From 1725a577cf881ae5478dbe08cef19b4b3f5a4f55 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sat, 21 Mar 2020 14:52:17 -0400
Subject: [PATCH 01/29] cmake function to install python package once make
 install is completed

---
 cmake/GtsamCythonWrap.cmake | 7 +++++++
 cython/CMakeLists.txt       | 2 ++
 2 files changed, 9 insertions(+)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index f1382729f..3ca8b903f 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -279,3 +279,10 @@ function(install_cython_files source_files dest_directory)
 
 endfunction()
 
+function(install_python_package install_path)
+  set(package_path "${install_path}${GTSAM_BUILD_TAG}")
+  # set cython directory permissions to user so we don't get permission denied
+  install(CODE "execute_process(COMMAND sh \"-c\" \"chown -R $(logname):$(logname) ${package_path}\")")
+  # go to cython directory and run setup.py
+  install(CODE "execute_process(COMMAND sh \"-c\" \"cd ${package_path} && python setup.py install\")")
+endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 4cc9d2f5d..96503b82f 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,4 +45,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
+  install_python_package("${GTSAM_CYTHON_INSTALL_PATH}")
+
 endif ()

From 93a00a38a40a21e21a1c20da9209192a7076fc85 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Mon, 22 Jun 2020 20:14:03 -0500
Subject: [PATCH 02/29] add new make command for installing python wrapper

---
 cmake/GtsamCythonWrap.cmake | 17 ++++++++++++-----
 cython/CMakeLists.txt       |  3 +++
 cython/scripts/install.bat  |  0
 cython/scripts/install.sh   | 21 +++++++++++++++++++++
 4 files changed, 36 insertions(+), 5 deletions(-)
 create mode 100755 cython/scripts/install.bat
 create mode 100755 cython/scripts/install.sh

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 3ca8b903f..361038ce0 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -280,9 +280,16 @@ function(install_cython_files source_files dest_directory)
 endfunction()
 
 function(install_python_package install_path)
-  set(package_path "${install_path}${GTSAM_BUILD_TAG}")
-  # set cython directory permissions to user so we don't get permission denied
-  install(CODE "execute_process(COMMAND sh \"-c\" \"chown -R $(logname):$(logname) ${package_path}\")")
-  # go to cython directory and run setup.py
-  install(CODE "execute_process(COMMAND sh \"-c\" \"cd ${package_path} && python setup.py install\")")
+#TODO this will only work for Linux. Need to make it work on macOS and Windows as well
+#TODO Running `sudo make install` makes this run in admin space causing Python 2.7 to be picked up.
+  # # go to cython directory and run setup.py
+  # install(CODE "execute_process(COMMAND sh \"-c\" \"cd ${package_path} && python setup.py install\")")
+  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    set(PYTHON_INSTALL_SCRIPT "install.bat")
+  elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+    set(PYTHON_INSTALL_SCRIPT "install.sh")
+  endif()
+
+  configure_file(${PROJECT_SOURCE_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT} ${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT})
+  add_custom_target(python-install "${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT}")
 endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 96503b82f..638bdfb2d 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,6 +45,9 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
+  # file(GLOB GTSAM_PYTHON_INSTALL_SCRIPTS "scripts/*")
+  # file(COPY ${GTSAM_PYTHON_INSTALL_SCRIPTS} DESTINATION ${PROJECT_BINARY_DIR}/cython/scripts)
+
   install_python_package("${GTSAM_CYTHON_INSTALL_PATH}")
 
 endif ()
diff --git a/cython/scripts/install.bat b/cython/scripts/install.bat
new file mode 100755
index 000000000..e69de29bb
diff --git a/cython/scripts/install.sh b/cython/scripts/install.sh
new file mode 100755
index 000000000..04759ca5e
--- /dev/null
+++ b/cython/scripts/install.sh
@@ -0,0 +1,21 @@
+#!/bin/sh
+echo "Installing GTSAM Python Wrapper"
+
+PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
+
+if [ ! -d "$PACKAGE_PATH" ]
+then 
+    echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
+    exit 1;
+fi
+
+# set cython directory permissions to user so we don't get permission denied
+if [ "$(whoami)" != "root" ]
+then
+    sudo chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
+else
+    chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
+fi
+
+echo "Running setup.py in $PACKAGE_PATH"
+${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install

From ca46ebfda81d8b54b1098cce83a41f0c664ee8b8 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Mon, 22 Jun 2020 20:20:50 -0500
Subject: [PATCH 03/29] added comments and removed unnecessary code

---
 cmake/GtsamCythonWrap.cmake |  8 ++++----
 cython/CMakeLists.txt       |  3 ---
 cython/scripts/install.sh   | 10 +++++++++-
 3 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 361038ce0..4cd061852 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -280,16 +280,16 @@ function(install_cython_files source_files dest_directory)
 endfunction()
 
 function(install_python_package install_path)
-#TODO this will only work for Linux. Need to make it work on macOS and Windows as well
-#TODO Running `sudo make install` makes this run in admin space causing Python 2.7 to be picked up.
-  # # go to cython directory and run setup.py
-  # install(CODE "execute_process(COMMAND sh \"-c\" \"cd ${package_path} && python setup.py install\")")
+  # Select the correct install script based on the OS
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
     set(PYTHON_INSTALL_SCRIPT "install.bat")
   elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
     set(PYTHON_INSTALL_SCRIPT "install.sh")
   endif()
 
+  # Configure the variables in the script
   configure_file(${PROJECT_SOURCE_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT} ${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT})
+
+  # Add the new make target command
   add_custom_target(python-install "${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT}")
 endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 638bdfb2d..96503b82f 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,9 +45,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
-  # file(GLOB GTSAM_PYTHON_INSTALL_SCRIPTS "scripts/*")
-  # file(COPY ${GTSAM_PYTHON_INSTALL_SCRIPTS} DESTINATION ${PROJECT_BINARY_DIR}/cython/scripts)
-
   install_python_package("${GTSAM_CYTHON_INSTALL_PATH}")
 
 endif ()
diff --git a/cython/scripts/install.sh b/cython/scripts/install.sh
index 04759ca5e..8e409803d 100755
--- a/cython/scripts/install.sh
+++ b/cython/scripts/install.sh
@@ -1,15 +1,22 @@
 #!/bin/sh
+
+# This script runs the installation flow for python wrapped GTSAM.
+# It does so by first setting the correct ownership permissions on the package directory,
+# and then running `python setup.py install` to install the wrapped package.
+
 echo "Installing GTSAM Python Wrapper"
 
+# Set the package path
 PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
 
+# Check if package directory exists. If not, print warning and exit.
 if [ ! -d "$PACKAGE_PATH" ]
 then 
     echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
     exit 1;
 fi
 
-# set cython directory permissions to user so we don't get permission denied
+# Set cython directory permissions to user so we don't get permission denied
 if [ "$(whoami)" != "root" ]
 then
     sudo chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
@@ -17,5 +24,6 @@ else
     chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
 fi
 
+# Run setup.py install with full paths
 echo "Running setup.py in $PACKAGE_PATH"
 ${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install

From 6972a5c9a70e5ff8eaa3f8b5b0f9392c2829a195 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 11:06:01 -0500
Subject: [PATCH 04/29] updated comments in shell script

---
 cython/scripts/install.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/cython/scripts/install.sh b/cython/scripts/install.sh
index 8e409803d..fdf86f130 100755
--- a/cython/scripts/install.sh
+++ b/cython/scripts/install.sh
@@ -11,12 +11,13 @@ PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
 
 # Check if package directory exists. If not, print warning and exit.
 if [ ! -d "$PACKAGE_PATH" ]
-then 
+then
     echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
     exit 1;
 fi
 
-# Set cython directory permissions to user so we don't get permission denied
+# Set cython directory permissions to user so we don't get permission denied.
+# This also works inside Docker containers.
 if [ "$(whoami)" != "root" ]
 then
     sudo chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
@@ -24,6 +25,6 @@ else
     chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
 fi
 
-# Run setup.py install with full paths
+# Run setup.py install with full paths.
 echo "Running setup.py in $PACKAGE_PATH"
 ${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install

From 530016edf00e9a56cbdb4de27ce612580337a66a Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 11:06:35 -0500
Subject: [PATCH 05/29] added Windows batch script to install python wrapped
 package

---
 cython/scripts/install.bat | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/cython/scripts/install.bat b/cython/scripts/install.bat
index e69de29bb..4dbd2051f 100755
--- a/cython/scripts/install.bat
+++ b/cython/scripts/install.bat
@@ -0,0 +1,18 @@
+:: This script runs the installation flow for python wrapped GTSAM.
+:: It does so by running `python setup.py install` to install the wrapped package.
+
+echo "Installing GTSAM Python Wrapper"
+
+:: Set the package path
+PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
+
+:: Check if package directory exists. If not, print warning and exit.
+if [ ! -d "$PACKAGE_PATH" ]
+then
+    echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
+    exit 1;
+fi
+
+:: Run setup.py install with full paths.
+echo "Running setup.py in $PACKAGE_PATH"
+${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install

From efde078b944e1865ea9e53e68726c48c5cf2d2e7 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 14:05:17 -0500
Subject: [PATCH 06/29] pure CMake script to install Python wrapper after
 compiling

---
 cmake/GtsamCythonWrap.cmake | 15 ---------------
 cython/CMakeLists.txt       |  3 ++-
 cython/scripts/install.bat  | 18 ------------------
 cython/scripts/install.sh   | 30 ------------------------------
 4 files changed, 2 insertions(+), 64 deletions(-)
 delete mode 100755 cython/scripts/install.bat
 delete mode 100755 cython/scripts/install.sh

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 4cd061852..6331d1e95 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -278,18 +278,3 @@ function(install_cython_files source_files dest_directory)
   endif()
 
 endfunction()
-
-function(install_python_package install_path)
-  # Select the correct install script based on the OS
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    set(PYTHON_INSTALL_SCRIPT "install.bat")
-  elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux" OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
-    set(PYTHON_INSTALL_SCRIPT "install.sh")
-  endif()
-
-  # Configure the variables in the script
-  configure_file(${PROJECT_SOURCE_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT} ${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT})
-
-  # Add the new make target command
-  add_custom_target(python-install "${PROJECT_BINARY_DIR}/cython/scripts/${PYTHON_INSTALL_SCRIPT}")
-endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 96503b82f..bce9f2308 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,6 +45,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
-  install_python_package("${GTSAM_CYTHON_INSTALL_PATH}")
+  # Add the new make target command
+  add_custom_target(python-install COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/setup.py install)
 
 endif ()
diff --git a/cython/scripts/install.bat b/cython/scripts/install.bat
deleted file mode 100755
index 4dbd2051f..000000000
--- a/cython/scripts/install.bat
+++ /dev/null
@@ -1,18 +0,0 @@
-:: This script runs the installation flow for python wrapped GTSAM.
-:: It does so by running `python setup.py install` to install the wrapped package.
-
-echo "Installing GTSAM Python Wrapper"
-
-:: Set the package path
-PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
-
-:: Check if package directory exists. If not, print warning and exit.
-if [ ! -d "$PACKAGE_PATH" ]
-then
-    echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
-    exit 1;
-fi
-
-:: Run setup.py install with full paths.
-echo "Running setup.py in $PACKAGE_PATH"
-${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install
diff --git a/cython/scripts/install.sh b/cython/scripts/install.sh
deleted file mode 100755
index fdf86f130..000000000
--- a/cython/scripts/install.sh
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/bin/sh
-
-# This script runs the installation flow for python wrapped GTSAM.
-# It does so by first setting the correct ownership permissions on the package directory,
-# and then running `python setup.py install` to install the wrapped package.
-
-echo "Installing GTSAM Python Wrapper"
-
-# Set the package path
-PACKAGE_PATH=${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}
-
-# Check if package directory exists. If not, print warning and exit.
-if [ ! -d "$PACKAGE_PATH" ]
-then
-    echo "Directory $PACKAGE_PATH DOES NOT exist. Please run 'make install' first.";
-    exit 1;
-fi
-
-# Set cython directory permissions to user so we don't get permission denied.
-# This also works inside Docker containers.
-if [ "$(whoami)" != "root" ]
-then
-    sudo chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
-else
-    chown -R $(logname) ${GTSAM_CYTHON_INSTALL_PATH}
-fi
-
-# Run setup.py install with full paths.
-echo "Running setup.py in $PACKAGE_PATH"
-${PYTHON_EXECUTABLE} $PACKAGE_PATH/setup.py install

From 9698b032537e9a74a6414ff46e09f9cdef196bab Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 14:06:25 -0500
Subject: [PATCH 07/29] removed extra line

---
 cmake/GtsamCythonWrap.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 6331d1e95..b6c4c2856 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -277,4 +277,4 @@ function(install_cython_files source_files dest_directory)
     install(FILES "${source_files}" DESTINATION "${dest_directory}")
   endif()
 
-endfunction()
+endfunction()
\ No newline at end of file

From 5feaf6dd9da35b9a347dc5c0d006c72ab0a3f2d4 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 14:07:28 -0500
Subject: [PATCH 08/29] reset to previous version

---
 cmake/GtsamCythonWrap.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index b6c4c2856..6331d1e95 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -277,4 +277,4 @@ function(install_cython_files source_files dest_directory)
     install(FILES "${source_files}" DESTINATION "${dest_directory}")
   endif()
 
-endfunction()
\ No newline at end of file
+endfunction()

From 2475e6c68c6581cce518f22c8d6683c857b0fc1b Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 17:44:03 -0500
Subject: [PATCH 09/29] Load Cython requirements file instead of reading it in
 cmake

---
 cython/CMakeLists.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index bce9f2308..0d2af6a33 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -32,8 +32,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                     )
   endif()
 
-  file(READ "${PROJECT_SOURCE_DIR}/cython/requirements.txt" CYTHON_INSTALL_REQUIREMENTS)
-  file(READ "${PROJECT_SOURCE_DIR}/README.md" README_CONTENTS)
+  set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
 
   # Install the custom-generated __init__.py
   # This is to make the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable

From 453d3a74164613375a083566eea9f8b16c782d74 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 18:11:24 -0500
Subject: [PATCH 10/29] Added cmake variable GTSAM_CYTHON_INSTALL_FULLPATH to
 include build tag directly

---
 CMakeLists.txt                      | 4 +++-
 cmake/GtsamCythonWrap.cmake         | 2 +-
 cython/gtsam_eigency/CMakeLists.txt | 8 ++++----
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a810ac9df..2cbdbf00c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -458,7 +458,9 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   if(NOT GTSAM_CYTHON_INSTALL_PATH)
     set(GTSAM_CYTHON_INSTALL_PATH "${CMAKE_INSTALL_PREFIX}/cython")
   endif()
-  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
+  # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
+  set(GTSAM_CYTHON_INSTALL_FULLPATH "${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}")
+  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
   add_subdirectory(cython)
 else()
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 0) # This will go into config.h
diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 6331d1e95..851f53cfe 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -184,7 +184,7 @@ function(install_cython_wrapped_library interface_header generated_files_path in
   # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH/subdirectory if there is one
   get_filename_component(location "${install_path}" PATH)
   get_filename_component(name "${install_path}" NAME)
-  message(STATUS "Installing Cython Toolbox to ${location}${GTSAM_BUILD_TAG}/${name}") #${GTSAM_CYTHON_INSTALL_PATH}"
+  message(STATUS "Installing Cython Toolbox to ${location}${GTSAM_BUILD_TAG}/${name}") #${GTSAM_CYTHON_INSTALL_FULLPATH}"
 
   if(GTSAM_BUILD_TYPE_POSTFIXES)
     foreach(build_type ${CMAKE_CONFIGURATION_TYPES})
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index 77bead834..da174d690 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -39,11 +39,11 @@ add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigen
 
 # install
 install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        DESTINATION "${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}"
+        DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}"
         PATTERN "CMakeLists.txt" EXCLUDE
         PATTERN "__init__.py.in" EXCLUDE)
 install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
-        DESTINATION "${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/gtsam_eigency")
-install(FILES ${OUTPUT_DIR}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/gtsam_eigency)
+        DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency")
+install(FILES ${OUTPUT_DIR}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
 configure_file(__init__.py.in ${OUTPUT_DIR}/__init__.py)
-install(FILES ${OUTPUT_DIR}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/gtsam_eigency)
+install(FILES ${OUTPUT_DIR}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)

From 4f6f8216110a2db9d7a9be3fbdba65a967490793 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 18:39:49 -0500
Subject: [PATCH 11/29] Vastly improved setup.py template

---
 cython/setup.py.in | 27 +++++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/cython/setup.py.in b/cython/setup.py.in
index df92b564c..98a05c9f6 100644
--- a/cython/setup.py.in
+++ b/cython/setup.py.in
@@ -7,6 +7,22 @@ except ImportError:
 
 packages = find_packages()
 
+package_data = {
+    package:
+        [f for f in os.listdir(package.replace('.', os.path.sep)) if os.path.splitext(f)[1] in ('.so', '.pyd')]
+        for package in packages
+}
+
+cython_install_requirements = open("${CYTHON_INSTALL_REQUIREMENTS_FILE}").readlines()
+
+install_requires = [line.strip() \
+    for line in cython_install_requirements \
+    if len(line.strip()) > 0 and not line.strip().startswith('#')
+]
+
+# Cleaner to read in the contents rather than copy them over.
+readme_contents = open("${PROJECT_SOURCE_DIR}/README.md").read()
+
 setup(
     name='gtsam',
     description='Georgia Tech Smoothing And Mapping library',
@@ -16,7 +32,7 @@ setup(
     author_email='frank.dellaert@gtsam.org',
     license='Simplified BSD license',
     keywords='slam sam robotics localization mapping optimization',
-    long_description='''${README_CONTENTS}''',
+    long_description=readme_contents,
     long_description_content_type='text/markdown',
     python_requires='>=2.7',
     # https://pypi.org/pypi?%3Aaction=list_classifiers
@@ -34,11 +50,6 @@ setup(
     ],
 
     packages=packages,
-    package_data={package:
-        [f for f in os.listdir(package.replace('.', os.path.sep)) if os.path.splitext(f)[1] in ('.so', '.pyd')]
-        for package in packages
-    },
-    install_requires=[line.strip() for line in '''
-${CYTHON_INSTALL_REQUIREMENTS}
-'''.splitlines() if len(line.strip()) > 0 and not line.strip().startswith('#')]
+    package_data=package_data,
+    install_requires=install_requires
 )

From 192184b3b7c1efacb5a7608a7da4205fbba3536f Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 24 Jun 2020 18:40:03 -0500
Subject: [PATCH 12/29] Specify working directory from where to call setup.py

---
 cython/CMakeLists.txt | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 0d2af6a33..01b6c06d4 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,6 +45,8 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
   # Add the new make target command
-  add_custom_target(python-install COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/setup.py install)
+  add_custom_target(python-install
+    COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/setup.py install
+    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
 
 endif ()

From 54c29031839fe00d559e97e4b2014927667180d2 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Mon, 29 Jun 2020 16:53:42 -0500
Subject: [PATCH 13/29] make python-install command depends on gtsam target

---
 cython/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 01b6c06d4..2bfa8ae7c 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -47,6 +47,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   # Add the new make target command
   add_custom_target(python-install
     COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/setup.py install
+    DEPENDS gtsam
     WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
 
 endif ()

From 806e5b12a37462481f1d1e656835b0beab89a6f1 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Mon, 29 Jun 2020 19:29:52 -0500
Subject: [PATCH 14/29] cleaner version of execution script which only needs
 'make install'

---
 cython/CMakeLists.txt | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 2bfa8ae7c..75cbfea8a 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -45,9 +45,9 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
   # Add the new make target command
-  add_custom_target(python-install
-    COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}/setup.py install
-    DEPENDS gtsam
-    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
+  install(CODE
+    "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install
+    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})")
+
 
 endif ()

From 16532bff37a5eb991f639d682ae733d2f27650b2 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Mon, 29 Jun 2020 21:37:07 -0500
Subject: [PATCH 15/29] run setup.py after installing the gtsam_eigency module

---
 cython/CMakeLists.txt               | 10 ++++++----
 cython/gtsam_eigency/CMakeLists.txt | 22 ++++++++++++----------
 2 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 75cbfea8a..5569c0e47 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -44,10 +44,12 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
-  # Add the new make target command
+  # Adding custom function here so that gtsam_eigency is installed before
+  # the below execute_process runs.
+  install_gtsam_eigency(${PROJECT_BINARY_DIR}/cython/gtsam_eigency)
+
+  # Automatically run the python installation via the setup.py
   install(CODE
     "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install
-    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})")
-
-
+      WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})")
 endif ()
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index da174d690..5ea1c337c 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -8,7 +8,7 @@ set(OUTPUT_DIR "${PROJECT_BINARY_DIR}/cython/gtsam_eigency")
 set(EIGENCY_INCLUDE_DIR ${OUTPUT_DIR})
 
 # This is to make the build/cython/gtsam_eigency folder a python package
-configure_file(__init__.py.in ${PROJECT_BINARY_DIR}/cython/gtsam_eigency/__init__.py)
+configure_file(__init__.py.in ${OUTPUT_DIR}/__init__.py)
 
 # include eigency headers
 include_directories(${EIGENCY_INCLUDE_DIR})
@@ -38,12 +38,14 @@ add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
 
 # install
-install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-        DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}"
-        PATTERN "CMakeLists.txt" EXCLUDE
-        PATTERN "__init__.py.in" EXCLUDE)
-install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
-        DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency")
-install(FILES ${OUTPUT_DIR}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
-configure_file(__init__.py.in ${OUTPUT_DIR}/__init__.py)
-install(FILES ${OUTPUT_DIR}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+function(install_gtsam_eigency source_directory)
+  install(DIRECTORY ${source_directory}
+          DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}"
+          PATTERN "CMakeLists.txt" EXCLUDE
+          PATTERN "__init__.py.in" EXCLUDE)
+  install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
+          DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency")
+  install(FILES ${source_directory}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+  install(FILES ${source_directory}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+
+endfunction()
\ No newline at end of file

From 192bf870af28156de5808074f6a45aa36e962410 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 13:16:09 -0500
Subject: [PATCH 16/29] newline added to end of CMake file

---
 cython/gtsam_eigency/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index 5ea1c337c..6cff534c5 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -48,4 +48,4 @@ function(install_gtsam_eigency source_directory)
   install(FILES ${source_directory}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
   install(FILES ${source_directory}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
 
-endfunction()
\ No newline at end of file
+endfunction()

From 9cbabb2cb6e8bf7407f67cfa8026cd227f069f5d Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 20:45:55 -0500
Subject: [PATCH 17/29] Set high level Cython/Eigency variables to reduce
 duplication

---
 CMakeLists.txt | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2cbdbf00c..f8deebfcd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -454,13 +454,14 @@ endif()
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 1)
   # Set up cache options
-  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to CMAKE_INSTALL_PREFIX/cython")
-  if(NOT GTSAM_CYTHON_INSTALL_PATH)
-    set(GTSAM_CYTHON_INSTALL_PATH "${CMAKE_INSTALL_PREFIX}/cython")
-  endif()
+  set(GTSAM_CYTHON_PATH "${PROJECT_BINARY_DIR}/cython" CACHE PATH "Cython source files directory path")
   # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
-  set(GTSAM_CYTHON_INSTALL_FULLPATH "${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}")
-  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython.build<GTSAM_BUILD_TAG>")
+  if(NOT GTSAM_CYTHON_INSTALL_PATH)
+    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython.build${GTSAM_BUILD_TAG}")
+  endif()
+  set(GTSAM_EIGENCY_PATH ${GTSAM_CYTHON_PATH}/gtsam_eigency)
+  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
   add_subdirectory(cython)
 else()
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 0) # This will go into config.h

From 06476c8ee745deca1b188730b4cf881d48a0f668 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 20:46:55 -0500
Subject: [PATCH 18/29] Create and use cython build directory

---
 cython/CMakeLists.txt | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 5569c0e47..b0eb43c50 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,3 +1,6 @@
+# Create directory where cython build files will be placed
+file(MAKE_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})
+
 # Install cython components
 include(GtsamCythonWrap)
 
@@ -5,7 +8,7 @@ include(GtsamCythonWrap)
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   # build and include the eigency version of eigency
   add_subdirectory(gtsam_eigency)
-  include_directories(${PROJECT_BINARY_DIR}/cython/gtsam_eigency)
+  include_directories(${GTSAM_EIGENCY_PATH})
 
   # Fix for error "C1128: number of sections exceeded object file format limit"
   if(MSVC)
@@ -44,12 +47,13 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
   install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
-  # Adding custom function here so that gtsam_eigency is installed before
-  # the below execute_process runs.
-  install_gtsam_eigency(${PROJECT_BINARY_DIR}/cython/gtsam_eigency)
+  # Install gtsam_eigency.
+  # The paths are picked up directly from the parent CMakeLists.txt.
+  install_gtsam_eigency()
 
   # Automatically run the python installation via the setup.py
   install(CODE
     "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install
-      WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})")
+      WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})")
+
 endif ()

From c84060acea3321150f7fd5e652d0b8b8c5c90f53 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 20:47:32 -0500
Subject: [PATCH 19/29] Use the high level cython variables, improve install
 process

---
 cython/gtsam_eigency/CMakeLists.txt | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index 6cff534c5..f64e45cdb 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -4,7 +4,7 @@ include(GtsamCythonWrap)
 # so that the cython-generated header "conversions_api.h" can be found when cythonizing eigency's core
 # and eigency's cython pxd headers can be found when cythonizing gtsam
 file(COPY "." DESTINATION ".")
-set(OUTPUT_DIR "${PROJECT_BINARY_DIR}/cython/gtsam_eigency")
+set(OUTPUT_DIR "${GTSAM_CYTHON_PATH}/gtsam_eigency")
 set(EIGENCY_INCLUDE_DIR ${OUTPUT_DIR})
 
 # This is to make the build/cython/gtsam_eigency folder a python package
@@ -16,8 +16,8 @@ include_directories(${EIGENCY_INCLUDE_DIR})
 # Cythonize and build eigency
 message(STATUS "Cythonize and build eigency")
 # Important trick: use "../gtsam_eigency/conversions.pyx" to let cython know that the conversions module is
-# a part of the gtsam_eigency package and generate the function call import_gtsam_igency__conversions()
-# in conversions_api.h correctly!!!
+# a part of the gtsam_eigency package and generate the function call import_gtsam_eigency__conversions()
+# in conversions_api.h correctly!
 cythonize(cythonize_eigency_conversions "../gtsam_eigency/conversions.pyx" "conversions"
   "${OUTPUT_DIR}" "${EIGENCY_INCLUDE_DIR}" "" "" "")
 cythonize(cythonize_eigency_core "../gtsam_eigency/core.pyx" "core"
@@ -38,14 +38,16 @@ add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
 
 # install
-function(install_gtsam_eigency source_directory)
-  install(DIRECTORY ${source_directory}
-          DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}"
+function(install_gtsam_eigency)
+  install(DIRECTORY ${GTSAM_EIGENCY_PATH}
+          DESTINATION "${GTSAM_CYTHON_INSTALL_PATH}"
           PATTERN "CMakeLists.txt" EXCLUDE
-          PATTERN "__init__.py.in" EXCLUDE)
+          PATTERN "__init__.py.in" EXCLUDE
+          PATTERN "*.dir" EXCLUDE
+          PATTERN "*.make" EXCLUDE)
   install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
-          DESTINATION "${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency")
-  install(FILES ${source_directory}/conversions_api.h DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
-  install(FILES ${source_directory}/__init__.py DESTINATION ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+          DESTINATION "${GTSAM_EIGENCY_INSTALL_PATH}")
+  install(FILES ${GTSAM_EIGENCY_PATH}/conversions_api.h DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
+  install(FILES ${GTSAM_EIGENCY_PATH}/__init__.py DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
 
 endfunction()

From 7a725bf46af9fc069f4db772e4f191956a783e89 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 20:48:01 -0500
Subject: [PATCH 20/29] Remove redundant postfix checking since the postfix is
 already added at the top level

---
 cmake/GtsamCythonWrap.cmake | 75 ++++++-------------------------------
 1 file changed, 12 insertions(+), 63 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 851f53cfe..3ce7f4454 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -184,35 +184,16 @@ function(install_cython_wrapped_library interface_header generated_files_path in
   # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH/subdirectory if there is one
   get_filename_component(location "${install_path}" PATH)
   get_filename_component(name "${install_path}" NAME)
-  message(STATUS "Installing Cython Toolbox to ${location}${GTSAM_BUILD_TAG}/${name}") #${GTSAM_CYTHON_INSTALL_FULLPATH}"
+  message(STATUS "Installing Cython Toolbox to ${location}/${name}") #${GTSAM_CYTHON_INSTALL_PATH}"
 
-  if(GTSAM_BUILD_TYPE_POSTFIXES)
-    foreach(build_type ${CMAKE_CONFIGURATION_TYPES})
-      string(TOUPPER "${build_type}" build_type_upper)
-      if(${build_type_upper} STREQUAL "RELEASE")
-        set(build_type_tag "") # Don't create release mode tag on installed directory
-      else()
-        set(build_type_tag "${build_type}")
-      endif()
-
-      install(DIRECTORY "${generated_files_path}/" DESTINATION "${location}${build_type_tag}/${name}"
-          CONFIGURATIONS "${build_type}"
-          PATTERN "build" EXCLUDE
-          PATTERN "CMakeFiles" EXCLUDE
-          PATTERN "Makefile" EXCLUDE
-          PATTERN "*.cmake" EXCLUDE
-          PATTERN "*.cpp" EXCLUDE
-          PATTERN "*.py" EXCLUDE)
-    endforeach()
-  else()
-    install(DIRECTORY "${generated_files_path}/" DESTINATION ${install_path}
-        PATTERN "build" EXCLUDE
-        PATTERN "CMakeFiles" EXCLUDE
-        PATTERN "Makefile" EXCLUDE
-        PATTERN "*.cmake" EXCLUDE
-        PATTERN "*.cpp" EXCLUDE
-        PATTERN "*.py" EXCLUDE)
-  endif()
+  install(DIRECTORY "${generated_files_path}/" DESTINATION ${install_path}
+      CONFIGURATIONS "${CMAKE_BUILD_TYPE}"
+      PATTERN "build" EXCLUDE
+      PATTERN "CMakeFiles" EXCLUDE
+      PATTERN "Makefile" EXCLUDE
+      PATTERN "*.cmake" EXCLUDE
+      PATTERN "*.cpp" EXCLUDE
+      PATTERN "*.py" EXCLUDE)
 endfunction()
 
 # Helper function to install Cython scripts and handle multiple build types where the scripts
@@ -232,24 +213,9 @@ function(install_cython_scripts source_directory dest_directory patterns)
   foreach(pattern ${patterns})
     list(APPEND patterns_args PATTERN "${pattern}")
   endforeach()
-  if(GTSAM_BUILD_TYPE_POSTFIXES)
-    foreach(build_type ${CMAKE_CONFIGURATION_TYPES})
-      string(TOUPPER "${build_type}" build_type_upper)
-      if(${build_type_upper} STREQUAL "RELEASE")
-        set(build_type_tag "") # Don't create release mode tag on installed directory
-      else()
-        set(build_type_tag "${build_type}")
-      endif()
-      # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH if there is one
-      get_filename_component(location "${dest_directory}" PATH)
-      get_filename_component(name "${dest_directory}" NAME)
-      install(DIRECTORY "${source_directory}" DESTINATION "${location}/${name}${build_type_tag}" CONFIGURATIONS "${build_type}"
-            FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
-    endforeach()
-  else()
-    install(DIRECTORY "${source_directory}" DESTINATION "${dest_directory}" FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
-  endif()
 
+  install(DIRECTORY "${source_directory}" DESTINATION "${dest_directory}" CONFIGURATIONS "${CMAKE_BUILD_TYPE}"
+            FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
 endfunction()
 
 # Helper function to install specific files and handle multiple build types where the scripts
@@ -259,22 +225,5 @@ endfunction()
 #  source_files: The source files to be installed.
 #  dest_directory: The destination directory to install to.
 function(install_cython_files source_files dest_directory)
-
-  if(GTSAM_BUILD_TYPE_POSTFIXES)
-    foreach(build_type ${CMAKE_CONFIGURATION_TYPES})
-      string(TOUPPER "${build_type}" build_type_upper)
-      if(${build_type_upper} STREQUAL "RELEASE")
-        set(build_type_tag "") # Don't create release mode tag on installed directory
-      else()
-        set(build_type_tag "${build_type}")
-      endif()
-      # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH if there is one
-      get_filename_component(location "${dest_directory}" PATH)
-      get_filename_component(name "${dest_directory}" NAME)
-      install(FILES "${source_files}" DESTINATION "${location}/${name}${build_type_tag}" CONFIGURATIONS "${build_type}")
-    endforeach()
-  else()
-    install(FILES "${source_files}" DESTINATION "${dest_directory}")
-  endif()
-
+    install(FILES "${source_files}" DESTINATION "${dest_directory}" CONFIGURATIONS "${CMAKE_BUILD_TYPE}")
 endfunction()

From 54f2acd521b0531c9a727ee585cae7afcf5ef2bd Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 30 Jun 2020 20:57:31 -0500
Subject: [PATCH 21/29] updated cython wrapper README

---
 cython/README.md | 89 +++++++++++++++++++++---------------------------
 1 file changed, 38 insertions(+), 51 deletions(-)

diff --git a/cython/README.md b/cython/README.md
index bc6e346d9..0c59915a0 100644
--- a/cython/README.md
+++ b/cython/README.md
@@ -1,33 +1,36 @@
 # Python Wrapper
 
-This is the Cython/Python wrapper around the GTSAM C++ library.
+This is the Python wrapper around the GTSAM C++ library. We use Cython to generate the bindings to the underlying C++ code.
+
+## Requirements
+
+- If you want to build the gtsam python library for a specific python version (eg 2.7), use the `-DGTSAM_PYTHON_VERSION=2.7` option when running `cmake` otherwise the default interpreter will be used.
+    - If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
+- This wrapper needs `Cython(>=0.25.2)`, `backports_abc(>=0.5)`, and `numpy(>=1.11.0)`. These can be installed as follows:
+
+  ```bash
+  pip install -r <gtsam_folder>/cython/requirements.txt
+  ```
+
+- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
+named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
 
 ## Install
 
-- if you want to build the gtsam python library for a specific python version (eg 2.7), use the `-DGTSAM_PYTHON_VERSION=2.7` option when running `cmake` otherwise the default interpreter will be used.
-    - If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
-- This wrapper needs Cython(>=0.25.2), backports_abc>=0.5, and numpy. These can be installed as follows:
-
-```bash
- pip install -r <gtsam_folder>/cython/requirements.txt
-```
-
-- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
-named **gtsam_eigency**, to interface between C++'s Eigen and Python's numpy.
-
-- Build and install gtsam using cmake with `GTSAM_INSTALL_CYTHON_TOOLBOX` enabled.
-The wrapped module will be installed to `GTSAM_CYTHON_INSTALL_PATH`, which is
-by default: `<your CMAKE_INSTALL_PREFIX>/cython`
+- Run cmake with the `GTSAM_INSTALL_CYTHON_TOOLBOX` cmake flag enabled to configure building the wrapper. The wrapped module will be built and copied to the directory defined by `GTSAM_CYTHON_INSTALL_PATH`, which is by default: `<CMAKE_INSTALL_PREFIX>/cython.build`.
 
 - To use the library without installing system-wide: modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
-```bash
-export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
-```
-- To install system-wide: run `make install` then navigate to `GTSAM_CYTHON_INSTALL_PATH` and run `python setup.py install`
-    - (the same command can be used to install into a virtual environment if it is active)
-    - note: if you don't want gtsam to install to a system directory such as `/usr/local`, pass `-DCMAKE_INSTALL_PREFIX="./install"` to cmake to install gtsam to a subdirectory of the build directory.
-    - if you run `setup.py` from the build directory rather than the installation directory, the script will warn you with the message: `setup.py is being run from an unexpected location`.
-      Before `make install` is run, not all the components of the package have been copied across, so running `setup.py` from the build directory would result in an incomplete package.
+
+  ```bash
+  export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
+  ```
+
+- Build GTSAM and the wrapper with `make`.
+
+- To install system-wide, simply run `make install`.
+    - The same command can be used to install into a virtual environment if it is active.
+    - **NOTE**: if you don't want gtsam to install to a system directory such as `/usr/local`, pass `-DCMAKE_INSTALL_PREFIX="./install"` to cmake to install gtsam to a subdirectory of the build directory.
+    - If you run `setup.py` from the build directory rather than the installation directory, the script will warn you with the message: `setup.py is being run from an unexpected location`.
 
 ## Unit Tests
 
@@ -47,48 +50,32 @@ See the tests for examples.
 
 - Vector/Matrix:
   + GTSAM expects double-precision floating point vectors and matrices.
-    Hence, you should pass numpy matrices with dtype=float, or 'float64'.
+    Hence, you should pass numpy matrices with `dtype=float`, or `float64`.
   + Also, GTSAM expects *column-major* matrices, unlike the default storage
     scheme in numpy. Hence, you should pass column-major matrices to gtsam using
     the flag order='F'. And you always get column-major matrices back.
-    For more details, see: https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed
-  + Passing row-major matrices of different dtype, e.g. 'int', will also work
+    For more details, see [this link](https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed).
+  + Passing row-major matrices of different dtype, e.g. `int`, will also work
     as the wrapper converts them to column-major and dtype float for you,
     using numpy.array.astype(float, order='F', copy=False).
     However, this will result a copy if your matrix is not in the expected type
     and storage order.
 
 - Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>_ in Python.
-Examples: noiseModel_Gaussian, noiseModel_mEstimator_Tukey
+
+  Examples: `noiseModel_Gaussian`, `noiseModel_mEstimator_Tukey`
 
 - Casting from a base class to a derive class must be done explicitly.
-Examples:
-```Python
-      noiseBase = factor.noiseModel()
-      noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
-```
 
-## Wrapping Your Own Project That Uses GTSAM
+  Examples:
+  ```python
+  noiseBase = factor.noiseModel()
+  noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
+  ```
 
-- Set PYTHONPATH to include ${GTSAM_CYTHON_INSTALL_PATH}
-  + so that it can find gtsam Cython header: gtsam/gtsam.pxd
+## Wrapping Custom GTSAM-based Project
 
-- In your CMakeList.txt
-```cmake
-find_package(GTSAM REQUIRED) # Make sure gtsam's install folder is in your PATH
-set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${GTSAM_DIR}/../GTSAMCMakeTools")
-
-# Wrap
-include(GtsamCythonWrap)
-include_directories(${GTSAM_EIGENCY_INSTALL_PATH})
-wrap_and_install_library_cython("your_project_interface.h"
-                                "from gtsam.gtsam cimport *" # extra import of gtsam/gtsam.pxd Cython header
-                                "your_install_path"
-                                "libraries_to_link_with_the_cython_module"
-                                "dependencies_which_need_to_be_built_before_the_wrapper"
-                                )
-#Optional: install_cython_scripts and install_cython_files. See GtsamCythonWrap.cmake.
-```
+Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/gtsam-project-python).
 
 ## KNOWN ISSUES
 

From 8859b963a24db117fc51ea9532c310b6721c0fc1 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 1 Jul 2020 12:13:53 -0500
Subject: [PATCH 22/29] In-place cython build

Build everything inside the build/cython{BuildType} directory directly, so we can bypass the `make install` step and introduce the `make python-install` step which allows cmake to handle all dependencies.
---
 CMakeLists.txt                      |  8 ++---
 cmake/GtsamCythonWrap.cmake         |  6 ++--
 cython/CMakeLists.txt               | 51 ++++++++++++++---------------
 cython/gtsam_eigency/CMakeLists.txt | 17 +---------
 4 files changed, 31 insertions(+), 51 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f8deebfcd..a9966f5d3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -454,15 +454,13 @@ endif()
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 1)
   # Set up cache options
-  set(GTSAM_CYTHON_PATH "${PROJECT_BINARY_DIR}/cython" CACHE PATH "Cython source files directory path")
   # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
-  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython.build<GTSAM_BUILD_TAG>")
+  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython<GTSAM_BUILD_TAG>")
   if(NOT GTSAM_CYTHON_INSTALL_PATH)
-    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython.build${GTSAM_BUILD_TAG}")
+    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython${GTSAM_BUILD_TAG}" CACHE PATH "")
   endif()
-  set(GTSAM_EIGENCY_PATH ${GTSAM_CYTHON_PATH}/gtsam_eigency)
   set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
-  add_subdirectory(cython)
+  add_subdirectory(cython ${GTSAM_CYTHON_INSTALL_PATH})
 else()
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 0) # This will go into config.h
 endif()
diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 3ce7f4454..797745acf 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -41,9 +41,9 @@ execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
 function(wrap_and_install_library_cython interface_header extra_imports install_path libs dependencies)
   # Paths for generated files
   get_filename_component(module_name "${interface_header}" NAME_WE)
-  set(generated_files_path "${PROJECT_BINARY_DIR}/cython/${module_name}")
+  set(generated_files_path "${GTSAM_CYTHON_INSTALL_PATH}/${module_name}")
   wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${libs}" "${dependencies}")
-  install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
+  # install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
 endfunction()
 
 function(set_up_required_cython_packages)
@@ -214,7 +214,7 @@ function(install_cython_scripts source_directory dest_directory patterns)
     list(APPEND patterns_args PATTERN "${pattern}")
   endforeach()
 
-  install(DIRECTORY "${source_directory}" DESTINATION "${dest_directory}" CONFIGURATIONS "${CMAKE_BUILD_TYPE}"
+  file(COPY "${source_directory}" DESTINATION "${dest_directory}"
             FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
 endfunction()
 
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index b0eb43c50..74725c463 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,21 +1,37 @@
-# Create directory where cython build files will be placed
-file(MAKE_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})
-
 # Install cython components
 include(GtsamCythonWrap)
 
 # Create the cython toolbox for the gtsam library
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
+  # Add the new make target command
+  add_custom_target(python-install
+    COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}/setup.py install
+    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
+
   # build and include the eigency version of eigency
   add_subdirectory(gtsam_eigency)
-  include_directories(${GTSAM_EIGENCY_PATH})
+  include_directories(${GTSAM_EIGENCY_INSTALL_PATH})
 
   # Fix for error "C1128: number of sections exceeded object file format limit"
   if(MSVC)
     add_compile_options(/bigobj)
   endif()
 
-  # wrap gtsam
+  # First set up all the package related files.
+  # This also ensures the below wrap operations work correctly.
+  set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
+
+  # Install the custom-generated __init__.py
+  # This makes the cython (sub-)directories into python packages, so gtsam can be found while wrapping gtsam_unstable
+  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam/__init__.py COPYONLY)
+  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
+  configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
+  install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
+  # install scripts and tests
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
+  # Wrap gtsam
   add_custom_target(gtsam_header DEPENDS "../gtsam.h")
   wrap_and_install_library_cython("../gtsam.h" # interface_header
                                   ""                  # extra imports
@@ -23,8 +39,9 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                   gtsam  # library to link with
                                   "wrap;cythonize_eigency;gtsam;gtsam_header"  # dependencies which need to be built before wrapping
                                   )
+  add_dependencies(python-install gtsam gtsam_header)
 
-  # wrap gtsam_unstable
+  # Wrap gtsam_unstable
   if(GTSAM_BUILD_UNSTABLE)
     add_custom_target(gtsam_unstable_header DEPENDS "../gtsam_unstable/gtsam_unstable.h")
     wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
@@ -33,27 +50,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                     gtsam_unstable  # library to link with
                                     "gtsam_unstable;gtsam_unstable_header;cythonize_gtsam"  # dependencies to be built before wrapping
                                     )
+    add_dependencies(python-install gtsam_unstable gtsam_unstable_header)
   endif()
 
-  set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
-
-  # Install the custom-generated __init__.py
-  # This is to make the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
-  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py COPYONLY)
-  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${PROJECT_BINARY_DIR}/cython/gtsam_unstable/__init__.py COPYONLY)
-  configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${PROJECT_BINARY_DIR}/cython/setup.py)
-  install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
-  # install scripts and tests
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
-
-  # Install gtsam_eigency.
-  # The paths are picked up directly from the parent CMakeLists.txt.
-  install_gtsam_eigency()
-
-  # Automatically run the python installation via the setup.py
-  install(CODE
-    "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install
-      WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})")
-
 endif ()
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index f64e45cdb..7c215e89c 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -4,7 +4,7 @@ include(GtsamCythonWrap)
 # so that the cython-generated header "conversions_api.h" can be found when cythonizing eigency's core
 # and eigency's cython pxd headers can be found when cythonizing gtsam
 file(COPY "." DESTINATION ".")
-set(OUTPUT_DIR "${GTSAM_CYTHON_PATH}/gtsam_eigency")
+set(OUTPUT_DIR "${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency")
 set(EIGENCY_INCLUDE_DIR ${OUTPUT_DIR})
 
 # This is to make the build/cython/gtsam_eigency folder a python package
@@ -36,18 +36,3 @@ target_include_directories(cythonize_eigency_core PUBLIC
 add_dependencies(cythonize_eigency_core cythonize_eigency_conversions)
 add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
-
-# install
-function(install_gtsam_eigency)
-  install(DIRECTORY ${GTSAM_EIGENCY_PATH}
-          DESTINATION "${GTSAM_CYTHON_INSTALL_PATH}"
-          PATTERN "CMakeLists.txt" EXCLUDE
-          PATTERN "__init__.py.in" EXCLUDE
-          PATTERN "*.dir" EXCLUDE
-          PATTERN "*.make" EXCLUDE)
-  install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
-          DESTINATION "${GTSAM_EIGENCY_INSTALL_PATH}")
-  install(FILES ${GTSAM_EIGENCY_PATH}/conversions_api.h DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
-  install(FILES ${GTSAM_EIGENCY_PATH}/__init__.py DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
-
-endfunction()

From 74591eece60b45342a865474fef452a7683430c7 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 1 Jul 2020 14:36:16 -0500
Subject: [PATCH 23/29] fixed CYTHON_INSTALL_PATH cmake variable wrt cache

---
 CMakeLists.txt | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a9966f5d3..f5b9c5e22 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -455,10 +455,8 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 1)
   # Set up cache options
   # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
-  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython<GTSAM_BUILD_TAG>")
-  if(NOT GTSAM_CYTHON_INSTALL_PATH)
-    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython${GTSAM_BUILD_TAG}" CACHE PATH "")
-  endif()
+  # This does not override custom values set from the command line
+  set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython${GTSAM_BUILD_TAG}" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython<GTSAM_BUILD_TAG>")
   set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
   add_subdirectory(cython ${GTSAM_CYTHON_INSTALL_PATH})
 else()

From 59968fddc5d7e0ded0102a8ac310602b9dd5c4b9 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 1 Jul 2020 14:36:57 -0500
Subject: [PATCH 24/29] Python Wrapper CMake update

- Added python-install target variable for easy updating.
- Fixed/Added all dependencies so that everything is built automatically.
- Removed unnecessary install commands
---
 cmake/GtsamCythonWrap.cmake         | 26 +++-----------------------
 cython/CMakeLists.txt               | 14 ++++++++------
 cython/gtsam_eigency/CMakeLists.txt |  2 ++
 3 files changed, 13 insertions(+), 29 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 797745acf..7597834c9 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -43,7 +43,6 @@ function(wrap_and_install_library_cython interface_header extra_imports install_
   get_filename_component(module_name "${interface_header}" NAME_WE)
   set(generated_files_path "${GTSAM_CYTHON_INSTALL_PATH}/${module_name}")
   wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${libs}" "${dependencies}")
-  # install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
 endfunction()
 
 function(set_up_required_cython_packages)
@@ -170,32 +169,13 @@ function(wrap_library_cython interface_header generated_files_path extra_imports
   cythonize(cythonize_${module_name} ${generated_pyx} ${module_name}
     ${generated_files_path} "${include_dirs}" "${libs}" ${interface_header} cython_wrap_${module_name}_pyx)
 
+  add_dependencies(${python_install_target} cython_wrap_${module_name}_pyx)
+
   # distclean
   add_custom_target(wrap_${module_name}_cython_distclean
       COMMAND cmake -E remove_directory ${generated_files_path})
 endfunction()
 
-# Internal function that installs a wrap toolbox
-function(install_cython_wrapped_library interface_header generated_files_path install_path)
-  get_filename_component(module_name "${interface_header}" NAME_WE)
-
-  # NOTE: only installs .pxd and .pyx and binary files (not .cpp) - the trailing slash on the directory name
-  # here prevents creating the top-level module name directory in the destination.
-  # Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH/subdirectory if there is one
-  get_filename_component(location "${install_path}" PATH)
-  get_filename_component(name "${install_path}" NAME)
-  message(STATUS "Installing Cython Toolbox to ${location}/${name}") #${GTSAM_CYTHON_INSTALL_PATH}"
-
-  install(DIRECTORY "${generated_files_path}/" DESTINATION ${install_path}
-      CONFIGURATIONS "${CMAKE_BUILD_TYPE}"
-      PATTERN "build" EXCLUDE
-      PATTERN "CMakeFiles" EXCLUDE
-      PATTERN "Makefile" EXCLUDE
-      PATTERN "*.cmake" EXCLUDE
-      PATTERN "*.cpp" EXCLUDE
-      PATTERN "*.py" EXCLUDE)
-endfunction()
-
 # Helper function to install Cython scripts and handle multiple build types where the scripts
 # should be installed to all build type toolboxes
 #
@@ -225,5 +205,5 @@ endfunction()
 #  source_files: The source files to be installed.
 #  dest_directory: The destination directory to install to.
 function(install_cython_files source_files dest_directory)
-    install(FILES "${source_files}" DESTINATION "${dest_directory}" CONFIGURATIONS "${CMAKE_BUILD_TYPE}")
+    file(COPY "${source_files}" DESTINATION "${dest_directory}")
 endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 74725c463..ce93120c2 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -4,7 +4,8 @@ include(GtsamCythonWrap)
 # Create the cython toolbox for the gtsam library
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   # Add the new make target command
-  add_custom_target(python-install
+  set(python_install_target python-install)
+  add_custom_target(${python_install_target}
     COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}/setup.py install
     WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
 
@@ -27,9 +28,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
   configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
   install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
-  # install scripts and tests
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
 
   # Wrap gtsam
   add_custom_target(gtsam_header DEPENDS "../gtsam.h")
@@ -39,7 +37,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                   gtsam  # library to link with
                                   "wrap;cythonize_eigency;gtsam;gtsam_header"  # dependencies which need to be built before wrapping
                                   )
-  add_dependencies(python-install gtsam gtsam_header)
+  add_dependencies(${python_install_target} gtsam gtsam_header)
 
   # Wrap gtsam_unstable
   if(GTSAM_BUILD_UNSTABLE)
@@ -50,7 +48,11 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                     gtsam_unstable  # library to link with
                                     "gtsam_unstable;gtsam_unstable_header;cythonize_gtsam"  # dependencies to be built before wrapping
                                     )
-    add_dependencies(python-install gtsam_unstable gtsam_unstable_header)
+    add_dependencies(${python_install_target} gtsam_unstable gtsam_unstable_header)
   endif()
 
+  # install scripts and tests
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
 endif ()
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index 7c215e89c..663ea0a32 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -36,3 +36,5 @@ target_include_directories(cythonize_eigency_core PUBLIC
 add_dependencies(cythonize_eigency_core cythonize_eigency_conversions)
 add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
+
+add_dependencies(${python_install_target} cythonize_eigency)

From a6908cd1cb003ee184d0018a559075b319d65afe Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 1 Jul 2020 16:23:24 -0500
Subject: [PATCH 25/29] removed unneeded install commands and updated README

---
 cmake/GtsamCythonWrap.cmake | 10 -----
 cython/CMakeLists.txt       |  1 -
 cython/README.md            | 83 ++++++++++++++++++++-----------------
 3 files changed, 44 insertions(+), 50 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 7597834c9..c155cbbd8 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -197,13 +197,3 @@ function(install_cython_scripts source_directory dest_directory patterns)
   file(COPY "${source_directory}" DESTINATION "${dest_directory}"
             FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
 endfunction()
-
-# Helper function to install specific files and handle multiple build types where the scripts
-# should be installed to all build type toolboxes
-#
-# Arguments:
-#  source_files: The source files to be installed.
-#  dest_directory: The destination directory to install to.
-function(install_cython_files source_files dest_directory)
-    file(COPY "${source_files}" DESTINATION "${dest_directory}")
-endfunction()
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index ce93120c2..65a9e9c62 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -27,7 +27,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam/__init__.py COPYONLY)
   configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
   configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
-  install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
 
   # Wrap gtsam
   add_custom_target(gtsam_header DEPENDS "../gtsam.h")
diff --git a/cython/README.md b/cython/README.md
index 0c59915a0..f69b7a5a6 100644
--- a/cython/README.md
+++ b/cython/README.md
@@ -4,43 +4,48 @@ This is the Python wrapper around the GTSAM C++ library. We use Cython to genera
 
 ## Requirements
 
-- If you want to build the gtsam python library for a specific python version (eg 2.7), use the `-DGTSAM_PYTHON_VERSION=2.7` option when running `cmake` otherwise the default interpreter will be used.
-    - If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
+- If you want to build the GTSAM python library for a specific python version (eg 3.6),
+  use the `-DGTSAM_PYTHON_VERSION=3.6` option when running `cmake` otherwise the default interpreter will be used.
+- If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment),
+  then the environment should be active while building GTSAM.
 - This wrapper needs `Cython(>=0.25.2)`, `backports_abc(>=0.5)`, and `numpy(>=1.11.0)`. These can be installed as follows:
 
   ```bash
   pip install -r <gtsam_folder>/cython/requirements.txt
   ```
 
-- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
-named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
+- For compatibility with GTSAM's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
+  named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
 
 ## Install
 
-- Run cmake with the `GTSAM_INSTALL_CYTHON_TOOLBOX` cmake flag enabled to configure building the wrapper. The wrapped module will be built and copied to the directory defined by `GTSAM_CYTHON_INSTALL_PATH`, which is by default: `<CMAKE_INSTALL_PREFIX>/cython.build`.
-
-- To use the library without installing system-wide: modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
-
-  ```bash
-  export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
-  ```
+- Run cmake with the `GTSAM_INSTALL_CYTHON_TOOLBOX` cmake flag enabled to configure building the wrapper. The wrapped module will be built and copied to the directory defined by `GTSAM_CYTHON_INSTALL_PATH`, which is by default `<PROJECT_BINARY_DIR>/cython` in Release mode and `<PROJECT_BINARY_DIR>/cython<CMAKE_BUILD_TYPE>` for other modes.
 
 - Build GTSAM and the wrapper with `make`.
 
-- To install system-wide, simply run `make install`.
-    - The same command can be used to install into a virtual environment if it is active.
-    - **NOTE**: if you don't want gtsam to install to a system directory such as `/usr/local`, pass `-DCMAKE_INSTALL_PREFIX="./install"` to cmake to install gtsam to a subdirectory of the build directory.
-    - If you run `setup.py` from the build directory rather than the installation directory, the script will warn you with the message: `setup.py is being run from an unexpected location`.
+- To install, simply run `make python-install`.
+  - The same command can be used to install into a virtual environment if it is active.
+  - **NOTE**: if you don't want GTSAM to install to a system directory such as `/usr/local`, pass `-DCMAKE_INSTALL_PREFIX="./install"` to cmake to install GTSAM to a subdirectory of the build directory.
+
+- You can also directly run `make python-install` without running `make`, and it will compile all the dependencies accordingly.
 
 ## Unit Tests
 
 The Cython toolbox also has a small set of unit tests located in the
 test directory. To run them:
 
-```bash
- cd <your GTSAM_CYTHON_INSTALL_PATH>
- python -m unittest discover
-```
+  ```bash
+  cd <GTSAM_CYTHON_INSTALL_PATH>
+  python -m unittest discover
+  ```
+
+## Utils
+
+TODO
+
+## Examples
+
+TODO
 
 ## Writing Your Own Scripts
 
@@ -49,25 +54,27 @@ See the tests for examples.
 ### Some Important Notes:
 
 - Vector/Matrix:
-  + GTSAM expects double-precision floating point vectors and matrices.
+
+  - GTSAM expects double-precision floating point vectors and matrices.
     Hence, you should pass numpy matrices with `dtype=float`, or `float64`.
-  + Also, GTSAM expects *column-major* matrices, unlike the default storage
-    scheme in numpy. Hence, you should pass column-major matrices to gtsam using
+  - Also, GTSAM expects _column-major_ matrices, unlike the default storage
+    scheme in numpy. Hence, you should pass column-major matrices to GTSAM using
     the flag order='F'. And you always get column-major matrices back.
     For more details, see [this link](https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed).
-  + Passing row-major matrices of different dtype, e.g. `int`, will also work
+  - Passing row-major matrices of different dtype, e.g. `int`, will also work
     as the wrapper converts them to column-major and dtype float for you,
     using numpy.array.astype(float, order='F', copy=False).
     However, this will result a copy if your matrix is not in the expected type
     and storage order.
 
-- Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>_ in Python.
+- Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>\_ in Python.
 
   Examples: `noiseModel_Gaussian`, `noiseModel_mEstimator_Tukey`
 
 - Casting from a base class to a derive class must be done explicitly.
 
   Examples:
+
   ```python
   noiseBase = factor.noiseModel()
   noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
@@ -75,37 +82,35 @@ See the tests for examples.
 
 ## Wrapping Custom GTSAM-based Project
 
-Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/gtsam-project-python).
+Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/GTSAM-project-python).
 
 ## KNOWN ISSUES
 
-  - Doesn't work with python3 installed from homebrew
-    - size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
-    - Guess: 64 vs 32b? disutils Compiler flags?
-  - Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector<Key>
-    - Upgrading to 0.25 solves the problem
-  - Need default constructor and default copy constructor for almost every classes... :(
-    - support these constructors by default and declare "delete" for special classes?
-
+- Doesn't work with python3 installed from homebrew
+  - size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
+  - Guess: 64 vs 32b? disutils Compiler flags?
+- Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector<Key>
+  - Upgrading to 0.25 solves the problem
+- Need default constructor and default copy constructor for almost every classes... :(
+  - support these constructors by default and declare "delete" for special classes?
 
 ### TODO
 
 - [ ] allow duplication of parent' functions in child classes. Not allowed for now due to conflicts in Cython.
-- [ ] a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in gtsam?)
+- [ ] a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in GTSAM?)
 - [ ] inner namespaces ==> inner packages?
 - [ ] Wrap fixed-size Matrices/Vectors?
 
-
 ### Completed/Cancelled:
 
-- [x] Fix Python tests: don't use " import <package> * ": Bad style!!! (18-03-17 19:50)
+- [x] Fix Python tests: don't use " import <package> \* ": Bad style!!! (18-03-17 19:50)
 - [x] Unit tests for cython wrappers @done (18-03-17 18:45) -- simply compare generated files
 - [x] Wrap unstable @done (18-03-17 15:30)
-- [x] Unify cython/gtsam.h and the original gtsam.h @done (18-03-17 15:30)
+- [x] Unify cython/GTSAM.h and the original GTSAM.h @done (18-03-17 15:30)
 - [x] 18-03-17: manage to unify the two versions by removing std container stubs from the matlab version,and keeping KeyList/KeyVector/KeySet as in the matlab version. Probably Cython 0.25 fixes the casting problem.
 - [x] 06-03-17: manage to remove the requirements for default and copy constructors
 - [ ] 25-11-16: Try to unify but failed. Main reasons are: Key/size_t, std containers, KeyVector/KeyList/KeySet. Matlab doesn't need to know about Key, but I can't make Cython to ignore Key as it couldn't cast KeyVector, i.e. FastVector<Key>, to FastVector<size_t>.
-- [ ] Marginal and JointMarginal: revert changes @failed (17-03-17 11:00) -- Cython does need a default constructor! It produces cpp code like this: ```gtsam::JointMarginal __pyx_t_1;```  Users don't have to wrap this constructor, however.
+- [ ] Marginal and JointMarginal: revert changes @failed (17-03-17 11:00) -- Cython does need a default constructor! It produces cpp code like this: `GTSAM::JointMarginal __pyx_t_1;` Users don't have to wrap this constructor, however.
 - [x] Convert input numpy Matrix/Vector to float dtype and storage order 'F' automatically, cannot crash! @done (15-03-17 13:00)
 - [x] Remove requirements.txt - Frank: don't bother with only 2 packages and a special case for eigency! @done (08-03-17 10:30)
 - [x] CMake install script @done (25-11-16 02:30)
@@ -119,7 +124,7 @@ Please refer to the template project and the corresponding tutorial available [h
 - [x] Casting from parent and grandparents @done (16-11-16 17:00)
 - [x] Allow overloading constructors. The current solution is annoying!!! @done (16-11-16 17:00)
 - [x] Support "print obj" @done (16-11-16 17:00)
-- [x] methods for FastVector: at, [], ...  @done (16-11-16 17:00)
+- [x] methods for FastVector: at, [], ... @done (16-11-16 17:00)
 - [x] Cython: Key and size_t: traits<size_t> doesn't exist @done (16-09-12 18:34)
 - [x] KeyVector, KeyList, KeySet... @done (16-09-13 17:19)
 - [x] [Nice to have] parse typedef @done (16-09-13 17:19)

From d2f69eeab41044219f4a40314eaf98d62254d183 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Wed, 1 Jul 2020 17:07:31 -0500
Subject: [PATCH 26/29] Add python-install dependency for gtsam_unstable as
 well

---
 cmake/GtsamCythonWrap.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index c155cbbd8..2f5582513 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -137,6 +137,8 @@ function(cythonize target pyx_file output_lib_we output_dir include_dirs libs in
     target_link_libraries(${target} "${libs}")
   endif()
   add_dependencies(${target} ${target}_pyx2cpp)
+
+  add_dependencies(${python_install_target} ${target})
 endfunction()
 
 # Internal function that wraps a library and compiles the wrapper
@@ -169,8 +171,6 @@ function(wrap_library_cython interface_header generated_files_path extra_imports
   cythonize(cythonize_${module_name} ${generated_pyx} ${module_name}
     ${generated_files_path} "${include_dirs}" "${libs}" ${interface_header} cython_wrap_${module_name}_pyx)
 
-  add_dependencies(${python_install_target} cython_wrap_${module_name}_pyx)
-
   # distclean
   add_custom_target(wrap_${module_name}_cython_distclean
       COMMAND cmake -E remove_directory ${generated_files_path})

From cb151dd9ee9426f60c371c4a49c043726f7a4afa Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sat, 4 Jul 2020 20:42:15 -0400
Subject: [PATCH 27/29] update python build location in travis script

---
 .travis.python.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.python.sh b/.travis.python.sh
index 1ef5799aa..772311f38 100644
--- a/.travis.python.sh
+++ b/.travis.python.sh
@@ -34,7 +34,7 @@ cmake $CURRDIR -DCMAKE_BUILD_TYPE=Release \
 
 make -j$(nproc) install
 
-cd $CURRDIR/../gtsam_install/cython
+cd cython
 
 sudo $PYTHON setup.py install
 

From e08e39202074fed0b0a40fdb821e5f0726ec4799 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sun, 5 Jul 2020 21:57:18 -0500
Subject: [PATCH 28/29] Improved paths and added checks

---
 cmake/GtsamCythonWrap.cmake         | 13 +++++++++----
 cython/gtsam_eigency/CMakeLists.txt |  4 +++-
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 2f5582513..c8f876895 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -41,7 +41,7 @@ execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
 function(wrap_and_install_library_cython interface_header extra_imports install_path libs dependencies)
   # Paths for generated files
   get_filename_component(module_name "${interface_header}" NAME_WE)
-  set(generated_files_path "${GTSAM_CYTHON_INSTALL_PATH}/${module_name}")
+  set(generated_files_path "${install_path}")
   wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${libs}" "${dependencies}")
 endfunction()
 
@@ -138,7 +138,9 @@ function(cythonize target pyx_file output_lib_we output_dir include_dirs libs in
   endif()
   add_dependencies(${target} ${target}_pyx2cpp)
 
-  add_dependencies(${python_install_target} ${target})
+  if(TARGET ${python_install_target})
+    add_dependencies(${python_install_target} ${target})
+  endif()
 endfunction()
 
 # Internal function that wraps a library and compiles the wrapper
@@ -151,9 +153,12 @@ function(wrap_library_cython interface_header generated_files_path extra_imports
   get_filename_component(module_name "${interface_header}" NAME_WE)
 
   # Wrap module to Cython pyx
-  message(STATUS "Cython wrapper generating ${module_name}.pyx")
+  message(STATUS "Cython wrapper generating ${generated_files_path}/${module_name}.pyx")
   set(generated_pyx "${generated_files_path}/${module_name}.pyx")
-  file(MAKE_DIRECTORY "${generated_files_path}")
+  if(NOT EXISTS ${generated_files_path})
+    file(MAKE_DIRECTORY "${generated_files_path}")
+  endif()
+
   add_custom_command(
     OUTPUT ${generated_pyx}
     DEPENDS ${interface_header} wrap
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index 663ea0a32..a0cf0fbde 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -37,4 +37,6 @@ add_dependencies(cythonize_eigency_core cythonize_eigency_conversions)
 add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
 
-add_dependencies(${python_install_target} cythonize_eigency)
+if(TARGET ${python_install_target})
+  add_dependencies(${python_install_target} cythonize_eigency)
+endif()

From 66570469c5f890af0245ec0b1334c9a9c1294782 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Tue, 7 Jul 2020 17:38:27 -0400
Subject: [PATCH 29/29] fix working directory for python install target

---
 cython/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index 65a9e9c62..221025575 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -7,7 +7,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(python_install_target python-install)
   add_custom_target(${python_install_target}
     COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}/setup.py install
-    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
+    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})
 
   # build and include the eigency version of eigency
   add_subdirectory(gtsam_eigency)