The easiest way to install HyperSpy is to use theHyperSpy Bundle, which is available on Windows, MacOSand Linux.
Alternatively, hyperspy can be installed in an existing python distribution,read the conda installation andpip installation sections for instructions.
Install Python 3 using homebrew (brew install python) or by manually installing the package from Install python3 and python3-pip using the package manager of the Linux Distribution. Install conda using the Anaconda or miniconda installers or the miniforge installers (no administrator permission required for any of those). Conda install -c conda-forge fbprophet numpy=1.19.5 hdf5=1.10.5 poetry install poetry install -E prediction If you would like to set up a docker image: Build the docker: docker build. Run it: docker run -it gamestonkterminal:dev; Note: The problem with docker is that it won't output matplotlib figures.Commands that may help you in case of.
Note
To enable the context-menu (right-click) shortcut in a chosen folder, usethe start_jupyter_cm tool.
Note
If you want to be notified about new releases, please Watch (Releases only)the hyperspy repository on GitHub(requires a GitHub account).
Warning
Since version 0.8.4 HyperSpy only supports Python 3. If you need to installHyperSpy in Python 2.7 install HyperSpy 0.8.3.
HyperSpy Bundle¶
The HyperSpy bundle is very similar to the Anaconda distribution, and it includes:
HyperSpy
When it was still Lion DiskMaker, DiskMaker X had the ability to burn DVDs too. Older versions are available here. Download DiskMaker 2.0.2 ( ZIP file, about 3 MB). Step 4: Install macOS High Sierra The second item from the top of the macOS Utilities screen is “Install macOS”. Select this item by clicking on it, then click on Continue. In the installer screen, select “Macintosh HD” (or whatever your boot drive is actually named) as the disk for macOS High Sierra to be installed on. DiskMaker X will erase the volume or the drive you chose, according to the options you chose. Don’t forget to backup your data first! DiskMaker X is donationware. If you like it, you can make a small (or huge 😉 ) donation here. If you hate Paypal, but still want to show your support, please get in touch with me so we can find a. The Easy Way: With DiskMaker X The simplest way to create a boot USB drive is to download DiskMaker X and use it to create your drive. Generally, the latest version supports only the latest version of macOS; if you want to install something older than macOS High Sierra, check the list of older versions and download one that’s compatible with. Diskmaker x for high sierra.
HyperSpyUI
context menu shortcut (right-click) to Jupyter Notebook, Qtconsole or JupyterLab
For instructions and download links go to https://github.com/hyperspy/hyperspy-bundle
Portable distribution (Windows only)¶
A portable version of the HyperSpy bundlebased on the WinPython distribution is also available on Windows.
Installation in an Anaconda/Miniconda distribution¶
HyperSpy is packaged in the conda-forge channeland can be installed easily using the condapackage manager.
To install hyperspy run the following from the Anaconda Prompt on Windows orfrom a Terminal on Linux and Mac.
This will install also install the optional GUI packages hyperspy_gui_ipywidgets
and hyperspy_gui_traitsui
. To install hyperspy without the GUI packages, use:
Note
Install Conda Mac Terminal Linux
Depending on how Anaconda has been installed, it is possible that theconda
command is not avaible from the Terminal, read theAnaconda User Guide for details.
Note
Using -cconda-forge
is only necessary when the conda-forge
channelis not already added to the conda configuration, read theconda-forge documentationfor more details.
Note
Depending on the packages installed in Anaconda, conda
can be slow andin this case mamba
can be used as an alternative of conda
since theformer is significantly faster. Read themamba documentation for instructions.
Further information¶
When installing packages, conda
will verify that all requirements of allpackages installed in an environment are met. This can lead to situations wherea solution for dependencies resolution cannot be resolved or the solution mayinclude installing old or undesired versions of libraries. The requirementsdepend on which libraries are already present in the environment as satisfyingtheir respective dependencies may be problematic. In such a situation, possiblesolutions are:
use Miniconda instead of Anaconda, if you are installing a pythondistribution from scratch: Miniconda only installs very few packages so satisfyingall dependencies is simple.
install hyperspy in a new environment.The following example illustrates how to create a new environment named
hspy_environment
,activate it and install hyperspy in the new environment.Note
A consequence of installing hyperspy in a new environment is that you needto activate this environment using
condaactivateenvironment_name
whereenvironment_name
is the name of the environment, however shortcuts canbe created using different approaches:Install start_jupyter_cmin the hyperspy environment.
Install nb_conda_kernels.
Create IPython kernels for different environment.
To learn more about the Anaconda eco-system:
Choose between Anaconda or Miniconda?
Understanding conda and pip.
Installation using pip¶
HyperSpy is listed in the Python Package Index. Therefore, it can be automatically downloadedand installed pip. You may need toinstall pip for the following commands to run.
To install all hyperspy functionalities, run:
To install only the strictly required dependencies and limited functionalities,use:
See the following list of selectors to select the installation of optionaldependencies required by specific functionalities:
learning
for some machine learning features,gui-jupyter
to use the Jupyter widgetsGUI elements,gui-traitsui
to use the GUI elements based on traitsui,mrcz
to read mrcz file,speed
to speed up some functionalities,usid
to read usid file,tests
to install required libraries to run HyperSpy’s unit tests,build-doc
to install required libraries to build HyperSpy’s documentation,dev
to install all the above,all
to install all the above expect the development requirements(tests
,build-doc
anddev
).
For example: Tuxera ntfs for mac 2019 download mac.
Install Conda On Mac From Terminal
Finally, be aware that HyperSpy depends on a number of libraries that usuallyneed to be compiled and therefore installing HyperSpy may require developmenttools installed in the system. If the above does not work for you remember thatthe easiest way to install HyperSpy isusing the HyperSpy bundle.
Rolling release Linux distributions¶
Due to the requirement of up to date versions for dependencies such as numpy,scipy, etc., binary packages of HyperSpy are not provided for most linuxdistributions and the installation via Anaconda/Minicondaor Pip is recommended.
However, packages of the latest HyperSpy release and the relatedGUI packages are maintained for the rolling release distributionsArch-Linux (in the Arch User Repository) (AUR) andopenSUSE (Community Package)as python-hyperspy
and python-hyperspy-gui-traitsui
/python-hyperspy-gui-ipywidgets
.
A more up-to-date package that contains all updates to be includedin the next minor version release (likely including new features compared tothe stable release) is also available in the AUR as python-hyperspy-git
.
Install development version¶
Clone the hyperspy repository¶
To get the development version from our git repository you need to install git. Then just do:
Warning
When running hyperspy from a development version, it can happen that thedependency requirement changes in which you will need to keep thisthis requirement up to date (check dependency requirement in setup.py
)or run again the installation in development mode using pip
as explainedbelow.
Installation in a Anaconda/Minconda distribution¶
Install the runtime and development dependencies requirements using conda:
The package hyperspy-dev
will install the development dependencies requiredfor testing and building the documentation.
From the root folder of your hyperspy repository (folder containing thesetup.py
file) run pip in development mode:
Installation in other (non-system) Python distribution¶
From the root folder of your hyperspy repository (folder containing thesetup.py
file) run pip in development mode:
All required dependencies are automatically installed by pip. If you don’t wantto install all dependencies and only install some of the optional dependencies,use the corresponding selector as explained in the Installation using pip section
Installation in a system Python distribution¶
When using a system Python distribution, it is recommanded to install thedependencies using your system package manager.
From the root folder of your hyperspy repository (folder containing thesetup.py
file) run pip in development mode.
Creating Debian/Ubuntu binaries¶
You can create binaries for Debian/Ubuntu from the source by running therelease_debian script
Install Anaconda Mac Terminal
Warning
Install Conda Mac Terminal Command
For this to work, the following packages must be installed in your systempython-stdeb, debhelper, dpkg-dev and python-argparser are required.