     }
 
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer

src/adaptions/crystfel/projectionData.cpp

-#include "adaptions/crystfel/projectionData.h"
+#include <pinkIndexer/adaptions/crystfel/projectionData.h>
 
 void allocDetectorPeaks(detectorPeaks_m_t* detectorPeaks_m)
 {
@@ -39,4 +39,4 @@ void freeMillerIndices(millerIndices_t millerIndices)
     delete[] millerIndices.h;
     delete[] millerIndices.k;
     delete[] millerIndices.l;
-}
\ No newline at end of file
+}

src/main.cpp

 
 #define EIGEN_DONT_PARALLELIZE
 
-#include "Chronometer.h"
+#include <pinkIndexer/Chronometer.h>
 #include <Eigen/Dense>
 #include <iostream>
 

src/tests.cpp

@@ -19,16 +19,16 @@
 #include <sstream>
 #include <string>
 
-#include "Backprojection.h"
-#include "Chronometer.h"
-#include "ExperimentSettings.h"
-#include "PinkIndexer.h"
-#include "Refinement.h"
-#include "ReflectionsInRangeFinder.h"
-#include "SimpleDiffractionPatternPrediction.h"
-#include "SimpleProjection.h"
-#include "Sinogram.h"
-#include "eigenDiskImport.h"
+#include <pinkIndexer/Backprojection.h>
+#include <pinkIndexer/Chronometer.h>
+#include <pinkIndexer/ExperimentSettings.h>
+#include <pinkIndexer/PinkIndexer.h>
+#include <pinkIndexer/Refinement.h>
+#include <pinkIndexer/ReflectionsInRangeFinder.h>
+#include <pinkIndexer/SimpleDiffractionPatternPrediction.h>
+#include <pinkIndexer/SimpleProjection.h>
+#include <pinkIndexer/Sinogram.h>
+#include <pinkIndexer/eigenDiskImport.h>
 
 using namespace std;
 using namespace Eigen;
@@ -341,4 +341,4 @@ namespace pinkIndexer
         return ExperimentSettings(beamEenergy_eV, detectorDistance_m, detectorRadius_m, divergenceAngle_deg, nonMonochromaticity, sampleReciprocalLattice_1A,
                                   tolerance, reflectionRadius_1_per_A);
     }
-} // namespace pinkIndexer
\ No newline at end of file
+} // namespace pinkIndexer