From ed976221c1431a176a26784bbd2d481e6998acfd Mon Sep 17 00:00:00 2001 From: Pablo Date: Wed, 8 Oct 2025 13:25:31 +0200 Subject: [PATCH 1/6] update files to match zenodo release --- CHANGELOG.md | 2 +- CITATION.cff | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 79dce8c..ee53859 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ 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). -## [Unreleased] +## [1.0.0] - 2024-10-02 ### Changed - Parameter sets (pKa values and force field-related parameters) from previous work are now belong to the pyMBE package and are directly accesible from the root path of the package. For example, the path to the Lunkad2021 data set can be accessed as `pmb.root / "parameters" / "peptides" / "Lunkad2021.json"`. (#132) diff --git a/CITATION.cff b/CITATION.cff index cdef009..af4a7f5 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -86,9 +86,9 @@ references: - family-names: Pineda given-names: Sebastian P. orcid: "https://orcid.org/0000-0001-8270-2476" - - family-names: Narambuena - given-names: Claudio F. - orcid: "https://orcid.org/0000-0003-3862-6642" + - family-names: Kurahatti + given-names: Somesh + orcid: "https://orcid.org/0009-0003-2098-6583" - family-names: Grad given-names: Jean-Noël orcid: "https://orcid.org/0000-0002-5821-4912" @@ -134,8 +134,8 @@ references: orcid: "https://orcid.org/0000-0002-7603-8617" doi: 10.5281/zenodo.12102635 type: software - version: 0.8.0 + version: 1.0.0 title: pyMBE - date-released: "2024-06-18" + date-released: "2024-10-02" license: - GPL-3.0-or-later From 5082be0b5ca4dcceef335746deb702651ff56cb5 Mon Sep 17 00:00:00 2001 From: Pablo Date: Wed, 8 Oct 2025 13:30:38 +0200 Subject: [PATCH 2/6] fix citation file --- CITATION.cff | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index af4a7f5..818846d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -86,9 +86,9 @@ references: - family-names: Pineda given-names: Sebastian P. orcid: "https://orcid.org/0000-0001-8270-2476" - - family-names: Kurahatti - given-names: Somesh - orcid: "https://orcid.org/0009-0003-2098-6583" + - family-names: Narambuena + given-names: Claudio F. + orcid: "https://orcid.org/0000-0003-3862-6642" - family-names: Grad given-names: Jean-Noël orcid: "https://orcid.org/0000-0002-5821-4912" @@ -120,9 +120,9 @@ references: - family-names: Pineda given-names: Sebastian P. orcid: "https://orcid.org/0000-0001-8270-2476" - - family-names: Narambuena - given-names: Claudio F. - orcid: "https://orcid.org/0000-0003-3862-6642" + - family-names: Kurahatti + given-names: Somesh + orcid: "https://orcid.org/0009-0003-2098-6583" - family-names: Grad given-names: Jean-Noël orcid: "https://orcid.org/0000-0002-5821-4912" From dbe70f353ef6c5d83c7d03d8158e10b2ff706310 Mon Sep 17 00:00:00 2001 From: Pablo Date: Wed, 8 Oct 2025 13:52:44 +0200 Subject: [PATCH 3/6] correct date --- CHANGELOG.md | 2 +- CITATION.cff | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ee53859..15fb6f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ 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). -## [1.0.0] - 2024-10-02 +## [1.0.0] - 2025-10-02 ### Changed - Parameter sets (pKa values and force field-related parameters) from previous work are now belong to the pyMBE package and are directly accesible from the root path of the package. For example, the path to the Lunkad2021 data set can be accessed as `pmb.root / "parameters" / "peptides" / "Lunkad2021.json"`. (#132) diff --git a/CITATION.cff b/CITATION.cff index 818846d..df82cfc 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -136,6 +136,6 @@ references: type: software version: 1.0.0 title: pyMBE - date-released: "2024-10-02" + date-released: "2025-10-02" license: - GPL-3.0-or-later From 6ae6b7bd4e86064aa5474eb59208ecc72f95cc09 Mon Sep 17 00:00:00 2001 From: Pablo Date: Thu, 9 Oct 2025 11:10:55 +0200 Subject: [PATCH 4/6] amend doi for the citation to the software --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index df82cfc..6e51fce 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -132,7 +132,7 @@ references: - family-names: Blanco given-names: Pablo M. orcid: "https://orcid.org/0000-0002-7603-8617" - doi: 10.5281/zenodo.12102635 + doi: 10.5281/zenodo.12102634 type: software version: 1.0.0 title: pyMBE From 74f108b34ba77a8b99b0acf9f3314549e016dec4 Mon Sep 17 00:00:00 2001 From: "Pablo M. Blanco" <75744061+pm-blanco@users.noreply.github.com> Date: Thu, 9 Oct 2025 12:01:15 +0200 Subject: [PATCH 5/6] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Jean-Noël Grad --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 15fb6f8..70b66fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ 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). -## [1.0.0] - 2025-10-02 +## [1.0.0] - 2025-10-08 ### Changed - Parameter sets (pKa values and force field-related parameters) from previous work are now belong to the pyMBE package and are directly accesible from the root path of the package. For example, the path to the Lunkad2021 data set can be accessed as `pmb.root / "parameters" / "peptides" / "Lunkad2021.json"`. (#132) From c2b8deb9ecb8a5af98d052a8c96e5c66edcf94de Mon Sep 17 00:00:00 2001 From: Pablo Date: Thu, 9 Oct 2025 12:04:59 +0200 Subject: [PATCH 6/6] fix date --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 6e51fce..5f1ea54 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -136,6 +136,6 @@ references: type: software version: 1.0.0 title: pyMBE - date-released: "2025-10-02" + date-released: "2025-10-08" license: - GPL-3.0-or-later