Merge branch 'develop' into feature/constrained_optimization

.github/workflows/build-linux.yml

@@ -56,7 +56,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Dependencies
         run: |

.github/workflows/build-macos.yml

@@ -26,6 +26,7 @@ jobs:
         # See https://help.github.com/en/articles/workflow-syntax-for-github-actions.
         name: [
           macos-12-xcode-14.2,
+          macos-14-xcode-15.4,
         ]
 
         build_type: [Debug, Release]
@@ -36,9 +37,14 @@ jobs:
             compiler: xcode
             version: "14.2"
 
+          - name: macos-14-xcode-15.4
+            os: macos-14
+            compiler: xcode
+            version: "15.4"
+
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Dependencies
         run: |

.github/workflows/build-python.yml

@@ -29,9 +29,9 @@ jobs:
         name:
           [
             ubuntu-20.04-gcc-9,
-            ubuntu-20.04-gcc-9-tbb,
             ubuntu-20.04-clang-9,
             macos-12-xcode-14.2,
+            macos-14-xcode-15.4,
             windows-2022-msbuild,
           ]
 
@@ -43,12 +43,6 @@ jobs:
             compiler: gcc
             version: "9"
 
-          - name: ubuntu-20.04-gcc-9-tbb
-            os: ubuntu-20.04
-            compiler: gcc
-            version: "9"
-            flag: tbb
-
           - name: ubuntu-20.04-clang-9
             os: ubuntu-20.04
             compiler: clang
@@ -59,13 +53,18 @@ jobs:
             compiler: xcode
             version: "14.2"
 
+          - name: macos-14-xcode-15.4
+            os: macos-14
+            compiler: xcode
+            version: "15.4"
+
           - name: windows-2022-msbuild
             os: windows-2022
             platform: 64
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install (Linux)
         if: runner.os == 'Linux'
@@ -139,7 +138,12 @@ jobs:
 
           # Use the prebuilt binary for Windows
           $Url = "https://sourceforge.net/projects/boost/files/boost-binaries/$env:BOOST_VERSION/$env:BOOST_EXE-${{matrix.platform}}.exe"
-          (New-Object System.Net.WebClient).DownloadFile($Url, "$env:TEMP\boost.exe")
+
+          # Create WebClient with appropriate settings and download Boost exe
+          $wc = New-Object System.Net.Webclient
+          $wc.Headers.Add("User-Agent: Other");
+          $wc.DownloadFile($Url, "$env:TEMP\boost.exe")
+
           Start-Process -Wait -FilePath "$env:TEMP\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES","/DIR=$BOOST_PATH"
 
           # Set the BOOST_ROOT variable
@@ -162,6 +166,14 @@ jobs:
         run: |
           bash .github/scripts/python.sh -d
 
+      - name: Create virtual on MacOS
+        if: runner.os == 'macOS'
+        run: |
+          python$PYTHON_VERSION -m venv venv
+          source venv/bin/activate
+          echo "PATH=$(pwd)/venv/bin:$PATH" >> $GITHUB_ENV
+          python -m pip install --upgrade pip
+
       - name: Install Python Dependencies
         shell: bash
         run: python$PYTHON_VERSION -m pip install -r python/dev_requirements.txt

.github/workflows/build-special.yml

@@ -83,7 +83,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install (Linux)
         if: runner.os == 'Linux'

.github/workflows/build-windows.yml

@@ -44,7 +44,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup msbuild
         uses: ilammy/msvc-dev-cmd@v1
@@ -70,9 +70,6 @@ jobs:
           }
 
           if ("${{ matrix.compiler }}" -eq "gcc") {
-            # Chocolatey GCC is broken on the windows-2019 image.
-            # See: https://github.com/DaanDeMeyer/doctest/runs/231595515
-            # See: https://github.community/t5/GitHub-Actions/Something-is-wrong-with-the-chocolatey-installed-version-of-gcc/td-p/32413
             scoop install gcc --global
             echo "CC=gcc" >> $GITHUB_ENV
             echo "CXX=g++" >> $GITHUB_ENV
@@ -98,7 +95,12 @@ jobs:
 
           # Use the prebuilt binary for Windows
           $Url = "https://sourceforge.net/projects/boost/files/boost-binaries/$env:BOOST_VERSION/$env:BOOST_EXE-${{matrix.platform}}.exe"
-          (New-Object System.Net.WebClient).DownloadFile($Url, "$env:TEMP\boost.exe")
+
+          # Create WebClient with appropriate settings and download Boost exe
+          $wc = New-Object System.Net.Webclient
+          $wc.Headers.Add("User-Agent: Other");
+          $wc.DownloadFile($Url, "$env:TEMP\boost.exe")
+
           Start-Process -Wait -FilePath "$env:TEMP\boost.exe" "/SILENT","/SP-","/SUPPRESSMSGBOXES","/DIR=$BOOST_PATH"
 
           # Set the BOOST_ROOT variable

CMakeLists.txt

@@ -1,4 +1,16 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.5)
+if (POLICY CMP0082)
+    cmake_policy(SET CMP0082 NEW) # install from sub-directories immediately
+endif()
+if (POLICY CMP0102)
+cmake_policy(SET CMP0102 NEW) # set policy on advanced variables and cmake cache
+endif()
+if (POLICY CMP0156)
+cmake_policy(SET CMP0156 NEW) # new linker strategies
+endif()
+if (POLICY CMP0167)
+cmake_policy(SET CMP0167 OLD) # Don't complain about boost
+endif()
 
 # Set the version number for the library
 set (GTSAM_VERSION_MAJOR 4)

CppUnitLite/CMakeLists.txt

@@ -6,6 +6,7 @@ file(GLOB cppunitlite_src "*.cpp")
 add_library(CppUnitLite STATIC ${cppunitlite_src} ${cppunitlite_headers})
 list(APPEND GTSAM_EXPORTED_TARGETS CppUnitLite)
 set(GTSAM_EXPORTED_TARGETS "${GTSAM_EXPORTED_TARGETS}" PARENT_SCOPE)
+target_compile_features(CppUnitLite PUBLIC ${GTSAM_COMPILE_FEATURES_PUBLIC})
 
 gtsam_assign_source_folders("${cppunitlite_headers};${cppunitlite_src}") # MSVC project structure
 

cmake/Config.cmake.in

@@ -15,10 +15,12 @@ endif()
 # Find dependencies, required by cmake exported targets:
 include(CMakeFindDependencyMacro)
 # Allow using cmake < 3.8
-if(${CMAKE_VERSION} VERSION_LESS "3.8.0")
-find_package(Boost @BOOST_FIND_MINIMUM_VERSION@ COMPONENTS @BOOST_FIND_MINIMUM_COMPONENTS@)
-else()
-find_dependency(Boost @BOOST_FIND_MINIMUM_VERSION@ COMPONENTS @BOOST_FIND_MINIMUM_COMPONENTS@)
+if (@GTSAM_ENABLE_BOOST_SERIALIZATION@ OR @GTSAM_USE_BOOST_FEATURES@)
+  if(${CMAKE_VERSION} VERSION_LESS "3.8.0")
+    find_package(Boost @BOOST_FIND_MINIMUM_VERSION@ COMPONENTS @BOOST_FIND_MINIMUM_COMPONENTS@)
+  else()
+    find_dependency(Boost @BOOST_FIND_MINIMUM_VERSION@ COMPONENTS @BOOST_FIND_MINIMUM_COMPONENTS@)
+  endif()
 endif()
 
 if(@GTSAM_USE_TBB@)

cmake/HandleBoost.cmake

@@ -25,7 +25,7 @@ endif()
 set(BOOST_FIND_MINIMUM_VERSION 1.65)
 set(BOOST_FIND_MINIMUM_COMPONENTS serialization system filesystem thread program_options date_time timer chrono regex)
 
-find_package(Boost ${BOOST_FIND_MINIMUM_VERSION} COMPONENTS ${BOOST_FIND_MINIMUM_COMPONENTS})
+find_package(Boost ${BOOST_FIND_MINIMUM_VERSION} COMPONENTS ${BOOST_FIND_MINIMUM_COMPONENTS} REQUIRED)
 
 # Required components
 if(NOT Boost_SERIALIZATION_LIBRARY OR NOT Boost_SYSTEM_LIBRARY OR NOT Boost_FILESYSTEM_LIBRARY OR

cmake/example_cmake_find_gtsam/CMakeLists.txt

@@ -1,7 +1,7 @@
 # This file shows how to build and link a user project against GTSAM using CMake
 ###################################################################################
 # To create your own project, replace "example" with the actual name of your project
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.5)
 project(example CXX)
 
 # Find GTSAM, either from a local build, or from a Debian/Ubuntu package.

doc/Hybrid.lyx

@@ -191,17 +191,17 @@ E_{gc}(x,y)=\frac{1}{2}\|Rx+Sy-d\|_{\Sigma}^{2}.\label{eq:gc_error}
 \end_layout
 
 \begin_layout Subsubsection*
-GaussianMixture
+HybridGaussianConditional
 \end_layout
 
 \begin_layout Standard
 A 
 \emph on
-GaussianMixture
+HybridGaussianConditional
 \emph default
  (maybe to be renamed to 
 \emph on
-GaussianMixtureComponent
+HybridGaussianConditionalComponent
 \emph default
 ) just indexes into a number of 
 \emph on
@@ -233,7 +233,7 @@ GaussianConditional
  to a set of discrete variables.
  As 
 \emph on
-GaussianMixture
+HybridGaussianConditional
 \emph default
  is a 
 \emph on
@@ -324,7 +324,7 @@ The key point here is that
 \color inherit
  is the log-normalization constant for the complete 
 \emph on
-GaussianMixture
+HybridGaussianConditional
 \emph default
  across all values of 
 \begin_inset Formula $m$
@@ -548,15 +548,15 @@ with
 \end_layout
 
 \begin_layout Subsubsection*
-GaussianMixtureFactor
+HybridGaussianFactor
 \end_layout
 
 \begin_layout Standard
 Analogously, a 
 \emph on
-GaussianMixtureFactor
+HybridGaussianFactor
 \emph default
- typically results from a GaussianMixture by having known values 
+ typically results from a HybridGaussianConditional by having known values 
 \begin_inset Formula $\bar{x}$
 \end_inset
 
@@ -817,7 +817,7 @@ E_{mf}(y,m)=\frac{1}{2}\|A_{m}y-b_{m}\|_{\Sigma_{mfm}}^{2}=E_{gcm}(\bar{x},y)+K_
 
 \end_inset
 
-which is identical to the GaussianMixture error 
+which is identical to the HybridGaussianConditional error 
 \begin_inset CommandInset ref
 LatexCommand eqref
 reference "eq:gm_error"

gtsam/3rdparty/Eigen/Eigen/src/SparseCore/TriangularSolver.h

@@ -270,11 +270,9 @@ struct sparse_solve_triangular_sparse_selector<Lhs,Rhs,Mode,UpLo,ColMajor>
       }
 
 
-      Index count = 0;
       // FIXME compute a reference value to filter zeros
       for (typename AmbiVector<Scalar,StorageIndex>::Iterator it(tempVector/*,1e-12*/); it; ++it)
       {
-        ++ count;
 //         std::cerr << "fill " << it.index() << ", " << col << "\n";
 //         std::cout << it.value() << "  ";
         // FIXME use insertBack

gtsam/3rdparty/Eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h

@@ -75,8 +75,6 @@ void SparseLUImpl<Scalar,StorageIndex>::heap_relax_snode (const Index n, IndexVe
   // Identify the relaxed supernodes by postorder traversal of the etree
   Index snode_start; // beginning of a snode 
   StorageIndex k;
-  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
-  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
   StorageIndex l; 
   for (j = 0; j < n; )
   {
@@ -88,7 +86,6 @@ void SparseLUImpl<Scalar,StorageIndex>::heap_relax_snode (const Index n, IndexVe
       parent = et(j);
     }
     // Found a supernode in postordered etree, j is the last column 
-    ++nsuper_et_post;
     k = StorageIndex(n);
     for (Index i = snode_start; i <= j; ++i)
       k = (std::min)(k, inv_post(i));
@@ -97,7 +94,6 @@ void SparseLUImpl<Scalar,StorageIndex>::heap_relax_snode (const Index n, IndexVe
     {
       // This is also a supernode in the original etree
       relax_end(k) = l; // Record last column 
-      ++nsuper_et; 
     }
     else 
     {
@@ -107,7 +103,6 @@ void SparseLUImpl<Scalar,StorageIndex>::heap_relax_snode (const Index n, IndexVe
         if (descendants(i) == 0) 
         {
           relax_end(l) = l;
-          ++nsuper_et;
         }
       }
     }

gtsam/3rdparty/metis/GKlib/pdb.c

@@ -131,7 +131,7 @@ that structure.
 /************************************************************************/
 pdbf *gk_readpdbfile(char *fname) { /* {{{ */
 	int i=0, res=0; 
-	char linetype[6];
+	char linetype[7];
 	int  aserial;
 	char aname[5] = "    \0";
 	char altLoc   = ' ';

gtsam/discrete/AlgebraicDecisionTree.h

@@ -196,6 +196,42 @@ namespace gtsam {
       return this->apply(g, &Ring::div);
     }
 
+    /// Compute sum of all values
+    double sum() const {
+      double sum = 0;
+      auto visitor = [&](double y) { sum += y; };
+      this->visit(visitor);
+      return sum;
+    }
+
+    /**
+     * @brief Helper method to perform normalization such that all leaves in the
+     * tree sum to 1
+     *
+     * @param sum
+     * @return AlgebraicDecisionTree
+     */
+    AlgebraicDecisionTree normalize(double sum) const {
+      return this->apply([&sum](const double& x) { return x / sum; });
+    }
+
+    /// Find the minimum values amongst all leaves
+    double min() const {
+      double min = std::numeric_limits<double>::max();
+      auto visitor = [&](double x) { min = x < min ? x : min; };
+      this->visit(visitor);
+      return min;
+    }
+
+    /// Find the maximum values amongst all leaves
+    double max() const {
+      // Get the most negative value
+      double max = -std::numeric_limits<double>::max();
+      auto visitor = [&](double x) { max = x > max ? x : max; };
+      this->visit(visitor);
+      return max;
+    }
+
     /** sum out variable */
     AlgebraicDecisionTree sum(const L& label, size_t cardinality) const {
       return this->combine(label, cardinality, &Ring::add);

gtsam/discrete/DecisionTree-inl.h

@@ -91,7 +91,7 @@ namespace gtsam {
     void dot(std::ostream& os, const LabelFormatter& labelFormatter,
              const ValueFormatter& valueFormatter,
              bool showZero) const override {
-      std::string value = valueFormatter(constant_);
+      const std::string value = valueFormatter(constant_);
       if (showZero || value.compare("0"))
         os << "\"" << this->id() << "\" [label=\"" << value
            << "\", shape=box, rank=sink, height=0.35, fixedsize=true]\n";
@@ -306,7 +306,8 @@ namespace gtsam {
     void dot(std::ostream& os, const LabelFormatter& labelFormatter,
              const ValueFormatter& valueFormatter,
              bool showZero) const override {
-      os << "\"" << this->id() << "\" [shape=circle, label=\"" << label_
+      const std::string label = labelFormatter(label_);
+      os << "\"" << this->id() << "\" [shape=circle, label=\"" << label
           << "\"]\n";
       size_t B = branches_.size();
       for (size_t i = 0; i < B; i++) {