dev: merge dev branch with main

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.0
+current_version = 3.0.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved

.zenodo.json

@@ -1,42 +1,42 @@
 {
   "creators": [
     {
-      "affiliation": "Netherlands eScience Center, Amsterdam, NL",
+      "affiliation": "Netherlands eScience Center, Amsterdam, The Netherlands",
       "name": "Giulia Crocioni",
       "orcid": "0000-0002-0823-0121"
     },
     {
-      "affiliation": "Netherlands eScience Center, Amsterdam, NL",
+      "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, NL",
+      "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, NL",
+      "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, NL",
+      "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, NL",
+      "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, NL",
+      "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, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Dario F. Marzella",
       "orcid": "0000-0002-0043-3055"
     },
@@ -45,7 +45,7 @@
       "orcid": "0000-0002-9113-0622"
     },
     {
-      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL",
+      "affiliation": "Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands",
       "name": "Li C. Xue",
       "orcid": "0000-0002-2613-538X"
     }

CITATION.cff

@@ -12,44 +12,44 @@ authors:
   - given-names: Giulia
     family-names: Crocioni
     email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     orcid: "https://orcid.org/0000-0002-0823-0121"
   - given-names: Dani L.
     family-names: Bodor
     email: [email protected]
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0001-8203-2783"
   - given-names: Sven A.
     family-names: van der Burg
-    affiliation: Netherlands eScience Center, Amsterdam, NL
+    affiliation: Netherlands eScience Center, Amsterdam, The Netherlands
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0002-0043-3055"
   - given-names: João M.C.
     family-names: Teixeira
     affiliation: Independent Researcher
     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, NL
+    affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     orcid: "https://orcid.org/0000-0002-2613-538X"
 abstract: >-
   DeepRank2 is an open-source deep learning
@@ -68,5 +68,5 @@ keywords:
   - DeepRank
 license: Apache-2.0
 commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c
-version: "3.0.0"
-date-released: "2024-01-25"
+version: "3.0.1"
+date-released: "2024-02-22"

CONTRIBUTING.rst

@@ -37,8 +37,8 @@ You want to make some kind of change to the code base
 #. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions `here <https://help.github.com/articles/configuring-a-remote-for-a-fork/>`__ and `here <https://help.github.com/articles/syncing-a-fork/>`__);
 #. make sure the existing tests still work by running ``python setup.py test``;
 #. add your own tests (if necessary);
-#. ensure the code is correctly linted (`ruff .`) and formatted (`ruff format .`);
-#. see our `developer's readme <README.dev.md>`` for detailed information on our style conventions, etc.;
+#. ensure the code is correctly linted (``ruff .``) and formatted (``ruff format .``);
+#. see our `developer's readme <README.dev.md>`_ for detailed information on our style conventions, etc.;
 #. update or expand the documentation;
 #. `push <http://rogerdudler.github.io/git-guide/>`_ your feature branch to (your fork of) the DeepRank2 repository on GitHub;
 #. create the pull request, e.g. following the instructions `here <https://help.github.com/articles/creating-a-pull-request/>`__.

README.dev.md

@@ -79,7 +79,7 @@ During the development cycle, three main supporting branches are used:
 
 ## Making a release
 
-1. Branch from `dev` and prepare the branch for the release (e.g., removing the unnecessary dev files such as the current one, fix minor bugs if necessary).
+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).

deeprank2/__init__.py

@@ -1 +1 @@
-__version__ = "3.0.0"
+__version__ = "3.0.1"

paper/paper.bib

@@ -135,7 +135,8 @@ @article{gainza2023novo
   journal={Nature},
   pages={1--9},
   year={2023},
-  publisher={Nature Publishing Group UK London}
+  publisher={Nature Publishing Group UK London},
+  doi={10.1038/s41586-023-05993-x}
 }
 
 @article{dove_gnn,
@@ -224,6 +225,7 @@ @article{torchdrug
       title={TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery}, 
       author={Zhu, Zhaocheng and Shi, Chence and Zhang, Zuobai and Liu, Shengchao and Xu, Minghao and Yuan, Xinyu and Zhang, Yangtian and Chen, Junkun and Cai, Huiyu and Lu, Jiarui and Ma, Chang and Liu, Runcheng and Xhonneux, Louis-Pascal and Qu, Meng and Tang, Jian},
       journal={arXiv preprint arXiv:2202.08320},
+	  doi={10.48550/arXiv.2202.08320},
       year={2022}
 }
 
@@ -250,12 +252,13 @@ @article{rosetta
 	title = {Accurate prediction of protein structures and interactions using a three-track neural network},
 	author = {Baek, Minkyung and {DiMaio}, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N and Schaeffer, R Dustin and Millán, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R and {DeGiovanni}, Andy and Pereira, Jose H and Rodrigues, Andria V and van Dijk, Alberdina A and Ebrecht, Ana C and Opperman, Diederik J and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K and Dalwadi, Udit and Yip, Calvin K and Burke, John E and Garcia, K Christopher and Grishin, Nick V and Adams, Paul D and Read, Randy J and Baker, David},
 	date = {2021},
-	langid = {english}
+	langid = {english},
+	doi={10.1126/science.abj8754}
 }
 
 @article{modeller,
   title={Evaluation of comparative protein structure modeling by MODELLER-3, Proteins Suppl. 1, 50- 58},
   author={Sanchez, R and Sali, A},
-  journal={Google Scholar There is no corresponding record for this reference},
-  year={1997}
+  year={1997},
+  doi={10.1002/(SICI)1097-0134(1997)1+%3C50::AID-PROT8%3E3.0.CO;2-S}
 }

paper/paper.md

@@ -47,9 +47,9 @@ authors:
     orcid: 0000-0002-2613-538X
     affiliation: 2
 affiliations:
-  - name: Netherlands eScience Center, Amsterdam, NL
+  - name: Netherlands eScience Center, Amsterdam, The Netherlands
     index: 1
-  - name: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, NL
+  - name: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands
     index: 2
   - name: Independent Researcher
     index: 3

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deeprank2"
-version = "3.0.0"
+version = "3.0.1"
 description = "DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants."
 readme = "README.md"
 requires-python = ">=3.10"