Installation

RosettaSciIO can be installed with pip, conda, the 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.

With pip

RosettaSciIO is availabe from the Python Package Index (PyPI), and can therefore be installed with pip. 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

Some functionality is optional and requires extra dependencies which must be installed manually or by using extra:

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

With conda

To install with conda, we recommend you install it in a conda environment with the Miniforge distribution. 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 for more information.

With the HyperSpy Bundle

The HyperSpy Bundle comes with RosettaSciIO and all its extras pre-installed. See HyperSpy Bundle for instructions.

From source

To install RosettaSciIO from source, clone the repository from GitHub, and install with pip:

git clone https://github.com/hyperspy/rosettasciio.git
cd rosettasciio
pip install --editable .

Note

If setuptools_scm 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 in order to get the correct development version, e.g. 0.3.dev14+g706deac:

pip install git+https://github.com/hyperspy/rosettasciio.git