From 96f14e32f9b2230a6204f300488b0aad04a676a1 Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 3 Jun 2020 09:39:28 +0200 Subject: Mention Joblib in installation doc --- src/python/doc/installation.rst | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'src/python/doc/installation.rst') diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index de09c5b3..a66e910e 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -260,6 +260,13 @@ a flag `enable_autodiff=True` is used). In order to reduce code duplication, we use `EagerPy `_ which wraps arrays from PyTorch, TensorFlow and JAX in a common interface. +Joblib +------ + +`Joblib `_ is used both as a dependency of `Scikit-learn`_, +and directly for parallelism in some modules (:class:`~gudhi.point_cloud.knn.KNearestNeighbors`, +:func:`~gudhi.representations.metrics.pairwise_persistence_diagram_distances`). + Hnswlib ------- -- cgit v1.2.3 From b50a41f53af6937c6f030d08f2b969b9024e17ac Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Fri, 12 Jun 2020 23:10:37 +0200 Subject: Mention pip package --- src/python/doc/installation.rst | 37 ++++++++++++++++++++++++++++++++----- 1 file changed, 32 insertions(+), 5 deletions(-) (limited to 'src/python/doc/installation.rst') diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index a66e910e..525ca84e 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -5,20 +5,47 @@ Installation ############ -Conda -***** -The easiest way to install the Python version of GUDHI is using -`conda `_. +Packages +******** +The easiest way to install the Python version of GUDHI is using pre-built packages. +We recommend `conda `_ + +.. code-block:: bash + + conda install -c conda-forge gudhi + +Gudhi is also available on `PyPI `_ + +.. code-block:: bash + + pip install gudhi + +Third party packages are also available, for instance on Debian or Ubuntu + +.. code-block:: bash + + apt install python3-gudhi + +In all cases, you may still want to install some of the optional `run time dependencies`_. 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 `_, +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/`. +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 `_ :math:`\geq` 1.56.0, `CMake `_ :math:`\geq` 3.1 to generate makefiles, `NumPy `_, `Cython `_ and `pybind11 `_ to compile the GUDHI Python module. It is a multi-platform library and compiles on Linux, Mac OSX and Visual -Studio 2017. +Studio 2017 or later. On `Windows `_ , only Python :math:`\geq` 3.5 are available because of the required Visual Studio version. -- cgit v1.2.3 From 39aff7e55beb318d1685dac410466414e69190ae Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 3 Aug 2020 16:22:59 +0200 Subject: doc review: Add LaTeX in optional runtime dependencies --- src/python/doc/installation.rst | 29 ++++++++++++++++++++++ .../doc/persistence_graphical_tools_user.rst | 21 ++-------------- 2 files changed, 31 insertions(+), 19 deletions(-) (limited to 'src/python/doc/installation.rst') diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 525ca84e..78e1af73 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -323,6 +323,35 @@ The following examples require the `Matplotlib `_: * :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>` +LaTeX +~~~~~ + +If a sufficiently complete LaTeX toolchain is available (including dvipng and ghostscript), the LaTeX option of +matplotlib is enabled for prettier captions (cf. +`matplotlib text rendering with LaTeX `_). +It also requires `type1cm` LaTeX package (not detected by matplotlib). + +If you are facing issues with LaTeX rendering, like this one: + +.. code-block:: none + + Traceback (most recent call last): + File "/usr/lib/python3/dist-packages/matplotlib/texmanager.py", line 302, in _run_checked_subprocess + report = subprocess.check_output(command, + ... + ! LaTeX Error: File `type1cm.sty' not found. + ... + +This is because the LaTeX package is not installed on your system. On Ubuntu systems you can install texlive-full +(for all LaTeX packages), or more specific packages like texlive-latex-extra, cm-super. + +You can still deactivate LaTeX rendering by saying: + +.. code-block:: python + + import gudhi + gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False + PyKeOps ------- diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst index 9954058d..d95b9d2b 100644 --- a/src/python/doc/persistence_graphical_tools_user.rst +++ b/src/python/doc/persistence_graphical_tools_user.rst @@ -94,25 +94,8 @@ If you want more information on a specific dimension, for instance: LaTeX support ------------- -By default, persistence graphical tools are using LaTeX support for matplotlib if available (cf. -`matplotlib text rendering with LaTeX `_). -It also requires `type1cm` LaTeX package (not detected by matplotlib). - -If you are facing issues with LaTeX rendering, like this one: - -.. code-block:: none - - Traceback (most recent call last): - File "/usr/lib/python3/dist-packages/matplotlib/texmanager.py", line 302, in _run_checked_subprocess - report = subprocess.check_output(command, - ... - ! LaTeX Error: File `type1cm.sty' not found. - ... - -This is because the LaTeX package is not installed on your system. On Ubuntu systems you can install texlive-full -(for all LaTeX packages), or more specific packages like texlive-latex-extra, cm-super. - -You can still deactivate LaTeX rendering by saying: +If you are facing issues with `LaTeX `_ rendering, you can still deactivate LaTeX rendering by +saying: .. code-block:: python -- cgit v1.2.3