smallbaselineApp.cfg not updated for --start reference_point option

[falkamelung]

I have modified the mintpy.reference.lalo option in my *template file and would expect that smallbaselineApp.py uses it. However, when I run smallbaselineApp.py $TE/PopocatepetlSenDT5.template --dir mintpy --start reference_point it does not update the smallbaselineApp.cfg file as you can see below. Is that a bug?

******************** step - reference_point ********************

generate_mask.py /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/inputs/ifgramStack.h5 --nonzero -o /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/maskConnComp.h5 --update
input ifgramStack file: /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/inputs/ifgramStack.h5
--------------------------------------------------
update mode: ON
1) output file /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/maskConnComp.h5 already exists.
2) output file is newer than input dataset: connectComponent.
run or skip: skip.

temporal_average.py /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/inputs/ifgramStack.h5 --dataset coherence -o /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/avgSpatialCoh.h5 --update
output file: /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/avgSpatialCoh.h5
--------------------------------------------------
update mode: ON
1) output file /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/avgSpatialCoh.h5 already exists.
2) output file is newer than input dataset: coherence.
run or skip: skip.

reference_point.py /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/inputs/ifgramStack.h5 -t /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/smallbaselineApp.cfg -c /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/avgSpatialCoh.h5 --lookup /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/inputs/geometryRadar.h5
--------------------------------------------------
reading reference info from template: /scratch1/05861/tg851601/PopocatepetlSenDT5/mintpy/smallbaselineApp.cfg
input reference point in lat/lon: (19.07, -98.672)
input reference point in y/x: (567, 543)
mask: maskConnComp.h5
Traceback (most recent call last):
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/smallbaselineApp.py", line 1288, in <module>
    main(sys.argv[1:])
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/smallbaselineApp.py", line 1270, in main
    app.run(steps=inps.runSteps)
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/smallbaselineApp.py", line 1041, in run
    self.run_reference_point(sname)
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/smallbaselineApp.py", line 481, in run_reference_point
    mintpy.reference_point.main(iargs)
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/reference_point.py", line 488, in main
    inps = read_reference_input(inps)
  File "/work2/05861/tg851601/stampede2/codet/rsmas_insar/sources/MintPy/mintpy/reference_point.py", line 447, in read_reference_input
    raise ValueError(msg)
ValueError: input reference point is in masked OUT area defined by maskConnComp.h5!

grep reference.lalo mintpy/smallbaselineApp.cfg  /work2/05861/tg851601/stampede2/insarlab/infiles/famelung/TEMPLATES/PopocatepetlSenDT5.template 
mintpy/smallbaselineApp.cfg:mintpy.reference.lalo          = 19.07,-98.672   #[31.8,130.8 / auto]

grep reference.lalo /work2/05861/tg851601/stampede2/insarlab/infiles/famelung/TEMPLATES/PopocatepetlSenDT5.template 
#mintpy.reference.lalo               = 19.071,-98.670                                                                                  
#mintpy.reference.lalo               = 19.0695,-98.6672                                                                                  
#mintpy.reference.lalo               = 19.07,-98.672