Doi and numpy (#85)

* added publication badge

* fixed badge

* future-proofing against numpy 2.0.0

* added CITATION.cff

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

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.

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"],