Installing transmorph
=====================

**transmorph** can be installed either from source of from the python repository PyPi. PyPi version is commonly more stable, but may not contain latest features, while you can find the development version on GitHub.

Using a python environment is highly recommended (for instance `pipenv`_) in order to easily handle dependencies and versions.

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Install from PyPi (recommended, latest stable version)
------------------------------------------------------

.. code-block:: console

    pip install transmorph

Install from source (dev version)
---------------------------------

.. code-block:: console

    git clone https://github.com/Risitop/transmorph
    pip install ./transmorph

Troubleshooting
---------------

Extra steps may be necessary to get **transmorph** properly working, especially on Windows systems. We would be grateful if you could to report any other installation error as a GitHub issue so that we can work on a fix. 

+ **numpy** package is not installed

.. code-block:: console

    pip install numpy

+ Microsoft Visual C++ >=14.0 is required

Fix: Grab the C++ SDK from https://visualstudio.microsoft.com/visual-cpp-build-tools/, ensure C++ development tools are ticked (C++ development tools are automatically installed on Linux distributions).

+ PyMDE install error, no graph.c file

.. code-block:: console

    pip install cython

What's next
-----------

Once the installation is completed, you can move on to :ref:`tutorials_section`.

.. _pipenv: https://pypi.org/project/pipenv/
.. _anndata: https://anndata.readthedocs.io/en/latest/
.. _igraph: https://igraph.org/
.. _leidenalg: https://leidenalg.readthedocs.io/en/stable/intro.html
.. _numba: https://numba.pydata.org/
.. _numpy: https://numpy.org/
.. _osqp: https://github.com/osqp/osqp-python
.. _POT: https://github.com/PythonOT/POT
.. _pymde: https://pymde.org/
.. _pynndescent: https://pynndescent.readthedocs.io/en/latest/
.. _scipy: https://www.scipy.org/
.. _scikit-learn: https://scikit-learn.org/stable/
.. _stabilized-ica: https://stabilized-ica.readthedocs.io/en/latest/
.. _umap-learn: https://umap-learn.readthedocs.io/en/latest/