Install Conda Mac Terminal



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.

Install Conda Mac Terminal

Installation in an Anaconda/Miniconda distribution¶

HyperSpy is packaged in the conda-forge channeland can be installed easily using the condapackage manager.

Install Conda Mac Terminal

To install hyperspy run the following from the Anaconda Prompt on Windows orfrom a Terminal on Linux and Mac.

Conda

This will install also install the optional GUI packages hyperspy_gui_ipywidgetsand 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 and dev).

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Install Conda On Mac From Terminal

Install

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¶

Terminal

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

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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.