Finish 4.2a1

.github/scripts/python.sh

@@ -75,7 +75,7 @@ cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
     -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
     -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
     -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
-    -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=OFF \
+    -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=OFF \
     -DCMAKE_INSTALL_PREFIX=$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=${GTSAM_BUILD_EXAMPLES_ALWAYS:-ON} \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=${GTSAM_ALLOW_DEPRECATED_SINCE_V41:-OFF} \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=${GTSAM_ALLOW_DEPRECATED_SINCE_V42:-OFF} \
       -DGTSAM_USE_QUATERNIONS=${GTSAM_USE_QUATERNIONS:-OFF} \
       -DGTSAM_ROT3_EXPMAP=${GTSAM_ROT3_EXPMAP:-ON} \
       -DGTSAM_POSE3_EXPMAP=${GTSAM_POSE3_EXPMAP:-ON} \

.github/workflows/build-special.yml

@@ -110,7 +110,7 @@ jobs:
       - name: Set Allow Deprecated Flag
         if: matrix.flag == 'deprecated'
         run: |
-          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V41=ON" >> $GITHUB_ENV
+          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V42=ON" >> $GITHUB_ENV
           echo "Allow deprecated since version 4.1"
 
       - name: Set Use Quaternions Flag

CMakeLists.txt

@@ -11,7 +11,7 @@ endif()
 set (GTSAM_VERSION_MAJOR 4)
 set (GTSAM_VERSION_MINOR 2)
 set (GTSAM_VERSION_PATCH 0)
-set (GTSAM_PRERELEASE_VERSION "a0")
+set (GTSAM_PRERELEASE_VERSION "a1")
 math (EXPR GTSAM_VERSION_NUMERIC "10000 * ${GTSAM_VERSION_MAJOR} + 100 * ${GTSAM_VERSION_MINOR} + ${GTSAM_VERSION_PATCH}")
 
 if (${GTSAM_VERSION_PATCH} EQUAL 0)

README.md

@@ -4,7 +4,7 @@
 
 As of Dec 2021, the `develop` branch is officially in "Pre 4.2" mode. A great new feature we will be adding in 4.2 is *hybrid inference* a la DCSLAM (Kevin Doherty et al) and we envision several API-breaking changes will happen in the discrete folder.
 
-In addition, features deprecated in 4.1 will be removed. Please use the last [4.1.1 release](https://github.com/borglab/gtsam/releases/tag/4.1.1) if you need those features. However, most (not all, unfortunately) are easily converted and can be tracked down (in 4.1.1) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V41`.
+In addition, features deprecated in 4.1 will be removed. Please use the last [4.1.1 release](https://github.com/borglab/gtsam/releases/tag/4.1.1) if you need those features. However, most (not all, unfortunately) are easily converted and can be tracked down (in 4.1.1) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42`.
 
 ## What is GTSAM?
 
@@ -57,7 +57,7 @@ GTSAM 4 introduces several new features, most notably Expressions and a Python t
 
 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_V41` for newly deprecated methods since the 4.1 release, which is on by default, allowing anyone to just pull version 4.1 and compile.
+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

Using-GTSAM-EXPORT.md

@@ -29,7 +29,7 @@ Rule #1 doesn't seem very bad, until you combine it with rule #2
 
 ***Compiler Rule #2*** Anything declared in a header file is not included in a DLL.
 
-When these two rules are combined, you get some very confusing results.  For example, a class which is completely defined in a header (e.g. LieMatrix) cannot use `GTSAM_EXPORT` in its definition.  If LieMatrix is defined with `GTSAM_EXPORT`, then the compiler _must_ find LieMatrix in a DLL.  Because LieMatrix is a header-only class, however, it can't find it, leading to a very confusing "I can't find this symbol" type of error.  Note that the linker says it can't find the symbol even though the compiler found the header file that completely defines the class.
+When these two rules are combined, you get some very confusing results.  For example, a class which is completely defined in a header (e.g. Foo) cannot use `GTSAM_EXPORT` in its definition.  If Foo is defined with `GTSAM_EXPORT`, then the compiler _must_ find Foo in a DLL.  Because Foo is a header-only class, however, it can't find it, leading to a very confusing "I can't find this symbol" type of error.  Note that the linker says it can't find the symbol even though the compiler found the header file that completely defines the class.
 
 Also note that when a class that you want to export inherits from another class that is not exportable, this can cause significant issues.  According to this [MSVC Warning page](https://docs.microsoft.com/en-us/cpp/error-messages/compiler-warnings/compiler-warning-level-2-c4275?view=vs-2019), it may not strictly be a rule, but we have seen several linker errors when a class that is defined with `GTSAM_EXPORT` extended an Eigen class.  In general, it appears that any inheritance of non-exportable class by an exportable class is a bad idea.
 

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_V41     "Allow use of methods/functions deprecated in GTSAM 4.1" ON)
+option(GTSAM_ALLOW_DEPRECATED_SINCE_V42     "Allow use of methods/functions deprecated in GTSAM 4.1" 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

@@ -86,7 +86,7 @@ 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(${GTSAM_ALLOW_DEPRECATED_SINCE_V41}  "Allow features deprecated in GTSAM 4.1")
+print_enabled_config(${GTSAM_ALLOW_DEPRECATED_SINCE_V42}  "Allow features deprecated in GTSAM 4.1")
 print_enabled_config(${GTSAM_SUPPORT_NESTED_DISSECTION}   "Metis-based Nested Dissection   ")
 print_enabled_config(${GTSAM_TANGENT_PREINTEGRATION}      "Use tangent-space preintegration")
 

examples/UGM_small.cpp

@@ -50,8 +50,7 @@ int main(int argc, char** argv) {
 
   // Print the UGM distribution
   cout << "\nUGM distribution:" << endl;
-  vector<DiscreteFactor::Values> allPosbValues = cartesianProduct(
-      Cathy & Heather & Mark & Allison);
+  auto allPosbValues = cartesianProduct(Cathy & Heather & Mark & Allison);
   for (size_t i = 0; i < allPosbValues.size(); ++i) {
     DiscreteFactor::Values values = allPosbValues[i];
     double prodPot = graph(values);

gtsam/3rdparty/Eigen/Eigen/src/Core/TriangularMatrix.h

@@ -440,7 +440,7 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
     EIGEN_DEVICE_FUNC
     void lazyAssign(const TriangularBase<OtherDerived>& other);
 
-    /** \deprecated */
+    /** @deprecated */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC
     void lazyAssign(const MatrixBase<OtherDerived>& other);
@@ -523,7 +523,7 @@ template<typename _MatrixType, unsigned int _Mode> class TriangularViewImpl<_Mat
       call_assignment(derived(), other.const_cast_derived(), internal::swap_assign_op<Scalar>());
     }
 
-    /** \deprecated
+    /** @deprecated
       * Shortcut for \code (*this).swap(other.triangularView<(*this)::Mode>()) \endcode */
     template<typename OtherDerived>
     EIGEN_DEVICE_FUNC

gtsam/base/CMakeLists.txt

@@ -5,8 +5,5 @@ install(FILES ${base_headers} DESTINATION include/gtsam/base)
 file(GLOB base_headers_tree "treeTraversal/*.h")
 install(FILES ${base_headers_tree} DESTINATION include/gtsam/base/treeTraversal)
 
-file(GLOB deprecated_headers "deprecated/*.h")
-install(FILES ${deprecated_headers} DESTINATION include/gtsam/base/deprecated)
-
 # Build tests
 add_subdirectory(tests)

gtsam/base/TestableAssertions.h

@@ -80,9 +80,10 @@ 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
+ * @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) {
@@ -108,6 +109,7 @@ bool GTSAM_DEPRECATED assert_equal(const std::vector<V>& expected, const std::ve
   }
   return true;
 }
+#endif
 
 /**
  * Function for comparing maps of testable->testable

gtsam/base/Vector.h

@@ -203,15 +203,16 @@ 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
+ * @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
+ * @deprecated: use operators instead
  */
 template<class V1, class V2>
 inline void GTSAM_DEPRECATED axpy(double alpha, const V1& x, V2& y) {
@@ -222,6 +223,7 @@ 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