Merge pull request #1399 from borglab/feature/remove_deprecated_code

Remove code deprecated in 4.2

.github/scripts/python.sh

@@ -79,7 +79,7 @@ function build()
       -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
       -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=OFF \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V43=OFF \
       -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install
 
 

.github/scripts/unix.sh

@@ -64,7 +64,7 @@ function configure()
       -DGTSAM_BUILD_UNSTABLE=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_WITH_TBB=${GTSAM_WITH_TBB:-OFF} \
       -DGTSAM_BUILD_EXAMPLES_ALWAYS=${GTSAM_BUILD_EXAMPLES_ALWAYS:-ON} \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=${GTSAM_ALLOW_DEPRECATED_SINCE_V42:-OFF} \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V43=${GTSAM_ALLOW_DEPRECATED_SINCE_V43:-OFF} \
       -DGTSAM_USE_QUATERNIONS=${GTSAM_USE_QUATERNIONS:-OFF} \
       -DGTSAM_ROT3_EXPMAP=${GTSAM_ROT3_EXPMAP:-ON} \
       -DGTSAM_POSE3_EXPMAP=${GTSAM_POSE3_EXPMAP:-ON} \

.github/workflows/build-special.yml

@@ -110,8 +110,8 @@ jobs:
       - name: Set Allow Deprecated Flag
         if: matrix.flag == 'deprecated'
         run: |
-          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V42=ON" >> $GITHUB_ENV
-          echo "Allow deprecated since version 4.1"
+          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V43=ON" >> $GITHUB_ENV
+          echo "Allow deprecated since version 4.3"
 
       - name: Set Use Quaternions Flag
         if: matrix.flag == 'quaternions'

CMakeLists.txt

@@ -6,8 +6,6 @@ if(NOT DEFINED CMAKE_MACOSX_RPATH)
   set(CMAKE_MACOSX_RPATH 0)
 endif()
 
-set(CMAKE_CXX_STANDARD 17)
-
 # Set the version number for the library
 set (GTSAM_VERSION_MAJOR 4)
 set (GTSAM_VERSION_MINOR 3)

README.md

@@ -55,11 +55,6 @@ Optional prerequisites - used automatically if findable by CMake:
 
 GTSAM 4 introduces several new features, most notably Expressions and a Python toolbox. It also introduces traits, a C++ technique that allows optimizing with non-GTSAM types. That opens the door to retiring geometric types such as Point2 and Point3 to pure Eigen types, which we also do. A significant change which will not trigger a compile error is that zero-initializing of Point2 and Point3 is deprecated, so please be aware that this might render functions using their default constructor incorrect.
 
-GTSAM 4 also deprecated some legacy functionality and wrongly named methods. If you are on a 4.0.X release, you can define the flag `GTSAM_ALLOW_DEPRECATED_SINCE_V4` to use the deprecated methods.
-
-GTSAM 4.1 added a new pybind wrapper, and **removed** the deprecated functionality. There is a flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42` for newly deprecated methods since the 4.1 release, which is on by default, allowing anyone to just pull version 4.1 and compile.
-
-
 ## Wrappers
 
 We provide support for [MATLAB](matlab/README.md) and [Python](python/README.md) wrappers for GTSAM. Please refer to the linked documents for more details.

cmake/GtsamBuildTypes.cmake

@@ -142,17 +142,14 @@ endif()
 if (NOT CMAKE_VERSION VERSION_LESS 3.8)
     set(GTSAM_COMPILE_FEATURES_PUBLIC "cxx_std_17" CACHE STRING "CMake compile features property for all gtsam targets.")
     # See: https://cmake.org/cmake/help/latest/prop_tgt/CXX_EXTENSIONS.html
-    # TODO(dellaert): is following line still needed or was that only for c++11?
     set(CMAKE_CXX_EXTENSIONS OFF)
     if (MSVC)
       # NOTE(jlblanco): seems to be required in addition to the cxx_std_17 above?
-      # TODO(dellaert): is this the right syntax below?
       list_append_cache(GTSAM_COMPILE_OPTIONS_PUBLIC /std:c++latest)
     endif()
 else()
   # Old cmake versions:
   if (NOT MSVC)
-    # TODO(dellaert): I just changed 11 to 17 below, hopefully that works
     list_append_cache(GTSAM_COMPILE_OPTIONS_PUBLIC $<$<COMPILE_LANGUAGE:CXX>:-std=c++17>)
   endif()
 endif()

cmake/HandleGeneralOptions.cmake

@@ -25,7 +25,7 @@ option(GTSAM_WITH_EIGEN_MKL_OPENMP          "Eigen, when using Intel MKL, will a
 option(GTSAM_THROW_CHEIRALITY_EXCEPTION     "Throw exception when a triangulated point is behind a camera" ON)
 option(GTSAM_BUILD_PYTHON                   "Enable/Disable building & installation of Python module with pybind11" OFF)
 option(GTSAM_INSTALL_MATLAB_TOOLBOX         "Enable/Disable installation of matlab toolbox"  OFF)
-option(GTSAM_ALLOW_DEPRECATED_SINCE_V42     "Allow use of methods/functions deprecated in GTSAM 4.1" ON)
+option(GTSAM_ALLOW_DEPRECATED_SINCE_V43     "Allow use of methods/functions deprecated in GTSAM 4.3" ON)
 option(GTSAM_SUPPORT_NESTED_DISSECTION      "Support Metis-based nested dissection" ON)
 option(GTSAM_TANGENT_PREINTEGRATION         "Use new ImuFactor with integration on tangent space" ON)
 option(GTSAM_SLOW_BUT_CORRECT_BETWEENFACTOR "Use the slower but correct version of BetweenFactor" OFF)

cmake/HandlePrintConfiguration.cmake

@@ -87,7 +87,7 @@ print_enabled_config(${GTSAM_USE_QUATERNIONS}             "Quaternions as defaul
 print_enabled_config(${GTSAM_ENABLE_CONSISTENCY_CHECKS}   "Runtime consistency checking    ")
 print_enabled_config(${GTSAM_ROT3_EXPMAP}                 "Rot3 retract is full ExpMap     ")
 print_enabled_config(${GTSAM_POSE3_EXPMAP}                "Pose3 retract is full ExpMap    ")
-print_enabled_config(${GTSAM_ALLOW_DEPRECATED_SINCE_V42}  "Allow features deprecated in GTSAM 4.1")
+print_enabled_config(${GTSAM_ALLOW_DEPRECATED_SINCE_V43}  "Allow features deprecated in GTSAM 4.3")
 print_enabled_config(${GTSAM_SUPPORT_NESTED_DISSECTION}   "Metis-based Nested Dissection   ")
 print_enabled_config(${GTSAM_TANGENT_PREINTEGRATION}      "Use tangent-space preintegration")
 

examples/StereoVOExample_large.cpp

@@ -27,6 +27,7 @@
 #include <gtsam/geometry/Pose3.h>
 #include <gtsam/geometry/Cal3_S2Stereo.h>
 #include <gtsam/nonlinear/Values.h>
+#include <gtsam/nonlinear/utilities.h>
 #include <gtsam/nonlinear/NonlinearEquality.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 #include <gtsam/nonlinear/LevenbergMarquardtOptimizer.h>
@@ -113,7 +114,7 @@ int main(int argc, char** argv) {
   Values result = optimizer.optimize();
 
   cout << "Final result sample:" << endl;
-  Values pose_values = result.filter<Pose3>();
+  Values pose_values = utilities::allPose3s(result);
   pose_values.print("Final camera poses:\n");
 
   return 0;

gtsam/base/TestableAssertions.h

@@ -80,37 +80,6 @@ bool assert_equal(const V& expected, const boost::optional<const V&>& actual, do
   return assert_equal(expected, *actual, tol);
 }
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-/**
- * Version of assert_equals to work with vectors
- * @deprecated: use container equals instead
- */
-template<class V>
-bool GTSAM_DEPRECATED assert_equal(const std::vector<V>& expected, const std::vector<V>& actual, double tol = 1e-9) {
-  bool match = true;
-  if (expected.size() != actual.size())
-    match = false;
-  if(match) {
-    size_t i = 0;
-    for(const V& a: expected) {
-      if (!assert_equal(a, actual[i++], tol)) {
-        match = false;
-        break;
-      }
-    }
-  }
-  if(!match) {
-    std::cout << "expected: " << std::endl;
-    for(const V& a: expected) { std::cout << a << " "; }
-    std::cout << "\nactual: " << std::endl;
-    for(const V& a: actual) { std::cout << a << " "; }
-    std::cout << std::endl;
-    return false;
-  }
-  return true;
-}
-#endif
-
 /**
  * Function for comparing maps of testable->testable
  * TODO: replace with more generalized version

gtsam/base/Vector.h

@@ -204,28 +204,6 @@ inline double inner_prod(const V1 &a, const V2& b) {
   return a.dot(b);
 }
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-/**
- * BLAS Level 1 scal: x <- alpha*x
- * @deprecated: use operators instead
- */
-inline void GTSAM_DEPRECATED scal(double alpha, Vector& x) { x *= alpha; }
-
-/**
- * BLAS Level 1 axpy: y <- alpha*x + y
- * @deprecated: use operators instead
- */
-template<class V1, class V2>
-inline void GTSAM_DEPRECATED axpy(double alpha, const V1& x, V2& y) {
-  assert (y.size()==x.size());
-  y += alpha * x;
-}
-inline void axpy(double alpha, const Vector& x, SubVector y) {
-  assert (y.size()==x.size());
-  y += alpha * x;
-}
-#endif
-
 /**
  * house(x,j) computes HouseHolder vector v and scaling factor beta
  *  from x, such that the corresponding Householder reflection zeroes out

gtsam/config.h.in

@@ -70,7 +70,7 @@
 #cmakedefine GTSAM_THROW_CHEIRALITY_EXCEPTION
 
 // Make sure dependent projects that want it can see deprecated functions
-#cmakedefine GTSAM_ALLOW_DEPRECATED_SINCE_V42
+#cmakedefine GTSAM_ALLOW_DEPRECATED_SINCE_V43
 
 // Support Metis-based nested dissection
 #cmakedefine GTSAM_SUPPORT_NESTED_DISSECTION

gtsam/discrete/DiscreteBayesNet.cpp

@@ -51,26 +51,6 @@ double DiscreteBayesNet::evaluate(const DiscreteValues& values) const {
   return result;
 }
 
-/* ************************************************************************* */
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-DiscreteValues DiscreteBayesNet::optimize() const {
-  DiscreteValues result;
-  return optimize(result);
-}
-
-DiscreteValues DiscreteBayesNet::optimize(DiscreteValues result) const {
-  // solve each node in turn in topological sort order (parents first)
-#ifdef _MSC_VER
-#pragma message("DiscreteBayesNet::optimize (deprecated) does not compute MPE!")
-#else
-#warning "DiscreteBayesNet::optimize (deprecated) does not compute MPE!"
-#endif
-  for (auto conditional : boost::adaptors::reverse(*this))
-    conditional->solveInPlace(&result);
-  return result;
-}
-#endif
-
 /* ************************************************************************* */
 DiscreteValues DiscreteBayesNet::sample() const {
   DiscreteValues result;

gtsam/discrete/DiscreteBayesNet.h

@@ -149,15 +149,6 @@ class GTSAM_EXPORT DiscreteBayesNet: public BayesNet<DiscreteConditional> {
 
     /// @}
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-    /// @name Deprecated functionality
-    /// @{
-
-    DiscreteValues GTSAM_DEPRECATED optimize() const;
-    DiscreteValues GTSAM_DEPRECATED optimize(DiscreteValues given) const;
-    /// @}
-#endif
-
  private:
     /** Serialization function */
     friend class boost::serialization::access;

gtsam/discrete/DiscreteConditional.cpp

@@ -235,57 +235,6 @@ DecisionTreeFactor::shared_ptr DiscreteConditional::likelihood(
   return likelihood(values);
 }
 
-/* ************************************************************************** */
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-void DiscreteConditional::solveInPlace(DiscreteValues* values) const {
-  ADT pFS = choose(*values, true);  // P(F|S=parentsValues)
-
-  // Initialize
-  DiscreteValues mpe;
-  double maxP = 0;
-
-  // Get all Possible Configurations
-  const auto allPosbValues = frontalAssignments();
-
-  // Find the maximum
-  for (const auto& frontalVals : allPosbValues) {
-    double pValueS = pFS(frontalVals);  // P(F=value|S=parentsValues)
-    // Update maximum solution if better
-    if (pValueS > maxP) {
-      maxP = pValueS;
-      mpe = frontalVals;
-    }
-  }
-
-  // set values (inPlace) to maximum
-  for (Key j : frontals()) {
-    (*values)[j] = mpe[j];
-  }
-}
-
-/* ************************************************************************** */
-size_t DiscreteConditional::solve(const DiscreteValues& parentsValues) const {
-  ADT pFS = choose(parentsValues, true);  // P(F|S=parentsValues)
-
-  // Then, find the max over all remaining
-  size_t max = 0;
-  double maxP = 0;
-  DiscreteValues frontals;
-  assert(nrFrontals() == 1);
-  Key j = (firstFrontalKey());
-  for (size_t value = 0; value < cardinality(j); value++) {
-    frontals[j] = value;
-    double pValueS = pFS(frontals); // P(F=value|S=parentsValues)
-    // Update solution if better
-    if (pValueS > maxP) {
-      maxP = pValueS;
-      max = value;
-    }
-  }
-  return max;
-}
-#endif
-
 /* ************************************************************************** */
 size_t DiscreteConditional::argmax() const {
   size_t maxValue = 0;

gtsam/discrete/DiscreteConditional.h

@@ -263,14 +263,6 @@ class GTSAM_EXPORT DiscreteConditional
 
   /// @}
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  /// @name Deprecated functionality
-  /// @{
-  size_t GTSAM_DEPRECATED solve(const DiscreteValues& parentsValues) const;
-  void GTSAM_DEPRECATED solveInPlace(DiscreteValues* parentsValues) const;
-  /// @}
-#endif
-
  protected:
   /// Internal version of choose
   DiscreteConditional::ADT choose(const DiscreteValues& given,

gtsam/discrete/DiscreteDistribution.h

@@ -93,12 +93,6 @@ class GTSAM_EXPORT DiscreteDistribution : public DiscreteConditional {
   std::vector<double> pmf() const;
 
   /// @}
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  /// @name Deprecated functionality
-  /// @{
-  size_t GTSAM_DEPRECATED solve() const { return Base::solve({}); }
-  /// @}
-#endif
 };
 // DiscreteDistribution
 

gtsam/discrete/tests/testDiscreteFactorGraph.cpp

@@ -209,13 +209,6 @@ TEST(DiscreteFactorGraph, marginalIsNotMPE) {
   auto actualMPE = graph.optimize();
   EXPECT(assert_equal(mpe, actualMPE));
   EXPECT_DOUBLES_EQUAL(0.315789, graph(mpe), 1e-5);  // regression
-
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  // Optimize on BayesNet maximizes marginal, then the conditional marginals:
-  auto notOptimal = bayesNet.optimize();
-  EXPECT(graph(notOptimal) < graph(mpe));
-  EXPECT_DOUBLES_EQUAL(0.263158, graph(notOptimal), 1e-5);  // regression
-#endif
 }
 
 /* ************************************************************************* */
@@ -246,10 +239,6 @@ TEST(DiscreteFactorGraph, testMPE_Darwiche09book_p244) {
   ordering += Key(0), Key(1), Key(2), Key(3), Key(4);
   auto chordal = graph.eliminateSequential(ordering);
   EXPECT_LONGS_EQUAL(5, chordal->size());
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  auto notOptimal = chordal->optimize();  // not MPE !
-  EXPECT(graph(notOptimal) < graph(mpe));
-#endif
 
   // Let us create the Bayes tree here, just for fun, because we don't use it
   DiscreteBayesTree::shared_ptr bayesTree =

gtsam/geometry/Cal3.h

@@ -170,11 +170,6 @@ class GTSAM_EXPORT Cal3 {
     return K;
   }
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  /** @deprecated The following function has been deprecated, use K above */
-  Matrix3 GTSAM_DEPRECATED matrix() const { return K(); }
-#endif
-
   /// Return inverted calibration matrix inv(K)
   Matrix3 inverse() const;
 

gtsam/geometry/Cal3Bundler.h

@@ -100,14 +100,6 @@ class GTSAM_EXPORT Cal3Bundler : public Cal3 {
 
   Vector3 vector() const;
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-  /// get parameter u0
-  inline double GTSAM_DEPRECATED u0() const { return u0_; }
-
-  /// get parameter v0
-  inline double GTSAM_DEPRECATED v0() const { return v0_; }
-#endif
-
   /**
    * @brief: convert intrinsic coordinates xy to image coordinates uv
    * Version of uncalibrate with derivatives

gtsam/geometry/Pose2.cpp

@@ -371,15 +371,5 @@ boost::optional<Pose2> Pose2::Align(const Matrix& a, const Matrix& b) {
   return Pose2::Align(ab_pairs);
 }
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-boost::optional<Pose2> align(const Point2Pairs& ba_pairs) {
-  Point2Pairs ab_pairs;
-  for (const Point2Pair &baPair : ba_pairs) {
-    ab_pairs.emplace_back(baPair.second, baPair.first);
-  }
-  return Pose2::Align(ab_pairs);
-}
-#endif
-
 /* ************************************************************************* */
 } // namespace gtsam

gtsam/geometry/Pose2.h

@@ -343,16 +343,6 @@ inline Matrix wedge<Pose2>(const Vector& xi) {
   return Matrix(Pose2::wedge(xi(0),xi(1),xi(2))).eval();
 }
 
-#ifdef GTSAM_ALLOW_DEPRECATED_SINCE_V42
-/**
- * @deprecated Use static constructor (with reversed pairs!)
- * Calculate pose between a vector of 2D point correspondences (p,q)
- * where q = Pose2::transformFrom(p) = t + R*p
- */
-GTSAM_EXPORT boost::optional<Pose2> 
-GTSAM_DEPRECATED align(const Point2Pairs& pairs);
-#endif
-
 // Convenience typedef
 using Pose2Pair = std::pair<Pose2, Pose2>;
 using Pose2Pairs = std::vector<Pose2Pair>;