The HyperSpy-bundle

What is the HyperSpy-bundle?

The hyperspy-bundle is a program, which installs a python distribution including hyperspy and other relevant scientific software and libraries for the analysis of multidimensional datasets. It aims at making the installation of a Python distribution very easy and integrating with existing established practices in the scientific research community. If you are brand new to python, this is the easiest way to install HyperSpy.

Table of Contents

Contents:

• Download
• Install
  • Windows
  • MacOS
  • Linux
• Usage
  • Managing libraries and conda environments
  • Context Menu Shortcuts
  • Start Menu (Windows only)
• Verify Installation
  • Jupyter QtConsole
  • Jupyter Lab / Notebook
• Development
  • How is the HyperSpy-bundle made
  • Release
  • Changelog
  • Documentation

Variants of the HyperSpy-bundle

It is compatible with Windows, MacOS (Intel and Apple Silicon), or Linux and comes with variants, which are optimised for AMD (using openblas) or Intel (using MKL) processors. The portable version is supported on windows only.

Standard Version

The standard version is very similar to the Anaconda / Miniforge distribution and it uses the conda / mamba package manager. It is built using the constructor tool, which is used to build the Anaconda / Miniforge distribution installer.

Difference with Anaconda/Miniconda

• Includes the libraries and software listed below.

• The packages are downloaded from the conda-forge channel only, to avoid incompatibilities between the anaconda defaults and conda-forge channels.

• Includes the mamba package manager, as faster alternative to conda.

• A configuration file .condarc is added in the root folder of the installation to save the channel’s settings and pin the blas implementation.

• Adds context menu entries (right-click shortcut) to start the Jupyter Notebook, Jupyter Lab or Juypter QtConsole. See start_jupyter_cm for details.

• Removes context menu entries when uninstalling on Windows only. For Linux and MaxOSX, no uninstall is provided and the context menu entries need to be removed manually using start_jupyter_cm --remove from the conda environment before deleting the distribution.

Portable Version

The portable version of the HyperSpy Bundle does not interact with other Python installations, and it can be safely installed alongside other Python distributions. As a portable distribution, no shortcut is installed and it can be installed on an external harddrive or it can be moved to any other folder.

It is based on the WinPython distribution.

Difference with WinPython

It includes the additional libraries listed below - except ovito and conda-related libraries.

Included Software and Libraries

The HyperSpy-bundle distribution includes the following software and libraries:

• abtem

• ase

• atomap >=0.4.0

• conda >=23.11

• dask >=2023.6.0

• dask-labextension

• exspy

• hdf5plugin

• holospy

• hyperspy >=2.0

• hyperspyui >=2.0

• ipympl

• jupyterlab

• lumispy >=0.2.2

• mamba >=1.5.6

• mamba_gator

• matplotlib-scalebar

• nb_conda_kernels

• nglview

• notebook

• particlespy

• pillow

• py4dstem

• pymatgen

• pystackreg

• python 3.11*

• python-graphviz

• python-rapidjson

• pyxem >=0.17

• openpyxl

• qtconsole >=5.4.3

• scanning_drift_corr

• spyder >=5.4.3

• start_jupyter_cm

• xlrd