Run executable from task dir

[SeanBryan51]

Currently, the CABLE executable is run from the current working directory instead of the task directory by using the absolute path to the executable. However, we should be running the executable from the task directory (otherwise CABLE will complain it cannot find the soil and PFT namelist files). This was a bug that was introduced in #99.

This change makes it so we change into the task directory before running the CABLE executable.

Fixes #123

[codecov]

Codecov Report

Merging #124 (b5c2169) into master (49da522) will decrease coverage by 0.02%.
Report is 1 commits behind head on master.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #124      +/-   ##
==========================================
- Coverage   88.46%   88.44%   -0.02%     
==========================================
  Files          26       27       +1     
  Lines        1387     1385       -2     
==========================================
- Hits         1227     1225       -2     
  Misses        160      160              

Files Changed	Coverage Δ
benchcab/repository.py	98.59% <100.00%> (-0.15%)	⬇️
benchcab/task.py	83.00% <100.00%> (ø)
benchcab/utils/os.py	100.00% <100.00%> (ø)
tests/test_task.py	100.00% <100.00%> (ø)

[SeanBryan51]

Integration tests

Test five site experiment:

#!/bin/bash
bench_example_dir='bench_example_test_five_site_experiment'
rm -rf $bench_example_dir
git clone git@github.com:CABLE-LSM/bench_example.git $bench_example_dir
cd $bench_example_dir
git reset --hard 6287539e96fc8ef36dc578201fbf9847314147fb
sed -i 's/project:.*/project: tm70/g' config.yaml
sed -i 's/experiment:.*/experiment: five-site-test/g' config.yaml
sed -i 's/ccc561\/v3.0-YP-changes/sb8430\/test-branch/g' config.yaml
benchcab run -v

CABLE standard output:

 THE NAME LIST IS cable.nml
 Use spatially-specific soil properties;          360         150
           0
           0
 When choosing spatially-specific soil properties,
 snow-free albedo is also overwritten by this data set.
 Reading CABLE_PFTPARM namelist...
 Reading CABLE_SOILPARM namelist...
 Total number of patches (countPatch):            1
 iveg           1           2
 patchfrac           1   1.000000    
  Could neither find restart file ./
  nor ./
  Pre-loaded default initialisations are used.
 Reading CABLE_PFTPARM namelist...
 Reading CABLE_SOILPARM namelist...
 
 time-space-averaged energy & water balances
 Ebal_tot[Wm-2], Wbal_tot[mm per timestep]  9.5453368E-07 -7.0809359E-03
 time-space-averaged latent heat and net photosynthesis
 sum_fe[Wm-2], sum_fpn[umol/m2/s]   61.4036706086355     
 -8.074845742925115E-005
 
 NB. Offline-serial runs spinup cycles:           1
 Internal check shows in this version new_sumbal != trunk sumbal
 Writing new_sumbal to the file:new_sumbal
 setting SPINON -> FALSE           0           1
 Finished.    80.06340      seconds needed for year
 Finished.    80.07153      seconds needed for       140256  hours

[ccarouge]

I have a small question but I'm happy for this to go in either way.

[ccarouge]

I'm suddenly wondering if exe_path and nml_path really need to exist? Could this assert be: assert f"./{internal.CABLE_EXE} {internal.CABLE_nml} in mock_subprocess.commands and remove the definition of exe_path and nml_path.

That's a detail, I'm happy to put things in as is. Just mentioning it as I like things as simple as possible when we think of it.