README.md

About nyxus-feedstock

Feedstock license: BSD-3-Clause

Home: https://github.com/PolusAI/nyxus

Package license: MIT

Summary: Scalable library for calculating features from intensity-label image data

Development: https://github.com/PolusAI/nyxus

Documentation: https://nyxus.readthedocs.io/en/latest/

Nyxus is a feature-rich, highly optimized, Python/C++ application capable of analyzing images of arbitrary size and assembling complex regions of interest (ROIs) split across multiple image tiles and files. Nyxus can be used via Python or command line and is available in containerized form for reproducible execution. Nyxus computes over 450 combined intensity, texture, and morphological features at the ROI or whole image level with more in development. Key features that make Nyxus unique among other image feature extraction applications is its ability to operate at any scale, its highly validated algorithms, and its modular nature that makes the addition of new features straightforward.

Current build status

Azure

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Current release info

Name	Downloads	Version	Platforms

Installing nyxus

Installing nyxus from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, nyxus can be installed with conda:

conda install nyxus

or with mamba:

mamba install nyxus

It is possible to list all of the versions of nyxus available on your platform with conda:

conda search nyxus --channel conda-forge

or with mamba:

mamba search nyxus --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search nyxus --channel conda-forge

# List packages depending on `nyxus`:
mamba repoquery whoneeds nyxus --channel conda-forge

# List dependencies of `nyxus`:
mamba repoquery depends nyxus --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating nyxus-feedstock

If you would like to improve the nyxus recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/nyxus-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

• If the version of a package is not being increased, please add or increase the build/number.
• If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

• @sameeul