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a diagnostic to evaluate the turnover times of land ecosystem carbon #1395
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I put some comments with regards to the documentation. Will take a look at the code now.
esmvaltool/diag_scripts/land_carbon_cycle/diag_zonal_turnover.py
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Depending on the python version, "/" will give a float, even with two int args. This version uses "//" + casting to avoid that problem and reduces some redundancy.
- wrapped lines to less than 80 chars - added newline at end of file - removed trailing whitespace
…minor formatting of code
In this case the cmorizer script should be provided, so that everyone is able to generate the observational data for the recipe after retrieving the original data from the respective source. See here. |
This PR should also be in the final release, since it's part of one of the already accepted ESMValTool papers. There are however two issues to be solved:
@koir-su any chance you can solve these issues before the final release (end of July)? |
Hi Mattia, we have had several discussions on the observation. The cmorization of observation is not a straightforward one here, as the variable compared is not a standard observation but rather a derived variable that is very specific. On top of that, every figure needs a derivation of the observation at the spatial and regional scale. For example, the uncertainty ranges cannot be aggregated, as has been discussed elsewhere within ESMValTool. So, the scripts to prepare observation is not a cmorization script but a rather complicated collection of derivations that produces the data up to the standard needed in the ESMValTool. Moreover, the derived observation-based data are provided in 11 different resolutions so that the evaluators have enough flexibility. I have pushed the changes to the filenames, as you suggested. |
Regarding previous discussion on the observations, it took place here #1395 (comment) and here #1395 (comment) |
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Are these scripts available somewhere publicly? In the interest of transparency and reproducibility, it would be really good if these could be made available somewhere, along with instructions on how to obtain the original input data and how to use the scripts. |
Damn! I use 2.2.4, and it does not complain. Can you please send me the yml for your esmvaltool environment so that I can try to fix it within that... |
No, but I can add the programs as is to a git repo. The full data will not be available publicly for the reasons mentioned before. The uncertainty bounds are based on the full cube of all realizations from Carvalhais, which is not available for public use (outside my hands). |
https://github.com/ESMValGroup/ESMValTool/blob/master/environment.yml and I'm using
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@mattiarighi, I have fixed the issue with the matplotlib version. Can you give it another go? |
There is something wrong with the provenance:
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@mattiarighi Can you attach the log so we can see which diagnostic it is? This happens when |
Could you also attach /mnt/lustre02/work/bd0854/b309057/ESMValTool/v2_output/recipe_carvalhais14nat_20200727_153204/run/diag_land_carbon_turnover/global_turnover_time/diagnostic_provenance.yml? It looks like the problem is in |
Ok, so the problem is in the files related to the figure with caption |
Thanks, both. Apparently, the problem was due to having a list as ancestor_files. Needed dictionary. Strangely, was not a problem with the older version of ESMValTool. |
Thank you, it works now. @bouweandela please cherry-pick. |
Thank you all for such a thorough review. I can say that I learned a lot from this. 🍻 |
@mattiarighi Done
@koir-su It would be great if you could do this and add a link in the recipe documentation. Make sure to add Zenodo integration to the repository and then make a release, so they have a DOI. If you have no intention of changing the scripts, you could also directly upload them to Zenodo. |
…1395) * a diagnostic to evaluate the turnover times of land ecosystem carbon stock * minor updates of land carbon cycle (recipe_carvalhais2014) * minor edits in land_carbon_cycle(recipe_carvalhais2014) * fully running recipe_carvalhais2014 for CRESCENDO_land_carbon_cycle * changes in handling NorESM resolution data * Fix float division in plot tick placement Depending on the python version, "/" will give a float, even with two int args. This version uses "//" + casting to avoid that problem and reduces some redundancy. * fixing issues with full run * minor fixes in all diagnostic scripts * additional documentation and full run * test compatibility * Move shared code to shared module * Remove dot dict and reformat issues * Simplify recipe * Simplify configuration handling * Refactor zonal turnover calculation to use cubes * Improved documentation * Improved formatting of documentation (see below) - wrapped lines to less than 80 chars - added newline at end of file - removed trailing whitespace * Fix docstring bug * Unified zonal observation handling * handling obs res * update of recipe documentation, clean up of obsolete fig_config, and minor formatting of code * Fix recipe * Fix zonal turnover calculation * Minor formatting issues * Minor formatting issues * Remove left-overs * Minor fixes * Minor formatting * Formatted documentation * Fixed reference link * Fixed math formatting * Fix Obs4MIPs link in documentation * Removed `.. _user settings:` anchor * Corrected tag in recipe * Updated figures of documentation * update on documentation and figures * update on documentation and figures * minor formatting for CI tests * Cleanup * Add provenance information for diag_zonal_turnover * Cleanup * provenance information for diag_zonal_correlation * provenance of diag_global_turnover * cleanup * minor changes in figure titles and labels * incorporate comments from pull request review and update of figures * cleanup for circleci test * circleci test fix * additional codacy checks fix and provenance update * update documentation regarding preprocessed observation at different resolutions * bug fix in location of doc file * fix provenance handling * fix codacy issues * fix generic variable names * fixing and cleaning provenance logging * Fix provenance if no netcdf output is requested * renaming recipe filenames to the standard * Fix recipe name in index * Add a note on data availability * fixing matplotlib issue with global * fix provenance issue with ancestor files Co-authored-by: Sujan Koirala <b301040@mlogin102.hpc.dkrz.de> Co-authored-by: Sujan Koirala <b301040@mlogin108.hpc.dkrz.de> Co-authored-by: Sujan Koirala <b301040@mistralpp2.hpc.dkrz.de> Co-authored-by: Klaus Zimmermann <klaus.zimmermann@smhi.se> Co-authored-by: Sujan Koirala <b301040@mlogin100.hpc.dkrz.de> Co-authored-by: Sujan Koirala <b301040@mlogin105.hpc.dkrz.de> Co-authored-by: koir-su <b301040@mlogin103.hpc.dkrz.de> Co-authored-by: koir-su <b301040@mlogin104.hpc.dkrz.de> Co-authored-by: koir-su <b301040@mlogin101.hpc.dkrz.de> Co-authored-by: Bouwe Andela <b.andela@esciencecenter.nl> Co-authored-by: Mattia Righi <mattia.righi@dlr.de>
…stock
Before you start, read CONTRIBUTING.md and the guide for diagnostic developers.
Please discuss your idea with the development team before getting started, to avoid disappointment later. The way to do this is to open a new issue on GitHub. If you are planning to modify existing functionality, please discuss it with the original author(s) by tagging them in the issue.
Tasks
yamllint
to check that your YAML files do not contain mistakesNew recipe/diagnostic
doc/sphinx/source/recipes
folder and add a new entry to index.rstIf you need help with any of the tasks above, please do not hesitate to ask by commenting in the issue or pull request.
Closes #1393