removed unneeded install commands and updated README
Varun Agrawal
parent
59968fddc5
commit
a6908cd1cb
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@ -197,13 +197,3 @@ function(install_cython_scripts source_directory dest_directory patterns)
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file(COPY "${source_directory}" DESTINATION "${dest_directory}"
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FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
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endfunction()
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# Helper function to install specific files and handle multiple build types where the scripts
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# should be installed to all build type toolboxes
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#
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# Arguments:
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# source_files: The source files to be installed.
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# dest_directory: The destination directory to install to.
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function(install_cython_files source_files dest_directory)
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file(COPY "${source_files}" DESTINATION "${dest_directory}")
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endfunction()
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@ -27,7 +27,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
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configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam/__init__.py COPYONLY)
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configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
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configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
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install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
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# Wrap gtsam
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add_custom_target(gtsam_header DEPENDS "../gtsam.h")
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@ -4,43 +4,48 @@ This is the Python wrapper around the GTSAM C++ library. We use Cython to genera
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## Requirements
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- 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.
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- If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
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- If you want to build the GTSAM python library for a specific python version (eg 3.6),
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use the `-DGTSAM_PYTHON_VERSION=3.6` option when running `cmake` otherwise the default interpreter will be used.
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- If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment),
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then the environment should be active while building GTSAM.
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- This wrapper needs `Cython(>=0.25.2)`, `backports_abc(>=0.5)`, and `numpy(>=1.11.0)`. These can be installed as follows:
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```bash
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pip install -r <gtsam_folder>/cython/requirements.txt
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```
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- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
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named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
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- For compatibility with GTSAM's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
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named `gtsam_eigency`, to interface between C++'s Eigen and Python's numpy.
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## Install
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- 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`.
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- To use the library without installing system-wide: modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
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```bash
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export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
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```
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- 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.
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- Build GTSAM and the wrapper with `make`.
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- To install system-wide, simply run `make install`.
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- The same command can be used to install into a virtual environment if it is active.
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- **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.
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- 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`.
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- To install, simply run `make python-install`.
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- The same command can be used to install into a virtual environment if it is active.
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- **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.
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- You can also directly run `make python-install` without running `make`, and it will compile all the dependencies accordingly.
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## Unit Tests
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The Cython toolbox also has a small set of unit tests located in the
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test directory. To run them:
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```bash
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cd <your GTSAM_CYTHON_INSTALL_PATH>
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python -m unittest discover
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```
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```bash
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cd <GTSAM_CYTHON_INSTALL_PATH>
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python -m unittest discover
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```
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## Utils
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TODO
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## Examples
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TODO
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## Writing Your Own Scripts
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@ -49,25 +54,27 @@ See the tests for examples.
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### Some Important Notes:
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- Vector/Matrix:
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+ GTSAM expects double-precision floating point vectors and matrices.
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- GTSAM expects double-precision floating point vectors and matrices.
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Hence, you should pass numpy matrices with `dtype=float`, or `float64`.
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+ Also, GTSAM expects *column-major* matrices, unlike the default storage
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scheme in numpy. Hence, you should pass column-major matrices to gtsam using
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- Also, GTSAM expects _column-major_ matrices, unlike the default storage
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scheme in numpy. Hence, you should pass column-major matrices to GTSAM using
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the flag order='F'. And you always get column-major matrices back.
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For more details, see [this link](https://github.com/wouterboomsma/eigency#storage-layout---why-arrays-are-sometimes-transposed).
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+ Passing row-major matrices of different dtype, e.g. `int`, will also work
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- Passing row-major matrices of different dtype, e.g. `int`, will also work
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as the wrapper converts them to column-major and dtype float for you,
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using numpy.array.astype(float, order='F', copy=False).
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However, this will result a copy if your matrix is not in the expected type
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and storage order.
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- Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>_ in Python.
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- Inner namespace: Classes in inner namespace will be prefixed by <innerNamespace>\_ in Python.
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Examples: `noiseModel_Gaussian`, `noiseModel_mEstimator_Tukey`
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- Casting from a base class to a derive class must be done explicitly.
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Examples:
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```python
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noiseBase = factor.noiseModel()
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noiseGaussian = dynamic_cast_noiseModel_Gaussian_noiseModel_Base(noiseBase)
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@ -75,37 +82,35 @@ See the tests for examples.
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## Wrapping Custom GTSAM-based Project
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Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/gtsam-project-python).
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Please refer to the template project and the corresponding tutorial available [here](https://github.com/borglab/GTSAM-project-python).
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## KNOWN ISSUES
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- Doesn't work with python3 installed from homebrew
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- size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
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- Guess: 64 vs 32b? disutils Compiler flags?
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- Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector<Key>
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- Upgrading to 0.25 solves the problem
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- Need default constructor and default copy constructor for almost every classes... :(
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- support these constructors by default and declare "delete" for special classes?
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- Doesn't work with python3 installed from homebrew
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- size-related issue: can only wrap up to a certain number of classes: up to mEstimator!
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- Guess: 64 vs 32b? disutils Compiler flags?
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- Bug with Cython 0.24: instantiated factor classes return FastVector<size_t> for keys(), which can't be casted to FastVector<Key>
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- Upgrading to 0.25 solves the problem
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- Need default constructor and default copy constructor for almost every classes... :(
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- support these constructors by default and declare "delete" for special classes?
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### TODO
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- [ ] allow duplication of parent' functions in child classes. Not allowed for now due to conflicts in Cython.
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- [ ] a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in gtsam?)
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- [ ] a common header for boost shared_ptr? (Or wait until everything is switched to std::shared_ptr in GTSAM?)
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- [ ] inner namespaces ==> inner packages?
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- [ ] Wrap fixed-size Matrices/Vectors?
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### Completed/Cancelled:
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- [x] Fix Python tests: don't use " import <package> * ": Bad style!!! (18-03-17 19:50)
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- [x] Fix Python tests: don't use " import <package> \* ": Bad style!!! (18-03-17 19:50)
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- [x] Unit tests for cython wrappers @done (18-03-17 18:45) -- simply compare generated files
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- [x] Wrap unstable @done (18-03-17 15:30)
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- [x] Unify cython/gtsam.h and the original gtsam.h @done (18-03-17 15:30)
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- [x] Unify cython/GTSAM.h and the original GTSAM.h @done (18-03-17 15:30)
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- [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.
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- [x] 06-03-17: manage to remove the requirements for default and copy constructors
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- [ ] 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>.
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- [ ] 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.
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- [ ] 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.
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- [x] Convert input numpy Matrix/Vector to float dtype and storage order 'F' automatically, cannot crash! @done (15-03-17 13:00)
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- [x] Remove requirements.txt - Frank: don't bother with only 2 packages and a special case for eigency! @done (08-03-17 10:30)
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- [x] CMake install script @done (25-11-16 02:30)
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@ -119,7 +124,7 @@ Please refer to the template project and the corresponding tutorial available [h
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- [x] Casting from parent and grandparents @done (16-11-16 17:00)
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- [x] Allow overloading constructors. The current solution is annoying!!! @done (16-11-16 17:00)
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- [x] Support "print obj" @done (16-11-16 17:00)
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- [x] methods for FastVector: at, [], ... @done (16-11-16 17:00)
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- [x] methods for FastVector: at, [], ... @done (16-11-16 17:00)
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- [x] Cython: Key and size_t: traits<size_t> doesn't exist @done (16-09-12 18:34)
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- [x] KeyVector, KeyList, KeySet... @done (16-09-13 17:19)
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- [x] [Nice to have] parse typedef @done (16-09-13 17:19)
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