diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..bac9ed4 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,80 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: ezomero +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Erick + orcid: 'https://orcid.org/0000-0002-7545-3675' + family-names: Martins Ratamero + affiliation: The Jackson Laboratory + - given-names: Kiya + family-names: Govek + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0002-2105-0715' + - given-names: Julio + family-names: Mateos-Langerak + affiliation: 'University of Montpellier, CNRS, INSERM' + orcid: 'https://orcid.org/0000-0003-1579-0773' + - given-names: Fernando + family-names: Cervantes Sanchez + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0003-0652-2750' + - given-names: David + family-names: Mellert + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0001-6606-0274' +repository-code: 'https://github.com/TheJacksonLaboratory/ezomero' +abstract: >- + Many research laboratories need to manage, process, and + analyze the increasingly large volumes and complexity of + data being produced by state-of-the-art bioimaging + platforms. OMERO is a popular open-source client-server + application that provides a unified interface for managing + and working with bioimages and their associated + measurements and metadata. Integrating OMERO into analysis + pipelines, such as those developed around the scientific + Python ecosystem, will thus be a common pattern across the + field of bioimaging. While OMERO has a powerful Python + API, it provides minimal abstraction from the underlying + OMERO object model and associated methods, which represent + more complexity than most users are interested in for the + context of an analysis script. We introduce ezomero, which + was designed to provide a convenience layer on top of + existing OMERO APIs and return data types that are either + Python primitive or commonly used in scientific Python. + Ezomero has minimal dependencies in addition to the OMERO + Python library itself and is installable directly from + PyPI. Here, we provide an overview of ezomero as well as + several vignettes to illustrate how it can be used to + accelerate discovery. +license: GPL-2.0 +preferred-citation: + type: article + authors: + - given-names: Erick + orcid: 'https://orcid.org/0000-0002-7545-3675' + family-names: Martins Ratamero + affiliation: The Jackson Laboratory + - given-names: Kiya + family-names: Govek + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0002-2105-0715' + - given-names: Julio + family-names: Mateos-Langerak + affiliation: 'University of Montpellier, CNRS, INSERM' + orcid: 'https://orcid.org/0000-0003-1579-0773' + - given-names: Fernando + family-names: Cervantes Sanchez + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0003-0652-2750' + - given-names: David + family-names: Mellert + affiliation: The Jackson Laboratory + orcid: 'https://orcid.org/0000-0001-6606-0274' + title: "Easing OMERO adoption with ezomero" + doi: 10.1101/2023.06.29.546930 \ No newline at end of file diff --git a/README.md b/README.md index 2a8fc10..5fe47bf 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -![Run Tests](https://github.com/TheJacksonLaboratory/ezomero/workflows/Run%20Tests/badge.svg?event=push) ![](https://raw.githubusercontent.com/TheJacksonLaboratory/ezomero/main/coverage.svg) +![](https://raw.githubusercontent.com/TheJacksonLaboratory/ezomero/main/coverage.svg) [![badge-doi](https://img.shields.io/badge/doi-10.1101%2F2023.06.29.546930-purple)](https://doi.org/10.1101/2023.06.29.546930) # ezomero A module with convenience functions for writing Python code that interacts with OMERO. diff --git a/setup.py b/setup.py index f262c74..7f60999 100644 --- a/setup.py +++ b/setup.py @@ -17,8 +17,8 @@ url="https://github.com/TheJacksonLaboratory/ezomero", packages=setuptools.find_packages(), install_requires=[ - 'omero-py==5.13.1', - 'numpy>=1.22' + 'omero-py == 5.13.1', + 'numpy >= 1.22, < 2.0' ], extras_require={ "tables": ["pandas"],