From e389853d891c037947c5efcc9e078a0df8fc650d Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Fri, 17 Aug 2018 18:06:14 -0700 Subject: [PATCH 1/4] stub for JOSS paper (Issue #147) --- paper/codemeta.json | 58 +++++++++++++++++++++++++++++++++++++++++++++ paper/paper.bib | 1 + paper/paper.md | 29 +++++++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 paper/codemeta.json create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/paper/codemeta.json b/paper/codemeta.json new file mode 100644 index 00000000..86cc0295 --- /dev/null +++ b/paper/codemeta.json @@ -0,0 +1,58 @@ +{ + "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld", + "@type": "Code", + "author": [ + { + "@id": "http://orcid.org/0000-0003-1340-0831", + "@type": "Person", + "email": "oliver.beckstein@asu.edu", + "name": "Oliver Beckstein", + "affiliation": "Arizona State University" + }, + { + "@id": "", + "@type": "Person", + "email": "", + "name": "Pedro Lacerda", + "affiliation": "" + }, + { + "@id": "", + "@type": "Person", + "email": "richardjgowers@gmail.com", + "name": "Richard Gowers", + "affiliation": "" + }, + { + "@id": "", + "@type": "Person", + "email": "ikenney@asu.edu", + "name": "Ian Kenney", + "affiliation": "Arizona State University" + }, + { + "@id": "", + "@type": "Person", + "email": "", + "name": "Andy Somogyi", + "affiliation": "" + }, + { + "@id": "", + "@type": "Person", + "email": "", + "name": "Philip Loche", + "affiliation": "" + } + ], + "identifier": "10.5281/zenodo.17901", + "codeRepository": "https://github.com/Becksteinlab/GromacsWrapper", + "datePublished": "2018-08-17", + "dateModified": "2018-08-17", + "dateCreated": "2018-08-17", + "description": "GromacsWrapper is a Python package that wraps system calls to the Gromacs molecular dynamics tools into thin classes and provides a Python-like API. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, all with the same Python code) into python scripts. ", + "keywords": "python, molecular-dynamics, gromacs", + "license": "GPL v3.0", + "title": "GromacsWrapper", + "version": "v0.7.0" +} diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 00000000..41de50be --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1 @@ +%%% paper.bib for GromacsWrapper paper.md diff --git a/paper/paper.md b/paper/paper.md new file mode 100644 index 00000000..13d176f0 --- /dev/null +++ b/paper/paper.md @@ -0,0 +1,29 @@ +--- +title: 'GromacsWrapper: A Python package for galactic dynamics' +tags: + - Python + - molecular-dynamics + - Gromacs +authors: + - name: Oliver Beckstein + orcid: 0000-0003-1340-0831 + affiliation: "1, 2" # (Multiple affiliations must be quoted) + - name: Pedro Lacerda + - name: Richard Gowers + - name: Ian Kenney + affiliation: 1 + - name: Philip Loche +affiliations: + - name: Department of Physics, Arizona State University + index: 1 + - name: Center for Biological Physics, Arizona State University + index: 2 +date: 17 August 2018 +bibliography: paper.bib +--- + +# Summary + +# Acknowledgments + +# References From 860d22b80d22b6276d561aea92d89be37fdb9c21 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Sat, 18 Aug 2018 14:08:48 -0500 Subject: [PATCH 2/4] Update codemeta.json --- paper/codemeta.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/paper/codemeta.json b/paper/codemeta.json index 86cc0295..f1282bed 100644 --- a/paper/codemeta.json +++ b/paper/codemeta.json @@ -17,11 +17,11 @@ "affiliation": "" }, { - "@id": "", + "@id": "https://orcid.org/0000-0002-3241-1846", "@type": "Person", "email": "richardjgowers@gmail.com", - "name": "Richard Gowers", - "affiliation": "" + "name": "Richard J. Gowers", + "affiliation": "University of New Hampshire" }, { "@id": "", From 37d44d73f9ba2fd8db093a7c5f7b1dca5db51db5 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Sat, 18 Aug 2018 14:15:12 -0500 Subject: [PATCH 3/4] Update paper.md --- paper/paper.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 13d176f0..f0daa5bc 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -9,7 +9,9 @@ authors: orcid: 0000-0003-1340-0831 affiliation: "1, 2" # (Multiple affiliations must be quoted) - name: Pedro Lacerda - - name: Richard Gowers + - name: Richard J. Gowers + orcid: 0000-0002-3241-1846 + affiliation: 3 - name: Ian Kenney affiliation: 1 - name: Philip Loche @@ -18,6 +20,8 @@ affiliations: index: 1 - name: Center for Biological Physics, Arizona State University index: 2 + - name: Department of Chemistry, University of New Hampshire + index: 3 date: 17 August 2018 bibliography: paper.bib --- From 03eac1a6db4be83d4db3e4e74e08fd6161be0eee Mon Sep 17 00:00:00 2001 From: Andrew White Date: Fri, 24 Aug 2018 14:24:59 -0400 Subject: [PATCH 4/4] Added Andrew White to paper.md and codemeta.json --- paper/codemeta.json | 7 +++++++ paper/paper.md | 5 +++++ 2 files changed, 12 insertions(+) diff --git a/paper/codemeta.json b/paper/codemeta.json index f1282bed..48cbad21 100644 --- a/paper/codemeta.json +++ b/paper/codemeta.json @@ -43,6 +43,13 @@ "email": "", "name": "Philip Loche", "affiliation": "" + }, + { + "@id": "http://orcid.org/0000-0002-6647-3965", + "@type": "Person", + "email": "andrew.white@rochester.edu", + "name": "Andrew D White", + "affiliation": "University of Rochester" } ], "identifier": "10.5281/zenodo.17901", diff --git a/paper/paper.md b/paper/paper.md index f0daa5bc..aac52e73 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -15,6 +15,9 @@ authors: - name: Ian Kenney affiliation: 1 - name: Philip Loche + - name: Andrew D. White + orcid: 0000-0002-6647-3965 + affiliation: 4 affiliations: - name: Department of Physics, Arizona State University index: 1 @@ -22,6 +25,8 @@ affiliations: index: 2 - name: Department of Chemistry, University of New Hampshire index: 3 + - name: Department of Chemical Engineering, University of Rochester + index: 4 date: 17 August 2018 bibliography: paper.bib ---