Geos 3.12 Update (#5361)

* Geos changes from updating to 3.12

* Added missing float include

* Updated tests

* Cleaned up environment.yml

* Removed pdal dep

* Set geos dep to proper version

* Embree3 update

* Final changes to embree shape/target

* Use find package shipped with embree and link against embree target

.gitignore

@@ -47,6 +47,7 @@ print.prt
 */tsts/*/output/*
 */build/
 build/
+*build*/
 install/
 
 # Unignore the documentation build

environment.yml

@@ -3,72 +3,74 @@ channels:
   - defaults
 
 dependencies:
-  - kalasiris 
-  - ale=0.9.1
+  - ale>=0.9.1, <1
   - armadillo
-  - boost=1.72
-  - boost-cpp=1.72
+  - boost>=1.72.0, <2
+  - boost-cpp>=1.72.0, <2
   - blas
   - usgs-astrogeology::bullet
   - bz2file
   - bzip2
-  - cmake >=3.15
+  - cmake >=3.15, <4
   - cspice=67
   - csm>=3.0.3,<3.0.4
-  - curl
-  - cxx-compiler=1.1.2
+  - curl>=8.3.0,<9.0a0
+  - cxx-compiler>=1.1.2
   - doxygen
-  - eigen < 3.4
-  - embree>=2.17,<3
+  - eigen>=3, <4
+  - embree>=3, <4
   - ffmpeg
-  - geos =3.11.1
+  - geos>=3.12.1, <4
   - geotiff
   - gmp
   - graphviz
   - gsl>=2.6
-  - hdf5
+  - hdf5>=1.14.2,<1.14.3.0a0
   - icu
   - inja
   - jama
-  - jpeg
   - usgs-astrogeology::kakadu==1
+  - kalasiris
   - krb5
-  - libopencv>=4.5.2
-  - libpng>=1.6.34
-  - libprotobuf<3.20
-  - libtiff>=4.0
+  - libboost>=1.72.0, <2
+  - libgdal >=3.7.2,<3.8.0a0
+  - libopencv>=4.5.2, <5
+  - libpng>=1.6.34, <2
+  - libprotobuf
+  - libtiff>=4.0, <5
   - libxml2
   - make
   - mesalib
   - mysql
   - mysql-connector-c
   - nanoflann<1.4
   - nlohmann_json
-  - ninja==1.7.2
+  - ninja>=1.7.2, <2
   - nn
-  - opencv>=4.5.2
-  - openssl>=1.1.1k
-  - pcl >= 1.10.0
+  - opencv>=4.5.2, <5
+  - openssl>=3.1.2,<4.0a0
+  - pcl >=1.10, <2
   - plio
-  - protobuf<3.20
-  - python>=3.7.11
+  - protobuf
+  - python=3.12
+  - python_abi=3.12
   - pytest
-  - rclone
   - qhull
-  - qt>=5.9.6,<5.15.0
+  - qt-main
   - qwt
-  - sqlite
+  - rclone
+  - sqlite>=3.43.0,<4.0a0
   - suitesparse
   - superlu
   - swig
   - texlive-core
   - tnt
   - x264
   - xalan-c
-  - xerces-c=3
+  - xerces-c>=3.2.4,<3.3.0a0
   - xorg-kbproto
   - xorg-libice
   - xorg-libsm
   - xorg-libx11
   - xorg-libxi
-  - zlib
+  - zlib>=1.2.13,<1.3.0a0

isis/CMakeLists.txt

@@ -161,7 +161,7 @@ endif()
 # sometimes third parties do not set their rpaths correctly
 set(thirdPartyCppFlags -Wall
                        -fPIC
-                       -std=c++14
+                       -std=c++17
                        -DISIS_LITTLE_ENDIAN=1
                        -Wno-unused-parameter
                        -Wno-overloaded-virtual
@@ -171,7 +171,7 @@ set(thirdPartyCppFlags -Wall
                        -DENABLEJP2K=${JP2KFLAG}
                      )
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 
 # Append CPP flags set in the third party lib file to the string set in this file.
 string(REPLACE ";" " " FLAGS_STR "${thirdPartyCppFlags}")
@@ -183,8 +183,8 @@ set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} ${FLAGS_STR}" )
 # Add gold linker (and therefore, phtread) to speed up linux (spec. Ubuntu18.04) builds
 if(NOT APPLE)
   set(thirdPartyCppFlags ${thirdPartyCppFlags} -fuse-ld=gold
-	                                       -pthread
-					       -fext-numeric-literals
+	                                             -pthread
+					                                     -fext-numeric-literals
                                                -Wl,-rpath,$ENV{CONDA_PREFIX}/lib)
 endif()
 
@@ -270,7 +270,7 @@ find_package(Cholmod   4.4.5   REQUIRED)
 find_package(CSM       3.0.3.3 REQUIRED)
 find_package(CSPICE    65      REQUIRED)
 find_package(Eigen             REQUIRED)
-find_package(Embree    2.15.0  REQUIRED)
+find_package(Embree    3.13.0  REQUIRED)
 find_package(GeoTIFF   2       REQUIRED)
 SET(GSL_ROOT_DIR $ENV{CONDA_PREFIX})
 find_package(GSL       2.2.1   REQUIRED)
@@ -279,7 +279,7 @@ find_package(Jama      125     REQUIRED)
 find_package(NN                REQUIRED)
 find_package(OpenCV    3.1.0   REQUIRED)
 find_package(PCL               REQUIRED)
-find_package(Protobuf  2.6.1   REQUIRED)
+find_package(protobuf          REQUIRED CONFIG)
 find_package(Qwt       6       REQUIRED)
 find_package(SuperLU   4.3     REQUIRED)
 find_package(TIFF      4.0.0   REQUIRED)
@@ -352,7 +352,7 @@ foreach (_variableName ${_variableNames})
 endforeach()
 
 # add target based linkages to ALLLIBS variable
-list(APPEND ALLLIBS pantor::inja sensorutilities)
+list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree)
 
 # Sometimes we add the same lib more than once (especially with LIBDIRS)
 list(REMOVE_DUPLICATES ALLLIBDIRS)

isis/cmake/FindGeos.cmake

@@ -6,7 +6,7 @@
 #   GEOS_LIBRARY
 
 find_path(GEOS_INCLUDE_DIR
-  NAMES geos.h
+  NAMES geos.h geos_c.h
   PATH_SUFFIXES "geos/geos${Geos_FIND_VERSION}" "geos"
 )
 

isis/cmake/FindPCL.cmake

@@ -7,7 +7,7 @@
 
 find_path(PCL_INCLUDE_DIR
   NAME pcl_base.h
-  PATH_SUFFIXES "pcl-1.8/pcl" "pcl-1.9/pcl" "pcl-1.11/pcl"
+  PATH_SUFFIXES "pcl-1.8/pcl" "pcl-1.9/pcl" "pcl-1.11/pcl" "pcl-1.12/pcl" "pcl-1.13/pcl"
 )
 
 find_library(PCL_COMMON_LIBRARY NAMES pcl_common)

isis/src/base/apps/caminfo/CamTools.cpp

@@ -734,7 +734,7 @@ namespace Isis {
     vector<const geos::geom::Geometry *> polys;
     polys.push_back(g);
     const geos::geom::GeometryFactory *gfactory = geos::geom::GeometryFactory::getDefaultInstance();
-    return (gfactory->createMultiPolygon(polys));
+    return (gfactory->createMultiPolygon(polys).release());
   }
 
 

isis/src/base/apps/cubediff/main.cpp

@@ -14,12 +14,11 @@
 #include "IString.h"
 #include "Pixel.h"
 
-using namespace std;
 using namespace Isis;
 
-void compare(vector<Buffer *> &in, vector<Buffer *> &out);
+void compare(std::vector<Buffer *> &in, std::vector<Buffer *> &out);
 
-void diffTable(ofstream &target, int precision);
+void diffTable(std::ofstream &target, int precision);
 
 // This is only used for the difference table
 struct Difference {
@@ -36,7 +35,7 @@ int sample, line, band, spCount, diffCount, colWidth;
 Statistics stats;
 bool doTable;
 unsigned int sigFigAccuracy = DBL_DIG; // DBL_DIG is maximum accuracy for a double
-vector<Difference> diffset;
+std::vector<Difference> diffset;
 int sigFigLine = 0;
 int sigFigSample = 0;
 int sigFigBand = 0;
@@ -64,7 +63,7 @@ void IsisMain() {
     doTable = true;
     diffCount = ui.GetInteger("COUNT");
     if(!ui.WasEntered("TO")) {
-      string message = "A target file is required for difference output";
+      std::string message = "A target file is required for difference output";
       throw IException(IException::User, message, _FILEINFO_);
     }
 
@@ -123,15 +122,15 @@ void IsisMain() {
   }
   if(doTable) {
     QString filename = FileName(ui.GetFileName("TO", "txt")).expanded();
-    ofstream ofile(filename.toLatin1().data(), ios_base::app);
+    std::ofstream ofile(filename.toLatin1().data(), std::ios_base::app);
     diffTable(ofile, ui.GetInteger("PRECISION"));
   }
 
   p.EndProcess();
   filesEqual = true;
 }
 
-void compare(vector<Buffer *> &in, vector<Buffer *> &out) {
+void compare(std::vector<Buffer *> &in, std::vector<Buffer *> &out) {
   Buffer &input1 = *in[0];
   Buffer &input2 = *in[1];
   int inputSize = input1.size();
@@ -252,8 +251,8 @@ void compare(vector<Buffer *> &in, vector<Buffer *> &out) {
 }
 
 //Function to prepare the table to append to the
-void diffTable(ofstream &target, int precision) {
-  vector<int> temp;
+void diffTable(std::ofstream &target, int precision) {
+  std::vector<int> temp;
 
   //Make a list of all samples present
   for(unsigned int i = 0; i < diffset.size(); i++) {
@@ -264,14 +263,14 @@ void diffTable(ofstream &target, int precision) {
   sort(temp.begin(), temp.end());
 
   //Remove duplicates
-  vector<int> samps;
+  std::vector<int> samps;
   samps.push_back(temp[0]);
   for(unsigned int i = 1; i < temp.size(); i++) {
     if(temp[i] != samps.back()) {
       samps.push_back(temp[i]);
     }
   }
-  vector<Column> cols;
+  std::vector<Column> cols;
   //Add the first Column
   Column first("Line#", 7, Column::Integer);
   cols.push_back(first);

isis/src/base/apps/fakecube/main.cpp

@@ -2,7 +2,6 @@
 #include "ProcessByLine.h"
 #include "SpecialPixel.h"
 
-using namespace std;
 using namespace Isis;
 
 void SumLineSample(Buffer &in, Buffer &out);

isis/src/base/apps/footprintmerge/main.cpp

@@ -83,7 +83,7 @@ void IsisMain() {
 
   //  Create union poly
   geos::geom::GeometryCollection *polyCollection =
-    Isis::globalFactory->createGeometryCollection(allPolys);
+    Isis::globalFactory->createGeometryCollection(allPolys).release();
   geos::geom::Geometry *unionPoly = polyCollection->buffer(0).release();
 
 

isis/src/base/objs/Chip/Chip.cpp

@@ -959,8 +959,8 @@ namespace Isis {
             interp.Interpolate(CubeSample(), CubeLine(), port.DoubleBuffer());
         }
         else {
-          geos::geom::Point *pnt = globalFactory->createPoint(
-                                     geos::geom::Coordinate(CubeSample(), CubeLine()));
+          std::unique_ptr<geos::geom::Point> pnt = globalFactory->createPoint(
+              geos::geom::Coordinate(CubeSample(), CubeLine()));
           if (pnt->within(m_clipPolygon)) {
             port.SetPosition(CubeSample(), CubeLine(), band);
             cube.read(port);
@@ -970,7 +970,7 @@ namespace Isis {
           else {
             m_buf[line-1][samp-1] = Isis::NULL8;
           }
-          delete pnt;
+          pnt.reset();
         }
       }
     }

isis/src/base/objs/Chip/unitTest.cpp

@@ -17,7 +17,7 @@ find files of those names at the top level of this repository. **/
 #include "Preference.h"
 #include "SpecialPixel.h"
 #include "geos/geom/Coordinate.h"
-#include "geos/geom/CoordinateArraySequence.h"
+#include "geos/geom/CoordinateSequence.h"
 #include "geos/geom/GeometryFactory.h"
 #include "geos/geom/Polygon.h"
 #include "geos/geom/MultiPolygon.h"
@@ -134,16 +134,16 @@ int main() {
   cout << "Test load chip from cube with rotation and clipping polygon " << endl;
   chip.TackCube(26.0, 25.0);
 
-  geos::geom::CoordinateArraySequence *pts = new geos::geom::CoordinateArraySequence();
-  pts->add(geos::geom::Coordinate(23.0, 22.0));
-  pts->add(geos::geom::Coordinate(28.0, 22.0));
-  pts->add(geos::geom::Coordinate(28.0, 27.0));
-  pts->add(geos::geom::Coordinate(25.0, 28.0));
-  pts->add(geos::geom::Coordinate(23.0, 22.0));
-  vector<geos::geom::Geometry *> *polys = new vector<geos::geom::Geometry *>;
+  geos::geom::CoordinateSequence pts;
+  pts.add(geos::geom::Coordinate(23.0, 22.0));
+  pts.add(geos::geom::Coordinate(28.0, 22.0));
+  pts.add(geos::geom::Coordinate(28.0, 27.0));
+  pts.add(geos::geom::Coordinate(25.0, 28.0));
+  pts.add(geos::geom::Coordinate(23.0, 22.0));
+  vector <const geos::geom::Geometry *> polys;
   geos::geom::GeometryFactory::Ptr gf = geos::geom::GeometryFactory::create();
-  polys->push_back(gf->createPolygon(gf->createLinearRing(pts), NULL));
-  geos::geom::MultiPolygon *mPolygon = gf->createMultiPolygon(polys);
+  polys.push_back(gf->createPolygon(gf->createLinearRing(pts)).release());
+  geos::geom::MultiPolygon *mPolygon = gf->createMultiPolygon(polys).release();
 
   chip.SetClipPolygon(*mPolygon);
   chip.Load(junk, 45.0);