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author | MathieuCarriere <mathieu.carriere3@gmail.com> | 2022-02-14 18:57:53 +0100 |
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committer | MathieuCarriere <mathieu.carriere3@gmail.com> | 2022-02-14 18:57:53 +0100 |
commit | fe3fb13a1a824ef0c915d626344d868eef6ecdcd (patch) | |
tree | d6caaf94666427f33c28bcfe39886ae1afc926ea /src/python/doc/installation.rst | |
parent | 041dfcf7cc72d3af78a20cfbd86ae629809ca13a (diff) | |
parent | 5e9f99b8b8ad7bf97a070b3578605a48fb484297 (diff) |
Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into diff
Diffstat (limited to 'src/python/doc/installation.rst')
-rw-r--r-- | src/python/doc/installation.rst | 97 |
1 files changed, 50 insertions, 47 deletions
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index bf0ee67a..dd476054 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` 1.66.0, `CMake <https://www.cmake.org/>`_ :math:`\geq` 3.5 to generate makefiles, -`NumPy <http://numpy.org>`_ :math:`\geq` 1.15.0, `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 @@ -142,54 +136,63 @@ 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_reader;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]: 1.5 + 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_reader;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 ============= @@ -345,8 +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 ------- |