errors & improvements in CLM-FATES tutorials - Githubissues

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A collection of Galaxy-related training material

https://training.galaxyproject.org

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errors & improvements in CLM-FATES tutorials #2099

Closed annefou closed 3 years ago

annefou commented 3 years ago

Fates Tutorials were used during a 2 day workshop EOSC-Life & EOSC-Nordic.

Feedback from "Online Galaxy Training on Functionally Assembled Terrestrial Ecosystem Simulator (FATES)":

CLM-FATES Galaxy tool Hands-on:

Add requirement on Extracting workflows from histories
Step-6 is unclear; learners need more explanations on how to customize their workflows.

CLM-FATES in Galaxy Climate JupyterLab:

lots of typos to be corrected

For instance:

Check your run (case name is wrong):

%%bash
cd $HOME/work/fates_alp1
ls -la

plotting (as we have only one month there is no time axis. Maybe we could run 3 or 6 months so we get more meangful outputs

Filename is wrong (remove _t).

import os
import xarray as xr
xr.set_options(display_style="html")
%matplotlib inline

case = 'fates_alp1'
path = os.path.join(os.getenv('HOME'), 'archive', case, 'lnd', 'hist')
dset = xr.open_dataset(path + '/fates_alp1.clm2.h0.2000-01.nc')
dset

Plotting `CANOPY_AREA_BY_AGE' is wrong too. (except if we run 3-6 months otherwise, one needs to remove col_wrap:

dset['CANOPY_AREA_BY_AGE'].plot(aspect=3, size=6)

annefou commented 3 years ago

Still broken (FATES with JupyterLab) in Hands-on: check your simulation:

As we now run 6 months, we should read all the files for analyzing the results and not the first one only e.g. replace:
```
dset = xr.open_dataset(path + '/fates_alp1.clm2.h0.2000-01.nc')
```

by

dset = xr.open_mfdataset(path + '/*.nc', combine='by_coords')