Merge pull request #2 from kerautret/FixCIFrechetFix

Fix ci frechet fix

.github/workflows/build-master.yml

@@ -10,7 +10,7 @@ env:
   CONFIG_GLOBAL:  -DBUILD_EXAMPLES=true -DBUILD_TESTING=true -DDGTAL_RANDOMIZED_TESTING_THRESHOLD=10 -DWITH_EIGEN=true 
   CONFIG_LINUX:   -DWITH_OPENMP=true -DWITH_GMP=true -DWITH_FFTW3=true -DWITH_CGAL=true -DWITH_LIBIGL=true  -DWARNING_AS_ERROR=ON -DWITH_HDF5=true -DWITH_QGLVIEWER=true -DWITH_CAIRO=true   -DWITH_ITK=true -DDGTAL_ENABLE_FLOATING_POINT_EXCEPTIONS=true -DBUILD_POLYSCOPE_EXAMPLES=true
   CONFIG_MAC:     -DWITH_GMP=true -DBUILD_POLYSCOPE_EXAMPLES=true -DWITH_CGAL=true -DWITH_LIBIGL=true 
-  CONFIG_WINDOWS: -DWITH_OPENMP=true -DENABLE_CONAN=true #-DWITH_FFTW3=true  #-DWITH_CAIRO=true #-DWITH_ITK=true  -DWITH_GMP=true
+  CONFIG_WINDOWS: -DWITH_OPENMP=true  #-DWITH_GMP=true #-DWITH_FFTW3=true  #-DWITH_CAIRO=true #-DWITH_ITK=true  
 
 jobs:
   build:
@@ -44,17 +44,18 @@ jobs:
        id: conan
        uses: turtlebrowser/get-conan@main
        with:
-         version: 1.57.0
+         version: 2.4.0
 
      - name: Create conan default profile
        if: matrix.os == 'windows-latest'
-       run: conan profile new default --detect
-
+       run: |
+          conan profile detect --force
+  
      - uses: actions/cache@v4
        if: matrix.os == 'windows-latest'
        with:
          path: ~/.conan
-         key: ${{ runner.os }}-conan-${{ matrix.BUILD_TYPE }}
+         key: ${{ runner.os }}-conan2-${{ matrix.BUILD_TYPE }}
 
      - name: Get white list of tests
        run: |
@@ -80,7 +81,9 @@ jobs:
        if: matrix.os == 'windows-latest'
        shell: bash
        working-directory: ${{runner.workspace}}/build
-       run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_GLOBAL $CONFIG_WINDOWS -DDGTAL_RANDOMIZED_TESTING_WHITELIST="${{ steps.whitelist.outputs.WHITELIST }}"
+       run: |
+            conan install $GITHUB_WORKSPACE --build=missing
+            cmake $GITHUB_WORKSPACE -DCMAKE_TOOLCHAIN_FILE="conan_toolchain.cmake" -DCMAKE_POLICY_DEFAULT_CMP0091=NEW -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_GLOBAL $CONFIG_WINDOWS -DDGTAL_RANDOMIZED_TESTING_WHITELIST="${{ steps.whitelist.outputs.WHITELIST }}"
 
      - name: Build
        working-directory: ${{runner.workspace}}/build

.github/workflows/buildAndDocumentation-PR.yml

@@ -6,12 +6,11 @@ on:
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE:    Debug
   TESTBLACKLIST: "(testLinearStructure|testIntegerConverter|testArithmeticalDSSComputerOnSurfels)"
   CONFIG_GLOBAL:  -DBUILD_EXAMPLES=true -DBUILD_TESTING=true -DDGTAL_RANDOMIZED_TESTING_THRESHOLD=10 -DWITH_EIGEN=true
   CONFIG_LINUX:   -DUSE_CCACHE=NO -DWITH_OPENMP=true -DWITH_GMP=true -DWITH_CGAL=true -DWITH_LIBIGL=true -DWITH_FFTW3=true -DWARNING_AS_ERROR=ON -DWITH_HDF5=true -DWITH_QGLVIEWER=true -DWITH_CAIRO=true   -DWITH_ITK=true -DDGTAL_ENABLE_FLOATING_POINT_EXCEPTIONS=true -DBUILD_POLYSCOPE_EXAMPLES=true
   CONFIG_MAC:     -DUSE_CCACHE=NO -DWITH_GMP=true -DBUILD_POLYSCOPE_EXAMPLES=true -DWITH_CGAL=true -DWITH_LIBIGL=true
-  CONFIG_WINDOWS: -DWITH_OPENMP=true -DENABLE_CONAN=true #-DWITH_FFTW3=true  #-DWITH_CAIRO=true #-DWITH_ITK=true  -DWITH_GMP=true
+  CONFIG_WINDOWS: -DWITH_OPENMP=true   #-DWITH_GMP=true #-DWITH_FFTW3=true  #-DWITH_CAIRO=true #-DWITH_ITK=true 
 
 jobs:
   build:
@@ -45,17 +44,19 @@ jobs:
        id: conan
        uses: turtlebrowser/get-conan@main
        with:
-         version: 1.57.0
+         version: 2.4.0
 
      - name: Create conan default profile
        if: matrix.os == 'windows-latest'
-       run: conan profile new default --detect
+       run: |
+         conan profile detect --force
+
 
      - uses: actions/cache@v4
        if: matrix.os == 'windows-latest'
        with:
-         path: ~/.conan
-         key: ${{ runner.os }}-conan-${{ matrix.BUILD_TYPE }}
+         path: ~/.conan2
+         key: ${{ runner.os }}-conan2-${{ matrix.BUILD_TYPE }}
 
      - name: Get white list of tests
        run: |
@@ -81,7 +82,9 @@ jobs:
        if: matrix.os == 'windows-latest'
        shell: bash
        working-directory: ${{runner.workspace}}/build
-       run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_GLOBAL $CONFIG_WINDOWS -DDGTAL_RANDOMIZED_TESTING_WHITELIST="${{ steps.whitelist.outputs.WHITELIST }}"
+       run: |
+          conan install $GITHUB_WORKSPACE --build=missing
+          cmake $GITHUB_WORKSPACE -DCMAKE_TOOLCHAIN_FILE="conan_toolchain.cmake" -DCMAKE_POLICY_DEFAULT_CMP0091=NEW -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_GLOBAL $CONFIG_WINDOWS -DDGTAL_RANDOMIZED_TESTING_WHITELIST="${{ steps.whitelist.outputs.WHITELIST }}"
 
      - name: Build
        working-directory: ${{runner.workspace}}/build

.github/workflows/pythonBindings-PR.yml

@@ -48,17 +48,18 @@ jobs:
         id: conan
         uses: turtlebrowser/get-conan@main
         with:
-          version: 1.57.0
+          version: 2.4.0
 
       - name: Install dependancies (conan - Windows 2/2)
         if: matrix.os == 'windows-latest'
-        run: conan profile new default --detect
-
+        run: |
+          conan profile detect --force
+  
       - uses: actions/cache@v3
         if: matrix.os == 'windows-latest'
         with:
-          path: ~/.conan
-          key: ${{ runner.os }}-conan-${{ matrix.BUILD_TYPE }}
+          path: ~/.conan2
+          key: ${{ runner.os }}-conan2-${{ matrix.BUILD_TYPE }}
 
 
       - name: Create Build Environment
@@ -80,7 +81,9 @@ jobs:
         if: matrix.os == 'windows-latest'
         shell: bash
         working-directory: ${{runner.workspace}}/build
-        run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_PYTHON $CONFIG_GLOBAL $CONFIG_WINDOWS
+        run: |
+            conan install $GITHUB_WORKSPACE --build=missing
+            cmake $GITHUB_WORKSPACE -DCMAKE_TOOLCHAIN_FILE="conan_toolchain.cmake" -DCMAKE_POLICY_DEFAULT_CMP0091=NEW -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} $CONFIG_PYTHON $CONFIG_GLOBAL $CONFIG_WINDOWS
 
 
       - name: Build

.github/workflows/pythonBindings-Pypi.yml

@@ -51,17 +51,19 @@ jobs:
         id: conan
         uses: turtlebrowser/get-conan@main
         with:
-          version: 1.57.0
+          version: 2.4.0
 
       - name: Install dependancies (conan - Windows 2/2)
         if: matrix.os == 'windows-latest'
-        run: conan profile new default --detect
+        run: |
+          conan profile new default --detect
+          conan install . --output-folder=build --build=missing
 
       - uses: actions/cache@v3
         if: matrix.os == 'windows-latest'
         with:
           path: ~/.conan
-          key: ${{ runner.os }}-conan-${{ matrix.BUILD_TYPE }}
+          key: ${{ runner.os }}-conan2-${{ matrix.BUILD_TYPE }}
 
       - name: Install python dependancies
         shell: bash

ChangeLog.md

@@ -5,13 +5,13 @@
   - Major update: C++17 is now required for DGtal. (David Coeurjolly,
     [#1682](https://github.com/DGtal-team/DGtal/pull/1682))
   - Mandatory dependencies and some optional ones can be setup by
-    conan.io, especially on windows, new `ENABLE_CONAN` cmake
+    conan.io, especially on Windows, new `ENABLE_CONAN` cmake
     option to activate this. (David Coeurjolly,
     [#1689](https://github.com/DGtal-team/DGtal/pull/1689))
   - Faster build using CPM for dependency download and ccache with the cmake `USE_CCACHE=YES`option 
     (ccache must be installed). (David Coeurjolly, [#1696](https://github.com/DGtal-team/DGtal/pull/1696)) 
   - Better documentation style using doxygen-awesome.css. (David Coeurjolly,
-  [#1697](https://github.com/DGtal-team/DGtal/pull/1697))
+    [#1697](https://github.com/DGtal-team/DGtal/pull/1697))
 
 - *Geometry*
   - New implicit shape from point cloud using LibIGL Winding Numbers. (David Coeurjolly,
@@ -23,24 +23,41 @@
     [#1699](https://github.com/DGtal-team/DGtal/pull/1699))
   - Python bindings and Pypi deploy are now handled by Github-Actions (Bastien Doignies,
     [#1721](https://github.com/DGtal-team/DGtal/pull/1721))
+  - Add CMake option DGTAL_WRAP_PYTHON (Pablo Hernandez-Cerdan,
+    [#1700](https://github.com/DGtal-team/DGtal/pull/1700))
+  - Upgrade of the conan scripts (for windows build) to conan 2, removing the ENABLE_CONAN option 
+    (documentation update instead) (David Coeurjolly, 
+    [#1729](https://github.com/DGtal-team/DGtal/pull/1729))
 
 - *IO*
   - New method to change the mode of the light position in Viewer3D (fixed to
     camera or the scene) (Bertrand Kerautret, [#1683](https://github.com/DGtal-team/DGtal/pull/1683))
   - Add a new method to store material information in obj file in MeshReader and MeshWriter.
     (Bertrand Kerautret, [#1686](https://github.com/DGtal-team/DGtal/pull/1686))
   - Fix duplicate symbols on Windows due to stb_image, see issue #1714 (David Coeurjolly,
-    [#1715](https://github.com/DGtal-team/DGtal/pull/1715)
+    [#1715](https://github.com/DGtal-team/DGtal/pull/1715))
 
 - *Shapes*
-  - Add flips to SurfaceMesh data structure
-    (Jacques-Olivier Lachaud, [#1702](https://github.com/DGtal-team/DGtal/pull/1702))
+  - Add flips to SurfaceMesh data structure (Jacques-Olivier Lachaud,
+    [#1702](https://github.com/DGtal-team/DGtal/pull/1702))
   - Add method to remove isolated vertices in Mesh, improve obj
     material reading from potential obsolete path. (Bertrand Kerautret,
     [#1709](https://github.com/DGtal-team/DGtal/issues/1709))
-  - Update of the WindingNumber constructor to allow external computation of point areas
+  - Update of the WindingNumberShape constructor to allow external computation of point areas
+    (David Coeurjolly,[#1719](https://github.com/DGtal-team/DGtal/issues/1719))
+  - The WindingNumberShape class can output the raw winding number values
     (David Coeurjolly,[#1719](https://github.com/DGtal-team/DGtal/issues/1719))
 
+- *DEC*
+  - New helper functor to construct an embedder to correct the PolygonalCalculs
+    (projection onto estimated tangent planes) (David Coeurjolly,
+    [#1730](https://github.com/DGtal-team/DGtal/issues/17309))
+
+- *Geometry package*
+  - Add creation of polytopes from segments and triangles in
+    ConvexityHelper and 3-5xfaster full subconvexity tests for triangles
+    in DigitalConvexity (Jacques-Olivier Lachaud,
+    [#1717](https://github.com/DGtal-team/DGtal/pull/1717))
 
 - *Project*
   - Add CMake option DGTAL_WRAP_PYTHON (Pablo Hernandez-Cerdan,
@@ -84,16 +101,25 @@
     [#1711](https://github.com/DGtal-team/DGtal/pull/1711))
   - Fixing install path of CPM in the DGtalConfig.cmake.in (David Coeurjolly,
     [#1713](https://github.com/DGtal-team/DGtal/pull/1713))
+  - DGTAL_LIBRARIES cmake flag now contains the Deps (David Coeurjolly,
+    [#1728](https://github.com/DGtal-team/DGtal/pull/1728))
 
 - *Topology package*
   - Fix KhalimskySpaceND to get it work with BigInteger (Tristan Roussillon,
-    [#1681](https://github.com/DGtal-team/DGtal/pull/1681)
+    [#1681](https://github.com/DGtal-team/DGtal/pull/1681))
 
 - *Geometry package*
   - Fix Issue #1676 in testStabbingCircleComputer (Tristan Roussillon,
     [#1688](https://github.com/DGtal-team/DGtal/pull/1688)
+  - Fix BoundedLatticePolytopeCounter::countInterior method (Jacques-Olivier Lachaud,
+    [#1717](https://github.com/DGtal-team/DGtal/pull/1717))
   - Fix const attribute that shouldn't be in FreemanChain (Colin Weill--Duflos,
-    [#1723](https://github.com/DGtal-team/DGtal/pull/1723))
+	  [#1723](https://github.com/DGtal-team/DGtal/pull/1723))
+  - Fix seg fault due to recent compilers in FrechetShortcut (Bertrand Kerautret, 
+     Isabelle Sivignon [#1726](https://github.com/DGtal-team/DGtal/pull/1726))
+  - Fix FrechetShortcut to enable the parameter error to be equal to 0 and add new 
+    tests in testFrechetShortcut (Isabelle Sivignon, [#1726](https://github.com/DGtal-team/DGtal/pull/1726))
+
 
 - *IO*
   - Fix of the `getHSV` method in the `Color` class. (David Coeurjolly,

README.md

@@ -17,6 +17,7 @@ and to construct a federative project. Another objective of DGtal is
 to simplify the construction of demonstration tools to share new
 results and potential efficiency of the proposed work.
 
+DGtal received the [Symposium on Geometry Processing Software Award in 2016](http://awards.geometryprocessing.org/).
 
 Quick Install
 =============

cmake/CheckDGtalDependencies.cmake

@@ -6,70 +6,6 @@ message(STATUS "----------------------------------------------------------------
 message(STATUS "DGtal required dependencies: ")
 
 
-# -----------------------------------------------------------------------------
-# Mandatory and optional deps via conan
-# -----------------------------------------------------------------------------
-option(ENABLE_CONAN "Enable conan for deps discovery (used for windows CI for instance) features." OFF)
-
-
-if (ENABLE_CONAN)
-  message(STATUS  "Conan enabled for deps")
-
-  if(NOT EXISTS "${CMAKE_BINARY_DIR}/conan.cmake")
-    message(STATUS "Downloading conan.cmake from https://github.com/conan-io/cmake-conan")
-    file(DOWNLOAD "https://raw.githubusercontent.com/conan-io/cmake-conan/0.18.1/conan.cmake"
-                "${CMAKE_BINARY_DIR}/conan.cmake"
-                 STATUS DOWNLOAD_STATUS
-                 TLS_VERIFY ON)
-    list(GET DOWNLOAD_STATUS 0 STATUS_CODE)
-    list(GET DOWNLOAD_STATUS 1 ERROR_MESSAGE)
-    # Check if download was successful.
-    if(${STATUS_CODE} EQUAL 0)
-       message(STATUS "Download completed successfully!")
-    else()
-       message(STATUS "Error occurred during download: ${ERROR_MESSAGE}")
-       message(STATUS "Trying turning TLS_VERIFY OFF")
-       file(DOWNLOAD "https://raw.githubusercontent.com/conan-io/cmake-conan/0.18.1/conan.cmake"
-                     "${CMAKE_BINARY_DIR}/conan.cmake"
-                      STATUS DOWNLOAD_STATUS
-                      TLS_VERIFY OFF)
-       list(GET DOWNLOAD_STATUS 0 STATUS_CODE)
-       list(GET DOWNLOAD_STATUS 1 ERROR_MESSAGE)                   
-       if(${STATUS_CODE} EQUAL 0)
-         message(STATUS "Download completed successfully!")
-       else()
-         message(FATAL_ERROR "Error occurred during download: ${ERROR_MESSAGE}")
-       endif()
-    endif()
-  endif()
-
-  include("${CMAKE_BINARY_DIR}/conan.cmake")
-
-  conan_cmake_configure(REQUIRES zlib/1.2.13
-                                 boost/1.81.0
-                                 gmp/6.2.1
-                                 fftw/3.3.9
-                                 #cairo/1.17.6
-                                 #libpng/1.6.39 #Explicit fix deps (compat issues)
-                                 #expat/2.5.0
-                                 #openssl/1.1.1s
-                                 #libiconv/1.17
-                      OPTIONS boost:header_only=True
-                              gmp:enable_cxx=True
-                      GENERATORS cmake_find_package)
-
-  conan_cmake_autodetect(settings)
-  conan_cmake_install(PATH_OR_REFERENCE .
-                    BUILD missing
-                    REMOTE conancenter
-                    SETTINGS ${settings})
-
-  set(FFTW3_DIR ${CONAN_FFTW_ROOT})
-  message(STATUS "Setting FFTW3_DIR to ${CONAN_FFTW_ROOT}")
-else()
-  message(STATUS "Conan disabled")
-endif()
-
 # -----------------------------------------------------------------------------
 # Looking for boost
 # -----------------------------------------------------------------------------

cmake/DGtalConfig.cmake.in

@@ -132,5 +132,5 @@ if(NOT TARGET DGtal)
   include ("${DGTAL_CMAKE_DIR}/DGtalLibraryDepends.cmake")
 endif()
 
-set(DGTAL_LIBRARIES DGtal Eigen3::Eigen)
+set(DGTAL_LIBRARIES DGtal ${DGtalLibDependencies})
 get_target_property(DGTAL_INCLUDE_DIRS DGtal INTERFACE_INCLUDE_DIRECTORIES)

conanfile.txt

@@ -0,0 +1,14 @@
+[requires]
+fmt/9.1.0
+zlib/1.2.13
+boost/1.81.0
+gmp/6.3.0
+fftw/3.3.9
+
+[generators]
+CMakeDeps
+CMakeToolchain
+
+[options] 
+boost*:header_only=True
+gmp*:enable_cxx=True

examples/polyscope-examples/dgtalCalculus-bunny.cpp

@@ -19,6 +19,7 @@
  * Laboratoire d'InfoRmatique en Image et Systemes d'information - LIRIS (CNRS, UMR 5205), CNRS, France
  *
  * @date 2021/09/02
+ * @ingroup Examples
  *
  * This file is part of the DGtal library.
  */

examples/polyscope-examples/dgtalCalculus-geodesic.cpp

@@ -17,6 +17,7 @@
  * @file
  * @author David Coeurjolly (\c david.coeurjolly@liris.cnrs.fr )
  * Laboratoire d'InfoRmatique en Image et Systemes d'information - LIRIS (CNRS, UMR 5205), CNRS, France
+ * @ingroup Examples
  *
  * @date 2021/09/02
  *
@@ -92,25 +93,11 @@ void precompute()
     auto surfels   = SH3::getSurfelRange( surface, params2 );
     iinormals = SHG3::getIINormalVectors(binary_image, surfels,params2);
     trace.info()<<iinormals.size()<<std::endl;
-    auto myProjEmbedder = [&](Face f, Vertex v)
-    {
-      const auto nn = iinormals[f];
-      RealPoint centroid(0.0,0.0,0.0); //centroid of the original face
-      auto cpt=0;
-      for(auto v: surfmesh.incidentVertices(f))
-      {
-        cpt++;
-        centroid += surfmesh.position(v);
-      }
-      centroid = centroid / (double)cpt;
-      RealPoint p = surfmesh.position(v);
-      auto cp = p-centroid;
-      RealPoint q = p - nn.dot(cp)*nn;
-      return q;
-    };
     psMesh->addFaceVectorQuantity("II normals", iinormals);
+
     calculus = new PolyCalculus(surfmesh);
-    calculus->setEmbedder( myProjEmbedder );
+    functors::EmbedderFromNormalVectors<Z3i::RealPoint, Z3i::RealVector> embedderFromNormals(iinormals,surfmesh);
+    calculus->setEmbedder( embedderFromNormals );
   }
 
   heat = new GeodesicsInHeat<PolyCalculus>(calculus);

examples/polyscope-examples/dgtalCalculus-halfsphere.cpp

@@ -19,6 +19,7 @@
  * Laboratory of Mathematics (CNRS, UMR 5127), University of Savoie, France
  *
  * @date 2022/04/10
+ * @ingroup Examples
  *
  * This file is part of the DGtal library.
  */