Installation

Dependencies

The latest stable version of giotto-tda requires:

  • Python (>= 3.6)

  • NumPy (>= 1.17.0)

  • SciPy (>= 0.17.0)

  • joblib (>= 0.13)

  • scikit-learn (>= 0.22.0)

  • pyflagser (>= 0.4.0)

  • python-igraph (>= 0.7.1.post6)

  • plotly (>= 4.4.1)

  • ipywidgets (>= 7.5.1)

To run the examples, jupyter is required.

User installation

The simplest way to install giotto-tda is using pip

pip install -U giotto-tda

If necessary, this will also automatically install all the above dependencies. Note: we recommend upgrading pip to a recent version as the above may fail on very old versions.

Pre-release, experimental builds containing recently added features, and/or bug fixes can be installed by running

pip install -U giotto-tda-nightly

The main difference between giotto-tda-nightly and the developer installation (see the section on contributing, below) is that the former is shipped with pre-compiled wheels (similarly to the stable release) and hence does not require any C++ dependencies. As the main library module is called gtda in both the stable and nightly versions, giotto-tda and giotto-tda-nightly should not be installed in the same environment.

Developer installation

Installing both the PyPI release and source of giotto-tda in the same environment is not recommended since it is known to cause conflicts with the C++ bindings.

The developer installation requires three important C++ dependencies:

  • A C++14 compatible compiler

  • CMake >= 3.9

  • Boost >= 1.56

Please refer to your system’s instructions and to the CMake and Boost websites for definitive guidance on how to install these dependencies. The instructions below are unofficial, please follow them at your own risk.

Linux

Most Linux systems should come with a suitable compiler pre-installed. For the other two dependencies, you may consider using your distribution’s package manager, e.g. by running

sudo apt-get install cmake libboost-dev

if apt-get is available in your system.

macOS

On macOS, you may consider using brew (https://brew.sh/) to install the dependencies as follows:

brew install gcc cmake boost

Windows

On Windows, you will likely need to have Visual Studio installed. At present, it appears to be important to have a recent version of the VS C++ compiler. One way to check whether this is the case is as follows:

  1. open the VS Installer GUI;

  2. under the “Installed” tab, click on “Modify” in the relevant VS version;

  3. in the newly opened window, select “Individual components” and ensure that v14.24 or above of the MSVC “C++ x64/x86 build tools” is selected. The CMake and Boost dependencies are best installed using the latest binary executables from the websites of the respective projects.

Boost

Some users are experiencing some issue when installation boost on Windows. To help them resolve this issue, we customized a little bit the detection of boost library. To install boost on windows, we (maintainers of giotto-tda) recommend 3 options:

  • Pre-built binaries,

  • Directly from source,

  • Use an already installed boost version that fulfills giotto-tda requirements.

Pre-built binaries

Boost propose for windows pre-built binaries to ease the installation of boost in your system. In the website, you’ll have access to all versions of boost. At the time of writing this documentation, the most recent version of boost is 1.72.0. If you go into the folder, you’ll find different executables - choose the version corresponding to your system (32, 64 bits). In our case, we downloaded boost_1_72_0-msvc-14.2-64.exe. Follow the installation instructions, and when prompted to specify the folder to install boost, go for C:\local\.

Source code

Boost proposes to download directly the source code of boost. You can choose from different sources (compressed in .7z or .zip). Download one and uncompress it in C:\local\, so you should have something like C:\local\boost_x_y_z\<boost_files>.

Already installed boost version

If by some obscure reason, you have boost installed in your system but the installation procedure cannot find it (can happen, no control on cmake …). You can help the installation script by adding the path to your installation in the following place gtda\cmake\HelperBoost.cmake. In HelperBoost.cmake file, line 7, you can add your path between the quotation marks, e.g.:

list(APPEND BOOST_ROOT "C:\\<path_to_your_boost_installation>").

Troubleshooting

If you need to understand where the compiler tries to look for boost headers, you can install giotto-tda with:

pip install -e . -v

Then you can look at the output for lines starting with:

Boost_INCLUDE_DIR: <path>
Boost_INCLUDE_DIRS: <path>

Also, if you have installed different versions of boost in the process of trying to instal giotto-tda, make sure to clear CMake cache entries:

rm -rf build/

Source code

You can obtain the latest state of the source code with the command:

git clone https://github.com/giotto-ai/giotto-tda.git

To install:

cd giotto-tda
python -m pip install -e ".[dev]"

This way, you can pull the library’s latest changes and make them immediately available on your machine. Note: we recommend upgrading pip and setuptools to recent versions before installing in this way.

Testing

After installation, you can launch the test suite from outside the source directory:

pytest gtda