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Diffstat (limited to 'src/python/doc/installation.rst')
| -rw-r--r-- | src/python/doc/installation.rst | 64 |
1 files changed, 57 insertions, 7 deletions
diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 77d9e8b3..40f3f44b 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -8,7 +8,7 @@ Installation Conda ***** The easiest way to install the Python version of GUDHI is using -`conda <https://gudhi.inria.fr/licensing/>`_. +`conda <https://gudhi.inria.fr/conda/>`_. Compiling ********* @@ -40,6 +40,20 @@ To build the GUDHI Python module, run the following commands in a terminal: cd python make +.. note:: + + :code:`make python` (or :code:`make` in python directory) is only a + `CMake custom targets <https://cmake.org/cmake/help/latest/command/add_custom_target.html>`_ + to shortcut :code:`python setup.py build_ext --inplace` command. + No specific other options (:code:`-j8` for parallel, or even :code:`make clean`, ...) are + available. + But one can use :code:`python setup.py ...` specific options in the python directory: + +.. code-block:: bash + + python setup.py clean --all # Clean former compilation + python setup.py build_ext -j 8 --inplace # Build in parallel + GUDHI Python module installation ================================ @@ -59,19 +73,40 @@ Or install it definitely in your Python packages folder: # May require sudo or administrator privileges make 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 Test suites =========== -To test your build, `py.test <http://doc.pytest.org>`_ is optional. Run the -following command in a terminal: +To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the +following `Ctest <https://cmake.org/cmake/help/latest/manual/ctest.1.html>`_ +(CMake test driver program) command in a terminal: .. code-block:: bash cd /path-to-gudhi/build/python # For windows, you have to set PYTHONPATH environment variable export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/python' - make test + ctest + +.. note:: + + One can use :code:`ctest` specific options in the python directory: + +.. code-block:: bash + + # Launch tests in parallel on 8 cores and set failing tests in verbose mode + ctest -j 8 --output-on-failure Debugging issues ================ @@ -215,12 +250,27 @@ The following examples require the `Matplotlib <http://matplotlib.org>`_: * :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>` +Python Optimal Transport +======================== + +The :doc:`Wasserstein distance </wasserstein_distance_user>` +module requires `POT <https://pot.readthedocs.io/>`_, a library that provides +several solvers for optimization problems related to Optimal Transport. + +Scikit-learn +============ + +The :doc:`persistence representations </representations>` module require +`scikit-learn <https://scikit-learn.org/>`_, a Python-based ecosystem of +open-source software for machine learning. + SciPy ===== -The :doc:`persistence graphical tools </persistence_graphical_tools_user>` -module requires `SciPy <http://scipy.org>`_, a Python-based ecosystem of -open-source software for mathematics, science, and engineering. +The :doc:`persistence graphical tools </persistence_graphical_tools_user>` and +:doc:`Wasserstein distance </wasserstein_distance_user>` modules require `SciPy +<http://scipy.org>`_, a Python-based ecosystem of open-source software for +mathematics, science, and engineering. Threading Building Blocks ========================= |