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Installation
============
RosettaSciIO can be installed with `pip <https://pip.pypa.io/>`_,
`conda <https://docs.conda.io/>`_, the
:ref:`hyperspy:hyperspy-bundle`, or from source, and supports Python >= 3.8.
All alternatives are available on Windows, macOS and Linux.
For using HyperSpy, it is not necessary to install RosettaSciIO separetely, as it would
be installed automatically when installing HyperSpy.
.. _install-with-pip:
With pip
--------
RosettaSciIO is availabe from the Python Package Index (PyPI), and can therefore be
installed with `pip <https://pip.pypa.io/en/stable>`__.
To install with all optional dependencies::
pip install rosettasciio[all]
To install without optional dependencies::
pip install rosettasciio
To update RosettaSciIO to the latest release::
pip install --upgrade rosettasciio
To install a specific version of RosettaSciIO (say version 0.1)::
pip install rosettasciio==0.1
.. _optional-dependencies:
Optional dependencies
*********************
Some functionality is optional and requires extra dependencies which must be installed
manually or by using `extra <https://peps.python.org/pep-0508/#extras>`_:
Install all optional dependencies::
pip install rosettasciio[all]
The list of *extras*:
+---------------------+-------------------------+------------------------------------------------------------------------------+
| Extra | Dependencies | Usage |
+=====================+=========================+==============================================================================+
| ``blockfile`` | ``scikit-image`` | Data normalisation |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``eds-steam`` | ``sparse`` | Loading EDS data stream (JEOL ``pts``, Velox ``emd``) |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``hdf5`` | ``h5py`` | Reading hdf5-based file formats (``hspy``, ``de5``, ``emd``, ``usid``, etc.) |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``image`` | ``imageio`` | Reading images, other than tiff format. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``mrcz`` | ``blosc``, ``mrcz`` | Readding ``mrc`` and ``mrcz`` format. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``scalebar_export`` | ``matplotlib-scalebar`` | Exporting image with scalebar. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``speed`` | ``numba`` | Speed up loading some data, for example EDS data. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``tiff`` | ``tifffile`` | Read ``tiff`` files. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``usid`` | ``pyUSID`` | Read ``usid`` files. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
| ``zspy`` | ``zarr`` | Read ``zspy`` files. |
+---------------------+-------------------------+------------------------------------------------------------------------------+
And for development, the following *extras* are available (see ``pyproject.toml`` for more information):
- tests
- doc
- dev
.. _install-with-conda:
With conda
----------
To install with conda, we recommend you install it in a
:doc:`conda environment <conda:user-guide/tasks/manage-environments>` with the
`Miniforge distribution <https://github.com/conda-forge/miniforge>`_.
To create an environment and activate it::
conda create --name rsciio python=3.11
conda activate rsciio
To install rosettasciio with all dependencies::
conda install rosettasciio
To install rosettasciio without any dependencies::
conda install rosettasciio-base
To update RosettaSciIO to the latest release::
conda update rosettasciio
To install a specific version of RosettaSciIO (say version 0.1)::
conda install rosettasciio=0.1
.. note::
Conda used to be slow to install dependencies in large enviroment and mamba could be
used as a fast drop-in replacement. However, since conda release 23.10, mamba and conda
use the same "solver" and therefore takes similar time to "solve environment".
See the `conda blog <https://conda.org/blog/2023-11-06-conda-23-10-0-release>`_ for more information.
.. _install-with-hyperspy-bundle:
With the HyperSpy Bundle
------------------------
The HyperSpy Bundle comes with RosettaSciIO and all its extras pre-installed.
See :ref:`hyperspy:hyperspy-bundle` for instructions.
.. _install-from-source:
From source
-----------
To install RosettaSciIO from source, clone the repository from `GitHub
<https://github.com/hyperspy/rosettasciio>`__, and install with ``pip``::
git clone https://github.com/hyperspy/rosettasciio.git
cd rosettasciio
pip install --editable .
.. note::
If `setuptools_scm <https://setuptools-scm.readthedocs.io>`_ is
installed, the version will be determined from the git repository
at runtime, otherwise, the version will be the one at build time.
To install a development version on CI, it is advised to use
`pip with vcs support <https://pip.pypa.io/en/stable/topics/vcs-support/>`_
in order to get the correct development version, e.g. ``0.3.dev14+g706deac``::
pip install git+https://github.com/hyperspy/rosettasciio.git
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