From 2b7d4877c3d113c27c944cc220b7cfa6fd0b95d2 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Sat, 6 Jun 2020 12:18:52 +0200 Subject: [PATCH] Working on LaTeX headers --- dmp.org | 154 +++++++++++++++++++++++++++++--------------------------- 1 file changed, 81 insertions(+), 73 deletions(-) diff --git a/dmp.org b/dmp.org index b9e8db9..2b9a735 100644 --- a/dmp.org +++ b/dmp.org @@ -1,7 +1,22 @@ -#+TITLE: ERC PTEROSOR : Data Management Plan -#+AUTHOR: A. Scemama, P.-F. Loos -#+DATE: 2020-06-05 +# -*- mode: org; org-confirm-babel-evaluate: nil; org-babel-noweb-wrap-start: "«"; org-babel-noweb-wrap-end: "»"; -*- +#+TITLE: ERC PTEROSOR +#+SUBTITLE: Data Management Plan +#+AUTHOR: A. Scemama, P.-F. Loos +#+EMAIL: scemama@irsamc.ups-tlse.fr +#+DATE: \today +#+LANGUAGE: English +#+EXPORT_FILE_NAME: DMP-PTEROSOR.pdf +#+LATEX_CLASS: revtex4-1 +#+LATEX_CLASS_OPTIONS: aip,jcp,showkeys +#+LATEX_HEADER: \usepackage{mathpazo,hyperref,amssymb} +#+LATEX_HEADER_EXTRA: +#+DESCRIPTION: Org-mode document for LaTeX export +#+KEYWORDS: Software, Notebooks, Publications, Presentations +#+LATEX_COMPILER: pdflatex +#+OPTIONS: tags:t tasks:t tex:t timestamp:t toc:nil todo:t |:t +#+SELECT_TAGS: export +#+EXCLUDE_TAGS: noexport nolatex * Project details @@ -37,23 +52,13 @@ PT-symmetric regions. 1. QuAcK (Software) 2. Quantum Package (Software) 3. Notebooks (Interactive Resource) - 4. Publications (Text) + 4. Textual data (Text) * QuAcK ** Dataset summary - #+BEGIN_EXAMPLE -This should include: - - dataset reference and name - - origin and expected size of the data generated/collected - - data types and formats - #+END_EXAMPLE - QuAcK is a small quantum chemistry package written in Fortran by the coordinator of the project. It is mostly used for prototyping. @@ -72,15 +77,30 @@ This should include: source files, Python, Bash scripts, Makefiles and standard atomic basis sets and pseudo-potentials. + All along the project, Mathematica / Jupyter / Org-mode notebooks will + be produced by researchers and students. Each notebook will take a + few megabytes. + + PDF files for reports, publications, presentations and posters will + be produced in this project. Each pdf file will take a few megabytes. + Care will be taken to maintain the size of these documents as small + as possible. + +*** Guidelines :noexport: + This should include: + + dataset reference and name + + origin and expected size of the data generated/collected + + data types and formats + + ** FAIR data and resources *** Making data findable - #+BEGIN_EXAMPLE -This should consider the dataset description: metadata, persistent -and unique identifiers e.g., DOI - #+END_EXAMPLE QuAcK is hosted on GitHub (https://github.com/pfloos/quack), with a mirror on the Git repository of the LCPQ @@ -103,17 +123,28 @@ and unique identifiers e.g., DOI (https://www.youtube.com/channel/UC3a7Yakg9gk36G3HKDIFaYw). Quantum Package has also a twitter account (=@quantum_package=). + All the notebooks will be versioned in the Git repository of the LCPQ + (https://git.irsamc.ups-tlse.fr), publicly accessible. + These documents will be archived on Figshare, and the DOIs will be + provided in publications. + + The LaTeX source files relative to reports, publications, + presentations and posters will be versioned in the Git repository + of the LCPQ, publicly accessible. + We plan to submit all the source codes involved in this project to the [[https://www.softwareheritage.org][Software Heritage]] archive. + A web site for the project will be created, centralizing all the + links to the archived data. Care will be taken to provide useful + metadata in the HTML headers to help the search engines reference + this web site. + +**** Guidelines :noexport: + This should consider the dataset description: metadata, persistent + and unique identifiers e.g., DOI + *** Making data openly accessible - #+BEGIN_EXAMPLE - * Which data will be made openly available and if some datasets remain closed, - the reasons for not giving access? - * Where the data and associated metadata, documentation and code are deposited - (which repository)? - * How the data can be accessed? Are relevant software tools/methods provided? - #+END_EXAMPLE QuAcK is released under the GPL v3 license. Quantum Package is released under the AGPL v3 license. @@ -125,12 +156,15 @@ and unique identifiers e.g., DOI The project doesn't require any part of the codes to be closed. -*** Making data interoperable - #+BEGIN_EXAMPLE - Which standard or field-specific data and metadata vocabularies - and methods will be used? - #+END_EXAMPLE +**** Guidelines :noexport: + * Which data will be made openly available and if some datasets remain closed, + the reasons for not giving access? + * Where the data and associated metadata, documentation and code are deposited + (which repository)? + * How the data can be accessed? Are relevant software tools/methods provided? + +*** Making data interoperable QuAcK operates internally with text files. Standard =xyz= format is used for atomic coordinates and =GAMESS/US= @@ -138,14 +172,12 @@ and unique identifiers e.g., DOI website (https://www.basissetexchange.org) provides data in this format. +**** Guidelines :noexport: + Which standard or field-specific data and metadata vocabularies + and methods will be used? + *** Increase data reuse - #+BEGIN_EXAMPLE - * What data will remain re-usable and for how long? - * Is embargo foreseen? - * How the data is licensed? - * Any data quality assurance procedures? - #+END_EXAMPLE Along the project, the code will be structured in independent inter-operating components to make easier the extraction of a @@ -155,15 +187,13 @@ and unique identifiers e.g., DOI functional in the main branch. Developments will be made in a secondary development branch. +**** Guidelines :noexport: + * What data will remain re-usable and for how long? + * Is embargo foreseen? + * How the data is licensed? + * Any data quality assurance procedures? *** Allocation of resources and data security - #+BEGIN_EXAMPLE - * Estimated costs for making the project data open access and potential value - of long-term data preservation. - * Procedures for data backup and recovery. - * Transfer of sensitive data and secure storage in repositories for long term - preservation and curation. - #+END_EXAMPLE The mirroring of the GitHub repository in the institute of the coordinator provides a backup. @@ -174,36 +204,14 @@ and unique identifiers e.g., DOI We also plan to upload the code in the Software Heritage digital archive. - - -** Quantum Package - -Quantum Package is an open-source quantum chemistry package for -performing selected configuration interaction calculations. It is -developed on three sites : Toulouse (LCPQ), Paris (LCT) and Argonne -(USA). - -The code is under the AGPL v3 license and is hosted on GitHub -(https://github.com/QuantumPackage/qp2), with a mirror on the Git -repository of the institute of the coordinator of the project -(https://git.irsamc.ups-tlse.fr/LCPQ/qp2). - -The latest version was uploaded on Zenodo -(doi:10.5281/zenodo.3677565), and the GitHub repository is set up to -automatically upload on Zenodo every new release. For each publication -requiring a modification of Quantum Package, a release will be made -and the zenodo DOI will be cited. - - -** Notebooks - -All along the project, Mathematica / Jupyter / Org-mode notebooks will -be produced. All this data will be versioned in the Git repository of -the LCPQ (https://git.irsamc.ups-tlse.fr), -publicly accessible. All the notebooks will be archived on Zenodo, and -the DOIs will be provided in publications. - -** Publications +**** Guidelines :noexport: + * Estimated costs for making the project data open access and potential value + of long-term data preservation. + * Procedures for data backup and recovery. + * Transfer of sensitive data and secure storage in repositories for long term + preservation and curation. + +