Eric R. Scott

`model2netcdf.ED2()` output isn't grouped by PFT

2

### Bug Description The .nc files resulting from conversion from ED2 output have variables that could be split up by PFT but aren't. For example NPP in the .nc file...

`download.MERRA()` doesn't fully respect overwrite arg

1

### Bug Description When `do_conversions(settings, overwrite.met = FALSE)` is run, files get overwritten. The `overwrite.met` arg isn't used to determine whether to write a .nc file in the following lines:...

### Bug Description `runModule.run.write.configs(settings)` appears to attempt to copy the files in `settings$outdir`/run/ to `settings$host$rundir`. This is currently failing for me (not sure why), but it doesn't seem to matter...

HPC jobs get checked too often

3

### Bug Description `qsub_run_finished()` has no delay so it checks if remote jobs are done about every 30s. This floods the console and probably annoys the HPC people. The delay...

## Description Now that pecanproject.r-universe.dev exists, it *should* be easier to run `devtools::check()` locally. For `devtools` to install all the dependencies of a particular package it just needs to know...

`PEcAn.utils::mstmipvar()` condition has length > 1 error

2

https://github.com/PecanProject/pecan/blob/fbfcd2f26e4bad20cff9009da49e04ad85c05314/base/utils/R/utils.R#L38 Should this line be `is.null()` instead of `is.na()`? When this gets called by `model2netcdf.ED2()`, `time` is a complex nested list. This results in a warning in older versions of...

Don't use `testthat` inside of functions

2

### Bug Description The `testthat` package is made for unit testing, not use inside of functions. `testhat` functions appear in at least a couple of places: - `check_ed_metheader()` - `check_ed_metfile()`...

`model2netcdf.ED2()` only converts data for first PFT

7

### Bug Description I open one of the .h5 files output by ED2 and confirm that there are multiple PFTs listed, then run `model2netcdf.ED2()` where `pfts = settings$pfts`, and the...

`run.write.configs()` fails without error

3

### Bug Description Still don't understand how to reproduce this, but I know where the bug is happening: https://github.com/PecanProject/pecan/blob/fbfcd2f26e4bad20cff9009da49e04ad85c05314/base/workflow/R/run.write.configs.R#L45 The result of this line is sometimes a 0x0 tibble (again,...

<bety><write> tag not respected by `get.trait.data()`

6

### Bug Description `get.trait.data()` seems to write to BETY (not in documentation), but it doesn't seem to check for `settings$database$bety$write`. ### To Reproduce run PEcAn workflow with `settings$database$bety$write