From d6c903603bbc8833aad92c7d8c09cf78e99f689d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Thu, 29 Aug 2019 16:50:12 +0200 Subject: Add conda installation. NumPy became mandatory --- src/cython/doc/installation.rst | 52 +++++++++++++++++------------------------ 1 file changed, 21 insertions(+), 31 deletions(-) diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index e40a2ef9..34156942 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -5,16 +5,22 @@ Installation ############ +Conda +***** +The easiest way to install the Python version of GUDHI is using +`conda `_. + Compiling ********* The library uses c++11 and requires `Boost `_ ≥ 1.56.0, -`CMake `_ ≥ 3.1 to generate makefiles, and -`Cython `_ to compile the GUDHI Python module. +`CMake `_ ≥ 3.1 to generate makefiles, +`NumPy `_ and `Cython `_ to compile +the GUDHI Python module. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. On `Windows `_ , only Python -3.5 and 3.6 are available because of the required Visual Studio version. +≥ 3.5 are available because of the required Visual Studio version. On other systems, if you have several Python/Cython installed, the version 2.X will be used by default, but you can force it by adding @@ -87,11 +93,14 @@ You shall have something like: 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; - persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;alpha_complex; + 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; - Missing modules are: bottleneck_distance;nerve_gic;subsampling;tangential_complex;persistence_graphical_tools; 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 @@ -99,7 +108,7 @@ You shall have something like: 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 numpy and matplotlib are not +persistence_graphical_tools is not available as matplotlib is not available. Unitary tests cannot be run as pytest is missing. @@ -113,9 +122,11 @@ A complete configuration would be : 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; + 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 GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so @@ -194,27 +205,6 @@ formats and interactive environments across platforms. The following examples require the `Matplotlib `_: -.. only:: builder_html - - * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` - * :download:`gudhi_graphical_tools_example.py <../example/gudhi_graphical_tools_example.py>` - * :download:`periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` - * :download:`rips_complex_diagram_persistence_from_off_file_example.py <../example/rips_complex_diagram_persistence_from_off_file_example.py>` - * :download:`rips_persistence_diagram.py <../example/rips_persistence_diagram.py>` - * :download:`rips_complex_diagram_persistence_from_distance_matrix_file_example.py <../example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py>` - * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` - * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` - * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` - -NumPy -===== - -The :doc:`persistence graphical tools ` -module requires `NumPy `_, a fundamental package for -scientific computing with Python. - -The following examples require the `NumPy `_: - .. only:: builder_html * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` -- cgit v1.2.3