wiki:GroupActivities/CodeAvalaibilityPublication

Version 19 (modified by luyssaert, 9 months ago) (diff)

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Code availability associated to a publication

To answer the GMD editors' demands for a standard procedure for all submissions, the orchidee-project group has taken the following decisions.

  • A branch named "publications" is created where each publication has an associated directory containing the ORCHIDEE code used in the publication. See here https://forge.ipsl.jussieu.fr/orchidee/browser/branches/publications
  • On the bottom of this page (the one you're reading now), you should manually add a link towards a specific page that is related to the publication. This page should include:
    • the link to the code,
    • the explanation on how to download it,
    • a short description of the model.
    • This specific page will be sent to IPSL, to ask for a doi.
  • Prior to submission the manuscript should be uploaded to https://sharebox.lsce.ipsl.fr/index.php/s/AhJk0Bk6rdySXKL and a mail should be send to the orchidee-project group to inform the group about this manuscript (standard demand from the Fair Use Policy). The orchidee-project group centralizes the doi demands.

How to create a new version in publications

Use following to copy revision X of version YYY into publications/ORCHIDEE_ZZZ:

svn cp -r X svn://forge.ipsl.jussieu.fr/orchidee/YYY svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_ZZZ

where YYY can be branches/... or trunk/ORCHIDEE. For example:

svn cp -r 4513 svn://forge.ipsl.jussieu.fr/orchidee/branches/ORCHIDEE-ROUTING/ORCHIDEE svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_gmd-2018-57

How to extract a version from publications

All versions copied into publications folder can be extracted with username anonymous with passwd anonymous. For example:

> svn co --username anonymous svn://forge.ipsl.jussieu.fr/orchidee/branches/publications/ORCHIDEE_gmd-2018-57 ORCHIDEE
Domaine d'authentification : <svn://forge.ipsl.jussieu.fr:3690> f489ceea-5127-0410-b15c-c4a6149ed9a7
Mot de passe pour 'anonymous' : 

answer anonymous.

Versions copied to publications

  • ORCHIDEE_gmd-2018-261: copy of revision 4999 of the branch ORCHIDEE-CN used in "Accounting for Carbon and Nitrogen interactions in the Global Terrestrial Ecosystem Model ORCHIDEE (rev 4999): multi-scale evaluation of gross primary production" by Nicolas Vuichard, Palmira Messina, Sebastiaan Luyssaert, Bertrand Guenet, Sönke Zaehle, Josefine Ghattas, Vladislav Bastrikov, Philippe Peylin
  • ORCHIDEE_gmd-2018-182: copy of revision 1311 of the Trunk used in "A generic pixel-to-point comparison for simulated large-scale ecosystem properties and ground-based observations: an example from the Amazon region" by Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley Christoffersen, Phillipe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith, Matthieu Guimberteau, Andreas Huth, Michelle Johnson, Bart Krujit, Fanny Langerwisch, Patrick Meir, Phillip Papastefanou, Gilvan Sampaio, Kirsten Thonicke, Celso von Randow, Christian Zang, and Edna Rödig
  • ORCHIDEE-CN-P_grl_2018GL077736: copy of revision 4630 of branch ORCHIDEE-CN-P used in publication "Low phosphorus availability decreases susceptibility of tropical primary productivity to droughts" by Daniel S. GOLL, Emilie JOETZJER, Mengtian HUANG, and Philippe CIAIS (in revision)
  • ORCHIDEE_CAN_r2290: copy of revision 2290 of the ORCHIDEE-CAN branch used in "A vertically discretised canopy description for ORCHIDEE (SVN r2290) and the modifications to the energy, water and carbon fluxes" by K. Naudts, J. Ryder, M. J. McGrath, J. Otto, Y. Chen, A. Valade, V. Bellasen, G. Berhongaray, G. Bönisch, M. Campioli, J. Ghattas, T. De Groote, V. Haverd, J. Kattge, N. MacBean, F. Maignan, P. Merilä, J. Penuelas, P. Peylin, B. Pinty, H. Pretzsch, E. D. Schulze, D. Solyga, N. Vuichard, Y. Yan, and S. Luyssaert. Geosci. Model Dev., 8, 2035–2065, 2015. doi:10.5194/gmd-8-2035-2015
  • ORCHIDEE_CAN_r3069: copy of revision 3069 of the ORCHIDEE-CAN branch used in "Tradeoffs in using European forests to meet climate objectives" by Sebastiaan Luyssaert, Guillaume Marie, Aude Valade, Yi-Ying Chen, Sylvestre Njakou Djomo, James Ryder, Juliane Otto, Kim Naudts, Anne Sofie Lansø, Josefine Ghattas, and Matthew J. McGrath
  • ORCHIDEE_CN_CAN_r5698: copy of revision 5698 of the ORCHIDEE-CN-CAN branch used in "Using the International Tree-Ring Data Bank (ITRDB) records as century-long benchmarks for land-surface models" by Jina Jeong, Jonathan Barichivich, Philippe Peylin, Vanessa Haverd, Matthew J. McGrath, Nicolas Vuichard, Mike Evans, and Sebastiaan Luyssaert (to be submitted)