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Diffstat (limited to 'src/python/doc/installation.rst')
| -rw-r--r-- | src/python/doc/installation.rst | 140 |
1 files changed, 73 insertions, 67 deletions
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 66efe45a..7200b2f0 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -33,25 +33,19 @@ Compiling These instructions are for people who want to compile gudhi from source, they are unnecessary if you installed a binary package of Gudhi as above. They assume that you have downloaded a `release <https://github.com/GUDHI/gudhi-devel/releases>`_, -with a name like `gudhi.3.2.0.tar.gz`, then run `tar xf gudhi.3.2.0.tar.gz`, which -created a directory `gudhi.3.2.0`, hereinafter referred to as `/path-to-gudhi/`. +with a name like `gudhi.3.X.Y.tar.gz`, then run `tar xf gudhi.3.X.Y.tar.gz`, which +created a directory `gudhi.3.X.Y`, hereinafter referred to as `/path-to-gudhi/`. If you are instead using a git checkout, beware that the paths are a bit different, and in particular the `python/` subdirectory is actually `src/python/` there. -The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.56.0, +The library uses c++17 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.66.0, `CMake <https://www.cmake.org/>`_ :math:`\geq` 3.5 to generate makefiles, -`NumPy <http://numpy.org>`_, `Cython <https://www.cython.org/>`_ and -`pybind11 <https://github.com/pybind/pybind11>`_ to compile -the GUDHI Python module. -It is a multi-platform library and compiles on Linux, Mac OSX and Visual -Studio 2017 or later. +Python :math:`\geq` 3.5, `NumPy <http://numpy.org>`_ :math:`\geq` 1.15.0, `Cython <https://www.cython.org/>`_ +:math:`\geq` 0.27 and `pybind11 <https://github.com/pybind/pybind11>`_ to compile the GUDHI Python module. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2017 or later. -On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python -:math:`\geq` 3.5 are available because of the required Visual Studio version. - -On other systems, if you have several Python/python installed, the version 2.X -will be used by default, but you can force it by adding +If you have several Python/python installed, the version 2.X may be used by default, but you can force it by adding :code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command. GUDHI Python module compilation @@ -99,20 +93,14 @@ Or install it definitely in your Python packages folder: .. code-block:: bash cd /path-to-gudhi/build/python - # May require sudo or administrator privileges - make install + python setup.py install # add --user to the command if you do not have the permission + # Or 'pip install .' .. note:: - :code:`make install` is only a - `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ - to shortcut :code:`python setup.py install` command. It does not take into account :code:`CMAKE_INSTALL_PREFIX`. - But one can use :code:`python setup.py install ...` specific options in the python directory: - -.. code-block:: bash - - python setup.py install --prefix /home/gudhi # Install in /home/gudhi directory + But one can use + `alternate location installation <https://docs.python.org/3/install/#alternate-installation>`_. Test suites =========== @@ -148,60 +136,71 @@ If :code:`import gudhi` succeeds, please have a look to debug information: .. code-block:: python - import gudhi - print(gudhi.__debug_info__) + import gudhi as gd + print(gd.__debug_info__) + print("+ Installed modules are: " + gd.__available_modules) + print("+ Missing modules are: " + gd.__missing_modules) You shall have something like: .. code-block:: none - Python version 2.7.15 - Cython version 0.26.1 - Numpy version 1.14.1 - Eigen3 version 3.1.1 - Installed modules are: off_reader;simplex_tree;rips_complex; - cubical_complex;periodic_cubical_complex;reader_utils;witness_complex; - strong_witness_complex;alpha_complex; - Missing modules are: bottleneck_distance;nerve_gic;subsampling; - tangential_complex;persistence_graphical_tools; - euclidean_witness_complex;euclidean_strong_witness_complex; - CGAL version 4.7.1000 - GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so - GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so - TBB version 9107 found and used + Pybind11 version 2.8.1 + Python version 3.7.12 + Cython version 0.29.25 + Numpy version 1.21.4 + Boost version 1.77.0 + + Installed modules are: off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex; + + Missing modules are: bottleneck;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex; + euclidean_strong_witness_complex; -Here, you can see that bottleneck_distance, nerve_gic, subsampling and -tangential_complex are missing because of the CGAL version. -persistence_graphical_tools is not available as matplotlib is not -available. +Here, you can see that the modules that need CGAL are missing, because CGAL is not installed. +:code:`persistence_graphical_tools` is installed, but +`its functions <https://gudhi.inria.fr/python/latest/persistence_graphical_tools_ref.html>`_ will produce an error as +matplotlib is not available. Unitary tests cannot be run as pytest is missing. A complete configuration would be : .. code-block:: none - Python version 3.6.5 - Cython version 0.28.2 - Pytest version 3.3.2 - Matplotlib version 2.2.2 - Numpy version 1.14.5 - Eigen3 version 3.3.4 - Installed modules are: off_reader;simplex_tree;rips_complex; - cubical_complex;periodic_cubical_complex;persistence_graphical_tools; - reader_utils;witness_complex;strong_witness_complex; - persistence_graphical_tools;bottleneck_distance;nerve_gic;subsampling; - tangential_complex;alpha_complex;euclidean_witness_complex; - euclidean_strong_witness_complex; - CGAL header only version 4.11.0 + Pybind11 version 2.8.1 + Python version 3.9.7 + Cython version 0.29.24 + Pytest version 6.2.5 + Matplotlib version 3.5.0 + Numpy version 1.21.4 + Scipy version 1.7.3 + Scikit-learn version 1.0.1 + POT version 0.8.0 + HNSWlib found + PyKeOps version [pyKeOps]: 2.1 + EagerPy version 0.30.0 + TensorFlow version 2.7.0 + Sphinx version 4.3.0 + Sphinx-paramlinks version 0.5.2 + python_docs_theme found + Eigen3 version 3.4.0 + Boost version 1.74.0 + CGAL version 5.3 GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so + MPFR_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpfr.so TBB version 9107 found and used + + Installed modules are: bottleneck;off_utils;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;nerve_gic;subsampling; + tangential_complex;alpha_complex;euclidean_witness_complex;euclidean_strong_witness_complex; + + Missing modules are: + Documentation ============= -To build the documentation, `sphinx-doc <http://www.sphinx-doc.org>`_ and -`sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io>`_ are +To build the documentation, `sphinx-doc <http://www.sphinx-doc.org>`_, +`sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io>`_, +`sphinxcontrib-paramlinks <https://github.com/sqlalchemyorg/sphinx-paramlinks>`_ and +`python-docs-theme <https://github.com/python/python-docs-theme>`_ are required. As the documentation is auto-tested, `CGAL`_, `Eigen`_, `Matplotlib`_, `NumPy`_, `POT`_, `Scikit-learn`_ and `SciPy`_ are also mandatory to build the documentation. @@ -349,8 +348,8 @@ You can still deactivate LaTeX rendering by saying: .. code-block:: python - import gudhi - gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False + import gudhi as gd + gd.persistence_graphical_tools._gudhi_matplotlib_use_tex=False PyKeOps ------- @@ -363,7 +362,7 @@ Python Optimal Transport ------------------------ The :doc:`Wasserstein distance </wasserstein_distance_user>` -module requires `POT <https://pot.readthedocs.io/>`_, a library that provides +module requires `POT <https://pythonot.github.io/>`_, a library that provides several solvers for optimization problems related to Optimal Transport. PyTorch @@ -392,18 +391,25 @@ The :doc:`persistence graphical tools </persistence_graphical_tools_user>` and mathematics, science, and engineering. :class:`~gudhi.point_cloud.knn.KNearestNeighbors` can use the Python package -`SciPy <http://scipy.org>`_ as a backend if explicitly requested. +`SciPy <http://scipy.org>`_ :math:`\geq` 1.6.0 as a backend if explicitly requested. TensorFlow ---------- -`TensorFlow <https://www.tensorflow.org>`_ is currently only used in some automatic differentiation tests. +:class:`~gudhi.tensorflow.perslay.Perslay` from the :doc:`persistence representations </representations>` module +requires `TensorFlow <https://www.tensorflow.org/>`_. +The :doc:`cubical complex </cubical_complex_tflow_itf_ref>`, :doc:`simplex tree </ls_simplex_tree_tflow_itf_ref>` +and :doc:`Rips complex </rips_complex_tflow_itf_ref>` modules require `TensorFlow`_ +for incorporating them in neural nets. + +`TensorFlow`_ is also used in some automatic differentiation tests. Bug reports and contributions ***************************** -Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: - - Contact: gudhi-users@lists.gforge.inria.fr +Please help us improving the quality of the GUDHI library. +You may `report bugs <https://github.com/GUDHI/gudhi-devel/issues>`_ or +`contact us <https://gudhi.inria.fr/contact/>`_ for any suggestions. -GUDHI is open to external contributions. If you want to join our development team, please contact us. +GUDHI is open to external contributions. If you want to join our development team, please take some time to read our +`contributing guide <https://github.com/GUDHI/gudhi-devel/blob/master/.github/CONTRIBUTING.md>`_. |