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TorecLuik committed Dec 20, 2023
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34 changes: 22 additions & 12 deletions CITATION.cff
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# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Omero Slurm Client
title: OMERO Slurm Client
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Torec
- given-names: Torec Tom
family-names: Luik
email: [email protected]
affiliation: Amsterdam UMC
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description: ZENODO DOI for all versions
repository-code: 'https://github.com/NL-BioImaging/omero-slurm-client'
url: 'https://nl-bioimaging.github.io/omero-slurm-client/'
repository: 'https://github.com/NL-BioImaging/biomero-scripts'
abstract: >-
The omero_slurm_client Python package is a library that
facilitates working with a Slurm cluster in the context of
the Omero platform.
This library is to be used within BIOMERO (an extension to
OMERO), together with the BIOMERO Scripts we also provide.
Together, BIOMERO allows you to run BioImage analysis
workflows directly from OMERO on a Slurm cluster, through
SSH.
The package includes the SlurmClient class, which extends
the Fabric librarys Connection class to provide SSH-based
the Fabric library's Connection class to provide SSH-based
connectivity and interaction with a Slurm cluster. The
package enables users to submit jobs, monitor job status,
retrieve job output, and perform other Slurm-related
tasks.
Additionally, the package offers functionality for
tasks. Additionally, the package offers functionality for
configuring and managing paths to Slurm data and
Singularity images, as well as specific image models and
their associated repositories.
Overall, the omero_slurm_client package simplifies the
integration of Slurm functionality within the Omero
integration of Slurm functionality within the OMERO
platform and provides an efficient workflow for working
with Slurm clusters.
keywords:
- python
- omero
- slurm
- jobs
- high-performance-computing
- fair
- image-analysis
- bioimaging
- cytomine
- biomero
- biaflows
- high-throughput-screening
- high-content-screening
license: Apache-2.0
2 changes: 1 addition & 1 deletion README.md
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# BIOMERO - the OMERO Slurm Client library
[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![DOI](https://zenodo.org/badge/638954891.svg)](https://zenodo.org/badge/latestdoi/638954891) ![Python](https://img.shields.io/badge/Python-3.6-blue.svg) ![Slurm](https://img.shields.io/badge/Slurm-21.08.6-blue.svg) ![OMERO](https://img.shields.io/badge/OMERO-5.6.8-blue.svg) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8F%20%20%E2%97%8F-yellow)](https://fair-software.eu) [![OpenSSF Best Practices](https://bestpractices.coreinfrastructure.org/projects/7530/badge)](https://bestpractices.coreinfrastructure.org/projects/7530) [![Sphinx build](https://github.com/NL-BioImaging/omero-slurm-client/actions/workflows/sphinx.yml/badge.svg?branch=main)](https://github.com/NL-BioImaging/omero-slurm-client/actions/workflows/sphinx.yml) [![pages-build-deployment](https://github.com/NL-BioImaging/omero-slurm-client/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/NL-BioImaging/omero-slurm-client/actions/workflows/pages/pages-build-deployment)

This library is to be used within BIOMERO (an extension to OMERO), together with the OMERO Slurm Scripts we also provide.
This library is to be used within BIOMERO (an extension to OMERO), together with the BIOMERO Scripts we also provide.

Together, BIOMERO allows you to run BioImage analysis workflows directly from OMERO on a Slurm cluster, through SSH.

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