Prepare release 0.8.0 (#73)

Adopt Semantic Versioning, Keep a Changelog, Citation File Format.

.github/workflows/testsuite.yml

@@ -13,13 +13,16 @@ jobs:
     env:
       FI_PROVIDER: "^psm3,psm3;ofi_rxd"
       OMPI_MCA_mtl_ofi_provider_exclude: psm3
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@main
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3
       - name: Setup EESSI
         uses: eessi/github-action-eessi@v3
         with:
           eessi_stack_version: "2023.06"
-      - name: Checkout repository
-        uses: actions/checkout@main
       - name: Install dependencies
         uses: ./.github/actions/dependencies
         with:

AUTHORS.md

@@ -9,11 +9,11 @@ The following people have contributed to pyMBE:
 ## Core developers
 - David Beyer (University of Stuttgart, Germany)
 - Sebastian P. Pineda (Charles University, Czech Republic)
-- Paola B. Torres (Universidad Tecnologica Nacional, Argentina)
+- Paola B. Torres (Universidad Tecnológica Nacional, Argentina)
 
 ## Contributors
 - Marius Aarsten (Norwegian University of Science and Tecnology, Norway)
-- Claudio F. Narambuena (Universidad Tecnologica Nacional, Argentina)
+- Claudio F. Narambuena (Universidad Tecnológica Nacional, Argentina)
 
 ## Early testers of the library
 - Corinna Dannert (Norwegian University of Science and Technology, Norway)

CHANGELOG.md

@@ -0,0 +1,12 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.8.0] - 2024-06-17
+
+### Added
+
+* Initial release of pyMBE.

CITATION.cff

@@ -0,0 +1,93 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata from this file."
+title: pyMBE
+type: software
+version: 0.8.0
+authors:
+  - given-names: David
+    family-names: Beyer
+    affiliation: Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
+    orcid: "https://orcid.org/0000-0001-6066-8043"
+  - given-names: Paola B.
+    family-names: Torres
+    affiliation: Grupo de Bionanotecnologia y Sistemas Complejos. Infap-CONICET & Facultad Regional San Rafael, Universidad Tecnológica Nacional, San Rafael, Argentina
+    orcid: "https://orcid.org/0000-0001-9335-8367"
+  - given-names: Sebastian P.
+    family-names: Pineda
+    affiliation: Department of Physical and Macromolecular Chemistry, Charles University, Prague, Czech Republic
+    orcid: "https://orcid.org/0000-0001-8270-2476"
+  - given-names: Claudio F.
+    family-names: Narambuena
+    affiliation: Grupo de Bionanotecnologia y Sistemas Complejos. Infap-CONICET & Facultad Regional San Rafael, Universidad Tecnológica Nacional, San Rafael, Argentina
+    orcid: "https://orcid.org/0000-0003-3862-6642"
+  - given-names: Jean-Noël
+    family-names: Grad
+    affiliation: Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
+    orcid: "https://orcid.org/0000-0002-5821-4912"
+  - given-names: Peter
+    family-names: Košovan
+    affiliation: Department of Physical and Macromolecular Chemistry, Charles University, Prague, Czech Republic
+    orcid: "https://orcid.org/0000-0002-6708-3344"
+  - given-names: Pablo M.
+    family-names: Blanco
+    affiliation: Department of Physics, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
+    orcid: "https://orcid.org/0000-0002-7603-8617"
+identifiers:
+  - type: doi
+    value: 10.48550/arXiv.2401.14954
+    description: The arXiv preprint
+repository-code: "https://github.com/pyMBE-dev/pyMBE"
+keywords:
+  - molecule builder
+  - coarse-grained molecular modelling
+  - constant pH simulation
+  - Reaction ensemble Monte Carlo
+  - charge regulation
+  - pKa
+  - protein
+  - peptide
+license: GPL-3.0-or-later
+preferred-citation:
+  authors:
+    - given-names: David
+      family-names: Beyer
+    - given-names: Paola B.
+      family-names: Torres
+    - given-names: Sebastian P.
+      family-names: Pineda
+    - given-names: Claudio F.
+      family-names: Narambuena
+    - given-names: Jean-Noël
+      family-names: Grad
+    - given-names: Peter
+      family-names: Košovan
+    - given-names: Pablo M.
+      family-names: Blanco
+  doi: 10.48550/arXiv.2401.14954
+  status: preprint
+  type: article
+  journal: "arXiv preprint arXiv:2401.14954"
+  title: "pyMBE: the Python-based Molecule Builder for ESPResSo"
+  year: 2024
+references:
+  - authors:
+      - given-names: David
+        family-names: Beyer
+      - given-names: Paola B.
+        family-names: Torres
+      - given-names: Sebastian P.
+        family-names: Pineda
+      - given-names: Claudio F.
+        family-names: Narambuena
+      - given-names: Jean-Noël
+        family-names: Grad
+      - given-names: Peter
+        family-names: Košovan
+      - given-names: Pablo M.
+        family-names: Blanco
+    doi: 10.48550/arXiv.2401.14954
+    status: preprint
+    type: article
+    journal: "arXiv preprint arXiv:2401.14954"
+    title: "pyMBE: the Python-based Molecule Builder for ESPResSo"
+    year: 2024

CONTRIBUTING.md

@@ -5,12 +5,17 @@ If you discover any strange feature or unexpected behaviour of the library, plea
 Once a ticket is open in GitHub, we will work to fix the issue as soon as possible.
 
 ## New contributors
-New developers are welcomed to contribute to extend the functionalities of the pyMBE library. 
+New developers are welcome to contribute to extend the functionalities of the pyMBE library.
 To contribute to the pyMBE library, first one needs to be added as a member of this GitHub repository.
 If you want to contribute to the development of the pyMBE library, please contact Dr. Pablo M. Blanco ([email protected])
 
 ## Rules to contribute to pyMBE
-Any new version of the code must reproduce all the data stored in `testsuite/data`. 
-The scripts provided in `testsuite/` and in `samples/Beyer2024` can be used to quickly set-up simulations with pyMBE to reproduce such data sets.
-All new code will be reviewed by at least one member of the pyMBE development team before being merged into the stable version of the library to ensure that a functional version of the code is always available.
+Create a fork of the repository and submit your contribution in the form of a pull request.
+Give your branch a short and meaningful name, and start your work from the most recent commit on the main branch.
+Any new version of the code must reproduce all the data stored in `testsuite/data`.
+Before pushing your code, run `make tests` to execute the full test suite,
+`make pylint` to check for code issues, and `make docs` to confirm sphinx can build the user guide.
+When rapidly prototyping code, run `make unit_tests` periodically to check for regressions.
+All new code will be reviewed by at least one member of the pyMBE development team before being merged into the main branch to ensure that a functional version of the code is always available.
 Class methods are sorted in alphabetical order.
+We follow semantic versioning and keep a changelog.

README.md

@@ -21,25 +21,19 @@ pyMBE provides tools to facilitate building up molecules with complex architectu
 - [SciPy](https://scipy.org/) 
 - [pdoc](https://pdoc.dev/) (for building the docs)
 
-## Branches
-
-A deprecated version of pyMBE compatible with ESPResSo v4.1.4 (under the historical name of pyMBE, Sugar)  can be found in the branch `sugar_espresso4.1.4`. Note that further development of pyMBE will only be carried out for ESPResSo v4.2.1 and its forthcoming releases, and no further support for that branch is planned.
-
 ## Contents
 
-- `docs/`: folder with the API documentation of pyMBE.
 - `figs/`: folder with various images used in the tutorials of pyMBE.
-- `libs/`: folder with various libraries.
-- `logo/`: folder with the logo of pyMBE.
+- `lib/`: folder with various libraries.
 - `maintainer/`: folder with various scripts used by the maintainers.
 - `parameters/`: folder with various sets of parameters from previous works.
 - `samples/`: folder with various sample scripts showcasing how to use pyMBE to setup different systems.
 - `testsuite/`: folder with several test scripts and data for continous integration of the library.
 - `tutorials/`: folder with the available tutorials on pyMBE.
 - `visualization/`: folder with helper scripts to aid the visualization of vtf trajectories from constant pH and Grand reaction simulations with [VMD](https://www.ks.uiuc.edu/Research/vmd/).
 - `AUTHORS.md`: list of authors and contributors of pyMBE.
-- `CONTRIBUTING`: rules on how to contribute to pyMBE.
-- `LICENSE.md`: license of pyMBE.
+- `CONTRIBUTING.md`: rules on how to contribute to pyMBE.
+- `LICENSE.txt`: license of pyMBE.
 - `pyMBE.py`: source code of pyMBE
 - `requirements.txt`: list of required libraries to use pyMBE.
 
@@ -186,3 +180,15 @@ If you use pyMBE in your research, please cite our preprint:
 
 Please also make sure to properly cite the original authors if you use the resources provided in the `parameters/` folder.
 The relevant references are provided as comments in the corresponding files.
+
+## License
+
+Copyright (C) 2023-2024 pyMBE-dev team
+
+pyMBE is free software: you can redistribute it and/or modify it
+under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License,
+or (at your option) any later version.
+
+You should have received a [copy](LICENSE.txt) of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.