1. Name of the meeting, 20/06/2011 Background¶ The current scientific documentation of ORCHIDEE is : - incomplete, - inconsistent in its level of detail, - tri-lingual, - fragmented and - published in black, grey and white literature. Although considerable work has been done in the past: - it is difficult to benefit from this work, - unlikely to attract new ORCHIDEE and - unlikely to meet any traceability or reproducibility standards.

2. Name of the meeting, 20/06/2011 Aims - re-organise, - complete and - harmonize the scientific documentation of ORCHIDEE. Benefits - increase the readability of the source code, - archive the scientific basis of the model, - state-of-the-art searchable archive (html, pdf) and - ready to better tackle potential criticism on ORCHIDEE.

3. Name of the meeting, 20/06/2011 The rest of this presentation (1) Tier 1, Tier 2 and Tier 3 (2) Planning for the coming weeks (3) Objectives of the retreat (4) Examples & protocol

4. Name of the meeting, 20/06/2011 Tier 1, Tier 2 and Tier 3 - Tier 1: Collect the content (scientific documentation) in a quasi-harmonized format (collective effort – RoI = 2000% before and during the retreat) > documented source code. - Tier 2: Add basic dOxgen tags (selective effort during and after the retreat) > basic html and pdf (code-based). - Tier 3: Use advanced scripts based on dOxgen to extract and re-order documentation for html and pdf (selective effort during and after the retreat) > advanced html and pdf (process-based).

5. Name of the meeting, 20/06/2011 Planning 1/12/2011 to 19/1/2012 - Workload table and protocol (to be discussed – today) - Update the wiki (tomorrow) - Fabienne and Sebastiaan will visit/call/mail the persons responsible for (a) routine(s) to check whether the protocol and instructions are clear. - Strongly advise to start next week and make it a distributed effort in time. - Intermediate reminders will be send to the responsible persons. - Fabienne, Martial and Sebastiaan are stand-by to answer all questions.

6. Name of the meeting, 20/06/2011 Objectives of the retreat > 90% of the work should be done BEFORE the retreat (i.e. draft version of Tier 1) During the retreat we aim for: - Consultancy with N. Viovy, N. de Noblet, A. Ducharne & Jan Polcher (phone) to check and clarify hard bits (the remaining <10%) - Documenting overlooked subroutines - Reviewing each others documentation - Compiling Tier 2 documentation - Adding internal hyperlinks for in and output variables (Tier 3)

7. Name of the meeting, 20/06/2011 Examples & protocol