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.
The simplest way to install giotto-tda is using
pip install -U giotto-tda
If necessary, this will also automatically install all the above dependencies. Note: we recommend
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
both the stable and nightly versions, giotto-tda and giotto-tda-nightly should not be installed in
the same environment.
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.
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
apt-get is available in your system.
On macOS, you may consider using
brew (https://brew.sh/) to install the dependencies as follows:
brew install gcc cmake boost
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:
open the VS Installer GUI;
under the “Installed” tab, click on “Modify” in the relevant VS version;
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.
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:
Directly from source,
Use an already installed boost version that fulfills giotto-tda requirements.
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\.
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>").
If you need to understand where the compiler tries to look for
you can install
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
make sure to clear CMake cache entries:
rm -rf build/
You can obtain the latest state of the source code with the command:
git clone https://github.com/giotto-ai/giotto-tda.git
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
setuptools to recent versions before installing in this way.
After installation, you can launch the test suite from outside the source directory: