merge dev with main

CITATION.cff

@@ -1,72 +1,88 @@
-# This CITATION.cff file was generated with cffinit.
-# Visit https://bit.ly/cffinit to generate yours today!
-
-cff-version: 1.2.0
-doi: 10.5281/zenodo.6674124
-title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning"
-message: >-
-  If you use this software, please cite it using the
-  metadata from this file.
-type: software
+cff-version: "1.2.0"
 authors:
-  - given-names: Giulia
-    family-names: Crocioni
-    email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
+- family-names: Crocioni
+  given-names: Giulia
+  orcid: "https://orcid.org/0000-0002-0823-0121"
+- family-names: Bodor
+  given-names: Dani L.
+  orcid: "https://orcid.org/0000-0003-2109-2349"
+- family-names: Baakman
+  given-names: Coos
+  orcid: "https://orcid.org/0000-0003-4317-1566"
+- family-names: Parizi
+  given-names: Farzaneh M.
+  orcid: "https://orcid.org/0000-0003-4230-7492"
+- family-names: Rademaker
+  given-names: Daniel-T.
+  orcid: "https://orcid.org/0000-0003-1959-1317"
+- family-names: Ramakrishnan
+  given-names: Gayatri
+  orcid: "https://orcid.org/0000-0001-8203-2783"
+- family-names: Burg
+  given-names: Sven A.
+  name-particle: van der
+  orcid: "https://orcid.org/0000-0003-1250-6968"
+- family-names: Marzella
+  given-names: Dario F.
+  orcid: "https://orcid.org/0000-0002-0043-3055"
+- family-names: Teixeira
+  given-names: João M. C.
+  orcid: "https://orcid.org/0000-0002-9113-0622"
+- family-names: Xue
+  given-names: Li C.
+  orcid: "https://orcid.org/0000-0002-2613-538X"
+contact:
+- family-names: Crocioni
+  given-names: Giulia
+  orcid: "https://orcid.org/0000-0002-0823-0121"
+doi: 10.5281/zenodo.10566809
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Crocioni
+    given-names: Giulia
     orcid: "https://orcid.org/0000-0002-0823-0121"
-  - given-names: Dani L.
-    family-names: Bodor
-    email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
+  - family-names: Bodor
+    given-names: Dani L.
     orcid: "https://orcid.org/0000-0003-2109-2349"
-  - given-names: Coos
-    family-names: Baakman
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Baakman
+    given-names: Coos
     orcid: "https://orcid.org/0000-0003-4317-1566"
-  - given-names: Farzaneh Meimandi
-    family-names: Parizi
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Parizi
+    given-names: Farzaneh M.
     orcid: "https://orcid.org/0000-0003-4230-7492"
-  - given-names: Daniel-T.
-    family-names: Rademaker
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Rademaker
+    given-names: Daniel-T.
     orcid: "https://orcid.org/0000-0003-1959-1317"
-  - given-names: Gayatri
-    family-names: Ramakrishnan
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Ramakrishnan
+    given-names: Gayatri
     orcid: "https://orcid.org/0000-0001-8203-2783"
-  - given-names: Sven A.
-    family-names: van der Burg
-    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
+  - family-names: Burg
+    given-names: Sven A.
+    name-particle: van der
     orcid: "https://orcid.org/0000-0003-1250-6968"
-  - given-names: Dario F.
-    family-names: Marzella
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Marzella
+    given-names: Dario F.
     orcid: "https://orcid.org/0000-0002-0043-3055"
-  - given-names: João M.C.
-    family-names: Teixeira
-    affiliation: Independent Researcher
+  - family-names: Teixeira
+    given-names: João M. C.
     orcid: "https://orcid.org/0000-0002-9113-0622"
-  - given-names: Li C.
-    family-names: Xue
-    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - family-names: Xue
+    given-names: Li C.
     orcid: "https://orcid.org/0000-0002-2613-538X"
-abstract: >-
-  DeepRank2 is an open-source deep learning
-  framework for data mining of protein-protein interfaces
-  or single-residue variants.
-keywords:
-  - Python
-  - PyTorch
-  - structural biology
-  - geometric deep learning
-  - 3D protein structures
-  - protein-protein interfaces
-  - single-residue variants
-  - graph neural networks
-  - convolutional neural networks
-  - DeepRank
-license: Apache-2.0
-commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c
-version: "3.0.1"
-date-released: "2024-02-22"
+  date-published: 2024-02-27
+  doi: 10.21105/joss.05983
+  issn: 2475-9066
+  issue: 94
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 5983
+  title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep
+    Learning"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.05983"
+  volume: 9
+title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep
+  Learning"

README.dev.md

@@ -81,9 +81,8 @@ During the development cycle, three main supporting branches are used:
 
 1. Branch from `dev` and prepare the branch for the release (e.g., removing the unnecessary dev files, fix minor bugs if necessary).
 2. [Bump the version](https://github.com/DeepRank/deeprank2/blob/dev/README.dev.md#versioning).
-3. Verify that the information in `CITATION.cff` is correct (update the release date), and that `.zenodo.json` contains equivalent data.
-4. Merge the release branch into `main` (and `dev`), and [run the tests](https://github.com/DeepRank/deeprank2/blob/dev/README.dev.md#running-the-tests).
-5. Go to https://github.com/DeepRank/deeprank2/releases and draft a new release; create a new tag for the release, generate release notes automatically and adjust them, and finally publish the release as latest. This will trigger [a GitHub action](https://github.com/DeepRank/deeprank2/actions/workflows/release.yml) that will take care of publishing the package on PyPi.
+3. Merge the release branch into `main` (and `dev`), and [run the tests](https://github.com/DeepRank/deeprank2/blob/dev/README.dev.md#running-the-tests).
+4. Go to https://github.com/DeepRank/deeprank2/releases and draft a new release; create a new tag for the release, generate release notes automatically and adjust them, and finally publish the release as latest. This will trigger [a GitHub action](https://github.com/DeepRank/deeprank2/actions/workflows/release.yml) that will take care of publishing the package on PyPi.
 
 ## UML
 

README.md

@@ -4,7 +4,7 @@
 | :------------: | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 |  **fairness**  | [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6403/badge)](https://bestpractices.coreinfrastructure.org/projects/6403)                                                                                                                                                                                                                                |
 |  **package**   | [![PyPI version](https://badge.fury.io/py/deeprank2.svg)](https://badge.fury.io/py/deeprank2) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/b1bde03fc0334e07b0cd8a69ce2adeb3)](https://app.codacy.com/gh/DeepRank/deeprank2/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)                                                                                                                                                                                                                                     |
-|    **docs**    | [![Documentation Status](https://readthedocs.org/projects/deeprank2/badge/?version=latest)](https://deeprank2.readthedocs.io/en/latest/?badge=latest) [![RSD](https://img.shields.io/badge/RSD-deeprank2-pink)](https://research-software-directory.org/software/deeprankcore) [![DOI](https://zenodo.org/badge/450496579.svg)](https://zenodo.org/badge/latestdoi/450496579)                                                                                                                                                                                    |
+|    **docs**    | [![Documentation Status](https://readthedocs.org/projects/deeprank2/badge/?version=latest)](https://deeprank2.readthedocs.io/en/latest/?badge=latest) [![RSD](https://img.shields.io/badge/RSD-deeprank2-pink)](https://research-software-directory.org/software/deeprankcore) [![DOI](https://zenodo.org/badge/450496579.svg)](https://zenodo.org/badge/latestdoi/450496579) [![DOI](https://joss.theoj.org/papers/10.21105/joss.05983/status.svg)](https://doi.org/10.21105/joss.05983)                                                                        |
 |   **tests**    | [![Build Status](https://github.com/DeepRank/deeprank2/actions/workflows/build-repo.yml/badge.svg)](https://github.com/DeepRank/deeprank2/actions) ![Linting status](https://github.com/DeepRank/deeprank2/actions/workflows/linting.yml/badge.svg?branch=main) [![Coverage Status](https://coveralls.io/repos/github/DeepRank/deeprank2/badge.svg?branch=main)](https://coveralls.io/github/DeepRank/deeprank2?branch=main) ![Python](https://img.shields.io/badge/python-3.10-blue.svg) <!--- ![Python](https://img.shields.io/badge/python-3.11-blue.svg) --> |
 | **running on** | ![Ubuntu](https://img.shields.io/badge/Ubuntu-E95420?style=for-the-badge&logo=ubuntu&logoColor=white)                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
 |  **license**   | [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0/)                                                                                                                                                                                                                                                                                                                                                                                                                                               |

paper/paper.md

@@ -44,12 +44,13 @@ authors:
     orcid: 0000-0002-9113-0622
     affiliation: 3
   - name: Li C. Xue
+    corresponding: true
     orcid: 0000-0002-2613-538X
     affiliation: 2
 affiliations:
   - name: Netherlands eScience Center, Amsterdam, The Netherlands
     index: 1
-  - name: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
+  - name: The Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
     index: 2
   - name: Independent Researcher
     index: 3