From 1f6df2ea69b70b24679b9f3e303465ca3adfd3a7 Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Wed, 28 Feb 2024 10:26:14 +0100 Subject: [PATCH 1/5] Update README.md with JOSS badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c4317c29..25acb670 100644 --- a/README.md +++ b/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) | | **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/) | From db3d061e35cce10eb9e38ca1c3c92f707d136c6f Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Wed, 28 Feb 2024 10:28:47 +0100 Subject: [PATCH 2/5] update CITATION.cff with JOSS paper data --- CITATION.cff | 138 ++++++++++++++++++++++++++++----------------------- 1 file changed, 77 insertions(+), 61 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 9b36bc2d..0fc0a42a 100644 --- a/CITATION.cff +++ b/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: g.crocioni@esciencecenter.nl - 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: d.bodor@esciencecenter.nl - 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" From fbef9684e4386580593897b171fd75fd70436c8d Mon Sep 17 00:00:00 2001 From: Giulia Crocioni <55382553+gcroci2@users.noreply.github.com> Date: Wed, 28 Feb 2024 10:30:48 +0100 Subject: [PATCH 3/5] Delete .zenodo.json --- .zenodo.json | 69 ---------------------------------------------------- 1 file changed, 69 deletions(-) delete mode 100644 .zenodo.json diff --git a/.zenodo.json b/.zenodo.json deleted file mode 100644 index 522d595e..00000000 --- a/.zenodo.json +++ /dev/null @@ -1,69 +0,0 @@ -{ - "creators": [ - { - "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", - "name": "Giulia Crocioni", - "orcid": "0000-0002-0823-0121" - }, - { - "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", - "name": "Dani L. Bodor", - "orcid": "0000-0003-2109-2349" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Coos Baakman", - "orcid": "0000-0003-4317-1566" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Farzaneh M. Parizi", - "orcid": "0000-0003-4230-7492" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Daniel T. Rademaker", - "orcid": "0000-0003-1959-1317" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Gayatri Ramakrishnan", - "orcid": "0000-0001-8203-2783" - }, - { - "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", - "name": "Sven van der Burg", - "orcid": "0000-0003-1250-6968" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Dario F. Marzella", - "orcid": "0000-0002-0043-3055" - }, - { - "name": "João M. C. Teixeira", - "orcid": "0000-0002-9113-0622" - }, - { - "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", - "name": "Li C. Xue", - "orcid": "0000-0002-2613-538X" - } - ], - "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": { - "id": "Apache-2.0" - }, - "title": "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning" -} From 577b8b4850e8a241e8140bb61f27c0f7bb5bbcf2 Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Wed, 28 Feb 2024 13:41:55 +0100 Subject: [PATCH 4/5] reinsert zenodo file --- .zenodo.json | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .zenodo.json diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 00000000..522d595e --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,69 @@ +{ + "creators": [ + { + "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", + "name": "Giulia Crocioni", + "orcid": "0000-0002-0823-0121" + }, + { + "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", + "name": "Dani L. Bodor", + "orcid": "0000-0003-2109-2349" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Coos Baakman", + "orcid": "0000-0003-4317-1566" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Farzaneh M. Parizi", + "orcid": "0000-0003-4230-7492" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Daniel T. Rademaker", + "orcid": "0000-0003-1959-1317" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Gayatri Ramakrishnan", + "orcid": "0000-0001-8203-2783" + }, + { + "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands", + "name": "Sven van der Burg", + "orcid": "0000-0003-1250-6968" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Dario F. Marzella", + "orcid": "0000-0002-0043-3055" + }, + { + "name": "João M. C. Teixeira", + "orcid": "0000-0002-9113-0622" + }, + { + "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands", + "name": "Li C. Xue", + "orcid": "0000-0002-2613-538X" + } + ], + "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": { + "id": "Apache-2.0" + }, + "title": "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning" +} From f01a808ff594ceb0724c4905fc2656f45a36117e Mon Sep 17 00:00:00 2001 From: gcroci2 Date: Wed, 28 Feb 2024 13:44:17 +0100 Subject: [PATCH 5/5] update readme.dev.mdf --- README.dev.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.dev.md b/README.dev.md index f4eb2b56..879257de 100644 --- a/README.dev.md +++ b/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