# Command lines for test_run_matches_the_pk_binary: each runs through phytkit.run and the
# pk binary, and the results must match. Paths are relative to the rust/ folder.

describe
describe fvcb
describe fvcbC4
describe empiricalA
describe raats
describe lightResponse
describe nope
fit --help
li600 estimate --help
--help

fit photosynthesis examples/aci.csv --model fvcb --set gm=1000000 --fix gm,alphaG
fit photosynthesis examples/aci.csv --model fvcb --predicted
fit photosynthesis examples/aci.csv --model fvcbC4
fit photosynthesis examples/aci.csv --model empiricalA
fit photosynthesis examples/aci.csv --model fvcb --no-constraint ap_nonneg --weight vj_ratio=0.5
fit photosynthesis examples/aci.csv --model fvcb --constraints none --fix gm,alphaG
fit photosynthesis examples/aci.csv --model fvcb --set gm=1000000 --fix gm,alphaG --survey examples/survey.csv --stat median
fit photosynthesis examples/aci.csv --model fvcb --group-by CurveID --format csv
fit photosynthesis examples/aci.csv examples/messy_aci.csv --model empiricalA
fit photosynthesis examples/aci.csv --model fvcb --fit nope
fit stomatal examples/bta.csv
fit stomatal examples/medlyn.csv --model medlyn --predicted
fit hydraulics examples/pv.csv --model pvcurve --group-by Leaf
fit hydraulics examples/pv.csv --model pvcurve --group-by Leaf --format csv
fit hydraulics examples/vulnerability.csv --group-by stem
fit hydraulics examples/vulnerability_k.csv
fit soil examples/soil.csv --group-by sample --units kPa
fit soil examples/soil.csv --group-by sample --units kPa --model raats
fit soil examples/soil.csv --group-by sample --units kPa --model brooksCorey
fit soil examples/soil.csv --group-by sample --units kPa --model fractalSWRC
fit soil examples/soil.csv --group-by sample --units kPa --model modifiedVanGenuchten
li600 correct examples/li600.csv --rows
li600 correct examples/li600.csv --sidedness 2 --format csv
li600 estimate examples/li600.csv --set Vcmax25=90 --set Jmax25=170 --rows
li600 estimate examples/li600.csv --model fvcbC4 --format csv
li600 estimate examples/li600.csv --model empiricalA --set Amax25=30 --ca 400 --absorptance 0.9 --min-gsw 0.01
concat examples/aci.csv examples/messy_aci.csv
concat examples/aci.csv examples/messy_aci.csv --format json

# Errors: each should give the same code, message, hint and help in both.
li600 correct examples/li600.csv --sidednes 2
li600 correct examples/li600.csv -rows
li600 correct examples/li600.csv extra.csv
li600 correct examples/li600.csv --sidedness
li600 correct examples/li600.csv --format xml
li600 correct missing.csv
li600 correct examples
li600 correct examples/aci.csv
li600 correct
li600 corect examples/li600.csv
li600
li600 estimate examples/li600.csv --ca -10
li600 estimate examples/li600.csv --model c4
li600 estimate examples/li600.csv --set Vcmax=90
fitt photosynthesis examples/aci.csv
fit photosynthsis examples/aci.csv
fit fvcb examples/aci.csv
fit examples/aci.csv
fit photosynthesis examples/aci.csv --modle fvcb
fit photosynthesis examples/aci.csv --rows
fit photosynthesis examples/aci.csv --model medlyn
fit photosynthesis examples/aci.csv --model fvcb --model empiricalA
fit photosynthesis examples/aci.csv --max-iter 2.5
fit photosynthesis examples/aci.csv --no-constraint ap_nonneg_x
fit photosynthesis examples/aci.csv --ref-ci 300
fit soil examples/aci.csv
fit stomatal examples/bta.csv --units kPa
describe fvcb extra
concat
