Modify minimal requirements for python typing. Fix no cgal compilation

6 files changed, 60 insertions, 50 deletions

diff --git a/.github/next_release.md b/.github/next_release.md
index 170c7494..0d4673bd 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -9,6 +9,9 @@ Below is a list of changes made since GUDHI 3.4.0:
 - [Coxeter triangulation](https://gudhi.inria.fr/doc/latest/group__coxeter__triangulation.html)
      - constructs a piecewise-linear approximation of an m-dimensional smooth manifold embedded in R^d using an ambient triangulation. 
 
+- [Python installation](link)
+     - Python >= 3.5 and cython >= 0.27 are now required for Python typing purpose.
+
 - [Module](link)
      - ...
 
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 023061f1..deaea588 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -6,6 +6,10 @@ find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framewo
 if(NOT Boost_VERSION)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
 endif(NOT Boost_VERSION)
+INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
+
 
 find_package(GMP)
 if(GMP_FOUND)
@@ -89,9 +93,6 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 # problem on Mac with boost_system and boost_thread
 add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
-message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
-message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
-
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
 find_package( PythonInterp )
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 4a017251..12534b86 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -175,6 +175,7 @@ if(PYTHONINTERP_FOUND)
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'euclidean_strong_witness_complex', ")
     endif ()
 
+    add_gudhi_debug_info("Boost version ${Boost_VERSION}")
     if(CGAL_FOUND)
       # Add CGAL compilation args
       if(CGAL_HEADER_ONLY)
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst
index 35c344e3..6ed53960 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.X.tar.gz`, then run `tar xf gudhi.3.X.X.tar.gz`, which
+created a directory `gudhi.3.X.X`, 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,
 `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
@@ -143,53 +137,62 @@ If :code:`import gudhi` succeeds, please have a look to debug information:
 .. code-block:: python
 
     import gudhi
-    print(gudhi.__debug_info__)
+print(gudhi.__debug_info__)
+print("+ Installed modules are: " + gudhi.__available_modules)
+print("+ Missing modules are: " + gudhi.__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
+    print("+ Installed modules are: " + gudhi.__available_modules)
+    + 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 are requiring 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
-    TBB version 9107 found and used
+    MPFR_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpfr.so
+    + 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
 =============
diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml
index a9fb4985..55b64466 100644
--- a/src/python/pyproject.toml
+++ b/src/python/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.15.0", "cython", "pybind11"]
+requires = ["setuptools>=24.2.0", "wheel", "numpy>=1.15.0", "cython>=0.27", "pybind11"]
 build-backend = "setuptools.build_meta"
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 23746998..2c67c2c5 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -5,6 +5,7 @@
    Copyright (C) 2019  Inria
 
    Modification(s):
+     - 2021/12 Vincent Rouvreau: Python 3.5 as minimal version
      - YYYY/MM Author: Description of the modification
 """
 
@@ -43,7 +44,7 @@ for module in cython_modules:
         include_dirs=include_dirs,
         runtime_library_dirs=runtime_library_dirs,))
 
-ext_modules = cythonize(ext_modules, compiler_directives={'language_level': str(sys.version_info[0])})
+ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'})
 
 for module in pybind11_modules:
     my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
@@ -86,6 +87,7 @@ setup(
     long_description_content_type='text/x-rst',
     long_description=long_description,
     ext_modules = ext_modules,
+    python_requires='>=3.5.0',
     install_requires = ['numpy >= 1.15.0',],
     package_data={"": ["*.dll"], },
 )