removed unneeded install commands and updated README

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()

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")

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 you want to build the GTSAM python library for a specific python version (eg 3.6),
-    - If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
+  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),
+- 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.
+  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`.
+- 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.
-
-- 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>
-  ```
 
 - Build GTSAM and the wrapper with `make`.
 
-- To install system-wide, simply run `make install`.
+- To install, simply run `make python-install`.
-    - The same command can be used to install into a virtual environment if it is active.
+  - 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.
+  - **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`.
+
+- 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
+  ```bash
- cd <your GTSAM_CYTHON_INSTALL_PATH>
+  cd <GTSAM_CYTHON_INSTALL_PATH>
- python -m unittest discover
+  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
+  - Also, GTSAM expects _column-major_ matrices, unlike the default storage
-    scheme in numpy. Hence, you should pass column-major matrices to gtsam using
+    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
+- Doesn't work with python3 installed from homebrew
-    - size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
+  - size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
-    - Guess: 64 vs 32b? disutils Compiler flags?
+  - 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>
+- 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
+  - Upgrading to 0.25 solves the problem
-  - Need default constructor and default copy constructor for almost every classes... :(
+- Need default constructor and default copy constructor for almost every classes... :(
-    - support these constructors by default and declare "delete" for special 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)