rbeyer / kalasiris

A Python library to wrap functions and functionality for the Integrated Software for Imagers and Spectrometers (ISIS).
https://kalasiris.readthedocs.io
BSD 3-Clause "New" or "Revised" License
9 stars 5 forks source link

When using a build version of ISIS3, apps are not discovered correctly #3

Closed jessemapel closed 5 years ago

jessemapel commented 5 years ago

Description

I was trying to run the tests locally and it didn't have the apps even though they were built and executable in my ISIS build.

What I Did

Checking what apps kalasiris found

(kalasiris) igswzawglt1183:kalasiris jmapel$ python
Python 3.7.2 (default, Dec 29 2018, 00:00:04) 
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import kalasiris
>>> dir(kalasiris)
['Histogram', 'Path', '__author__', '__builtins__', '__cached__', '__doc__', '__email__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', '__version__', 'clem2isis', 'cubenormDialect', 'dsk2isis', 'environ', 'getkey_k', 'hi2isis_k', 'hist_k', 'isis', 'k_funcs', 'kalasiris', 'os', 'p', 'param_fmt', 'pixel2map', 'subprocess', 'sys', 'tempfile']

My ISIS build

(kalasiris) igswzawglt1183:kalasiris jmapel$ ls /Users/jmapel/ISIS3/build/bin/
algebra        ckwriter   cubefunc       gllssi2isis   ifft        map2cam    mode        remrx          tabledump
amica2isis     clem2isis      cubeit         gllssical     interestcube    map2map    mosrange    rgb2hsv        tgocassis2isis
amicacal       clemhirescal   cubenorm       gradient      ipce        mapgrid    mrf2isis    ringsautomos       tgocassismos
apollo2isis    clemnircal     dawnfc2isis        greyscale     isis2ascii      maplab     mrf2pds     ringscam2map       tgocassisrdrgen
apollocal      clemnirclean   dawnvir2isis       grid      isis2fits       mapmos     mroctx2isis     ringsmappt         tgocassisstitch
apollofindrx       clemnirnoise   ddd2isis       handmos       isis2gml    mappt      msi2isis    ringspt        tgocassisunstitch
apollopaninit      clemuvviscal   decorstretch       hi2isis       isis2pds    mapsize    mvic2isis   rolo2isis      thm2isis
apollopanstitcher  cnet2dem   deltack        hical     isis2raw    maptemplate    mvstats     rososiris2isis     thmbasemap1
apolloremrx    cnet2mat   dempack        hicalbeta     isis2std    maptrim    nirs2isis   rosvirtis2isis     thmdriftcor
apollowarp     cnetadd    demprep        hicalproc     isiscomplete    mar102isis     nocam2map   rotate         thmnoseam
appjit         cnetbin2pvl    deriv          hiccdstitch   isisminer       mar10cal   noisefilter     seedgrid       thmproc
ascii2isis     cnetcheck      desmear        hicolormos    isisui      mar10clean     noproj      segment        thmvisflat
automos        cnetcombinept  desmile        hicrop    jigsaw      mar10nonoise   noseam      shade          thmvistrim
autoregtemplate    cnetdiff   divfilter      hicubeit      junocam2isis    mar10restore   ocams2isis      shadow         tonematch
autoseed       cnetedit   dsk2isis       hicubenorm    kaguyami2isis   marci2isis     outline     shadowtau      trackextract
bandnorm       cneteditor     dstripe        hideal2pds    kaguyasp2ascii  marcical   overlapstats    sharpen        translate
bandtrim       cnetextract    editlab        hidestripe    kaguyasp2isis   marciflip      pad         sigmastretch       trim
barscale       cnethist   edrget         hidtmgen      kaguyatc2isis   mask       pca         skymap         trimfilter
bit2bit        cnetmerge      enlarge        hiequal       kerneldbgen     mat2cnet   pds2hideal      skypt          uncrop
blend          cnetnewradii   equalizer      hifringe      kernfilter      mdis2isis      pds2isis    skyrange       vdcomp
blobdump       cnetpvl2bin    errors         hifurrows     kuwahara    mdis2pds   percent     slither        vicar2isis
butterworth    cnetref    explode        highpass      leisa2isis      mdiscal    phocube     slpmap         vik2isis
cam2cam        cnetsplit      fakecube       higlob    lineeq      mdisddr    phoempglobal    smtk           vikcal
cam2map        cnetstats      fft            hijitreg      lo2isis     mdisedrinfo    phoemplocal     socetframesettings     vikclean
camcoeffs      cnettable      fillgap        hijitter      lopdsgen    mdisproc   phohillier      socetlinescankeywords  vikfixtrx
camdev         cnetthinner    findfeatures       himos     lorri2isis      median     photemplate     specadd        viknobutter
caminfo        cnetwinnow     findgaps       hinoise       lowpass     mer2isis   photomet    specdivfilter      viknonoodle
campt          copylabel      findimageoverlaps  hirdr2isis    lromakeflat     messckgen      photrim     spechighpass       viknopepper
camrange       coreg      findrx         hirdrgen      lronac2isis     messspkgen     pixel2map   speclowpass        viknosalt
camstats       cosi       fits2isis      hisharpen     lronac2pds      mical      pointreg    specpix        vims2isis
camtest        crism2isis     flip           hist      lronaccal       mimap2isis     poly        spicefit       vimscal
camtrim        crop       footprintinit      histat    lronacecho      minmax     prtloganalyzer  spiceinit      voy2isis
cathist        cropspecial    footprintmerge     histeq    lronacpho       mirror     pvldiff     spiceserver        voycal
catlab         csspckgen      fplanemap      histitch      lrowac2isis     moc2isis   qmos        spkwriter      voyramp
catoriglab     csv2table      fx             histmatch     lrowac2pds      moccal     qnet        stats          warp
center         ctxcal     gauss          hrsc2isis     lrowaccal       mocevenodd     qtie        std2isis       xml
chan1m32isis       ctxevenodd     gaussstretch       hsv2rgb       lrowacpho       mocgap     qview       stretch
circle         cubeatt    getkey         hyb1pds4gen   m3loc2net       mocnoise50     ratio       sumspice
ciss2isis      cubeavg    getsn          hyb2onc2isis  makecube    mocproc    raw2isis    svfilter
cisscal        cubediff   gllnims2isis       hyb2onccal    makeflat    mocuncompress  reduce      table2cube

The xml directory

(kalasiris) igswzawglt1183:kalasiris jmapel$ ls /Users/jmapel/ISIS3/build/bin/xml/*.xml
/Users/jmapel/ISIS3/build/bin/xml/algebra.xml        /Users/jmapel/ISIS3/build/bin/xml/kerneldbgen.xml
/Users/jmapel/ISIS3/build/bin/xml/amica2isis.xml     /Users/jmapel/ISIS3/build/bin/xml/kernfilter.xml
/Users/jmapel/ISIS3/build/bin/xml/amicacal.xml       /Users/jmapel/ISIS3/build/bin/xml/kuwahara.xml
/Users/jmapel/ISIS3/build/bin/xml/apollo2isis.xml    /Users/jmapel/ISIS3/build/bin/xml/leisa2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/apollocal.xml      /Users/jmapel/ISIS3/build/bin/xml/lineeq.xml
/Users/jmapel/ISIS3/build/bin/xml/apollofindrx.xml   /Users/jmapel/ISIS3/build/bin/xml/lo2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/apollopaninit.xml  /Users/jmapel/ISIS3/build/bin/xml/lopdsgen.xml
/Users/jmapel/ISIS3/build/bin/xml/apollopanstitcher.xml  /Users/jmapel/ISIS3/build/bin/xml/lorri2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/apolloremrx.xml    /Users/jmapel/ISIS3/build/bin/xml/lowpass.xml
/Users/jmapel/ISIS3/build/bin/xml/apollowarp.xml     /Users/jmapel/ISIS3/build/bin/xml/lromakeflat.xml
/Users/jmapel/ISIS3/build/bin/xml/appjit.xml         /Users/jmapel/ISIS3/build/bin/xml/lronac2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/ascii2isis.xml     /Users/jmapel/ISIS3/build/bin/xml/lronac2pds.xml
/Users/jmapel/ISIS3/build/bin/xml/automos.xml        /Users/jmapel/ISIS3/build/bin/xml/lronaccal.xml
/Users/jmapel/ISIS3/build/bin/xml/autoregtemplate.xml    /Users/jmapel/ISIS3/build/bin/xml/lronacecho.xml
/Users/jmapel/ISIS3/build/bin/xml/autoseed.xml       /Users/jmapel/ISIS3/build/bin/xml/lronacpho.xml
/Users/jmapel/ISIS3/build/bin/xml/bandnorm.xml       /Users/jmapel/ISIS3/build/bin/xml/lrowac2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/bandtrim.xml       /Users/jmapel/ISIS3/build/bin/xml/lrowac2pds.xml
/Users/jmapel/ISIS3/build/bin/xml/barscale.xml       /Users/jmapel/ISIS3/build/bin/xml/lrowaccal.xml
/Users/jmapel/ISIS3/build/bin/xml/bit2bit.xml        /Users/jmapel/ISIS3/build/bin/xml/lrowacpho.xml
/Users/jmapel/ISIS3/build/bin/xml/blend.xml      /Users/jmapel/ISIS3/build/bin/xml/m3loc2net.xml
/Users/jmapel/ISIS3/build/bin/xml/blobdump.xml       /Users/jmapel/ISIS3/build/bin/xml/makecube.xml
/Users/jmapel/ISIS3/build/bin/xml/butterworth.xml    /Users/jmapel/ISIS3/build/bin/xml/makeflat.xml
/Users/jmapel/ISIS3/build/bin/xml/cam2cam.xml        /Users/jmapel/ISIS3/build/bin/xml/map2cam.xml
/Users/jmapel/ISIS3/build/bin/xml/cam2map.xml        /Users/jmapel/ISIS3/build/bin/xml/map2map.xml
/Users/jmapel/ISIS3/build/bin/xml/camcoeffs.xml      /Users/jmapel/ISIS3/build/bin/xml/mapgrid.xml
/Users/jmapel/ISIS3/build/bin/xml/camdev.xml         /Users/jmapel/ISIS3/build/bin/xml/maplab.xml
/Users/jmapel/ISIS3/build/bin/xml/caminfo.xml        /Users/jmapel/ISIS3/build/bin/xml/mapmos.xml
/Users/jmapel/ISIS3/build/bin/xml/campt.xml      /Users/jmapel/ISIS3/build/bin/xml/mappt.xml
/Users/jmapel/ISIS3/build/bin/xml/camrange.xml       /Users/jmapel/ISIS3/build/bin/xml/mapsize.xml
/Users/jmapel/ISIS3/build/bin/xml/camstats.xml       /Users/jmapel/ISIS3/build/bin/xml/maptemplate.xml
/Users/jmapel/ISIS3/build/bin/xml/camtest.xml        /Users/jmapel/ISIS3/build/bin/xml/maptrim.xml
/Users/jmapel/ISIS3/build/bin/xml/camtrim.xml        /Users/jmapel/ISIS3/build/bin/xml/mar102isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cathist.xml        /Users/jmapel/ISIS3/build/bin/xml/mar10cal.xml
/Users/jmapel/ISIS3/build/bin/xml/catlab.xml         /Users/jmapel/ISIS3/build/bin/xml/mar10clean.xml
/Users/jmapel/ISIS3/build/bin/xml/catoriglab.xml     /Users/jmapel/ISIS3/build/bin/xml/mar10nonoise.xml
/Users/jmapel/ISIS3/build/bin/xml/center.xml         /Users/jmapel/ISIS3/build/bin/xml/mar10restore.xml
/Users/jmapel/ISIS3/build/bin/xml/chan1m32isis.xml   /Users/jmapel/ISIS3/build/bin/xml/marci2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/circle.xml         /Users/jmapel/ISIS3/build/bin/xml/marcical.xml
/Users/jmapel/ISIS3/build/bin/xml/ciss2isis.xml      /Users/jmapel/ISIS3/build/bin/xml/marciflip.xml
/Users/jmapel/ISIS3/build/bin/xml/cisscal.xml        /Users/jmapel/ISIS3/build/bin/xml/mask.xml
/Users/jmapel/ISIS3/build/bin/xml/ckwriter.xml       /Users/jmapel/ISIS3/build/bin/xml/mat2cnet.xml
/Users/jmapel/ISIS3/build/bin/xml/clem2isis.xml      /Users/jmapel/ISIS3/build/bin/xml/mdis2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/clemhirescal.xml   /Users/jmapel/ISIS3/build/bin/xml/mdis2pds.xml
/Users/jmapel/ISIS3/build/bin/xml/clemnircal.xml     /Users/jmapel/ISIS3/build/bin/xml/mdiscal.xml
/Users/jmapel/ISIS3/build/bin/xml/clemnirclean.xml   /Users/jmapel/ISIS3/build/bin/xml/mdisddr.xml
/Users/jmapel/ISIS3/build/bin/xml/clemnirnoise.xml   /Users/jmapel/ISIS3/build/bin/xml/mdisedrinfo.xml
/Users/jmapel/ISIS3/build/bin/xml/clemuvviscal.xml   /Users/jmapel/ISIS3/build/bin/xml/mdisproc.xml
/Users/jmapel/ISIS3/build/bin/xml/cnet2dem.xml       /Users/jmapel/ISIS3/build/bin/xml/median.xml
/Users/jmapel/ISIS3/build/bin/xml/cnet2mat.xml       /Users/jmapel/ISIS3/build/bin/xml/mer2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetadd.xml        /Users/jmapel/ISIS3/build/bin/xml/messckgen.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetbin2pvl.xml    /Users/jmapel/ISIS3/build/bin/xml/messspkgen.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetcheck.xml      /Users/jmapel/ISIS3/build/bin/xml/mical.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetcombinept.xml  /Users/jmapel/ISIS3/build/bin/xml/mimap2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetdiff.xml       /Users/jmapel/ISIS3/build/bin/xml/minmax.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetedit.xml       /Users/jmapel/ISIS3/build/bin/xml/mirror.xml
/Users/jmapel/ISIS3/build/bin/xml/cneteditor.xml     /Users/jmapel/ISIS3/build/bin/xml/moc2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetextract.xml    /Users/jmapel/ISIS3/build/bin/xml/moccal.xml
/Users/jmapel/ISIS3/build/bin/xml/cnethist.xml       /Users/jmapel/ISIS3/build/bin/xml/mocevenodd.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetmerge.xml      /Users/jmapel/ISIS3/build/bin/xml/mocgap.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetnewradii.xml   /Users/jmapel/ISIS3/build/bin/xml/mocnoise50.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetpvl2bin.xml    /Users/jmapel/ISIS3/build/bin/xml/mocproc.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetref.xml        /Users/jmapel/ISIS3/build/bin/xml/mocuncompress.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetsplit.xml      /Users/jmapel/ISIS3/build/bin/xml/mode.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetstats.xml      /Users/jmapel/ISIS3/build/bin/xml/mosrange.xml
/Users/jmapel/ISIS3/build/bin/xml/cnettable.xml      /Users/jmapel/ISIS3/build/bin/xml/mrf2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetthinner.xml    /Users/jmapel/ISIS3/build/bin/xml/mrf2pds.xml
/Users/jmapel/ISIS3/build/bin/xml/cnetwinnow.xml     /Users/jmapel/ISIS3/build/bin/xml/mroctx2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/copylabel.xml      /Users/jmapel/ISIS3/build/bin/xml/msi2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/coreg.xml      /Users/jmapel/ISIS3/build/bin/xml/mvic2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cosi.xml       /Users/jmapel/ISIS3/build/bin/xml/mvstats.xml
/Users/jmapel/ISIS3/build/bin/xml/crism2isis.xml     /Users/jmapel/ISIS3/build/bin/xml/nirs2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/crop.xml       /Users/jmapel/ISIS3/build/bin/xml/nocam2map.xml
/Users/jmapel/ISIS3/build/bin/xml/cropspecial.xml    /Users/jmapel/ISIS3/build/bin/xml/noisefilter.xml
/Users/jmapel/ISIS3/build/bin/xml/csspckgen.xml      /Users/jmapel/ISIS3/build/bin/xml/noproj.xml
/Users/jmapel/ISIS3/build/bin/xml/csv2table.xml      /Users/jmapel/ISIS3/build/bin/xml/noseam.xml
/Users/jmapel/ISIS3/build/bin/xml/ctxcal.xml         /Users/jmapel/ISIS3/build/bin/xml/ocams2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/ctxevenodd.xml     /Users/jmapel/ISIS3/build/bin/xml/outline.xml
/Users/jmapel/ISIS3/build/bin/xml/cubeatt.xml        /Users/jmapel/ISIS3/build/bin/xml/overlapstats.xml
/Users/jmapel/ISIS3/build/bin/xml/cubeavg.xml        /Users/jmapel/ISIS3/build/bin/xml/pad.xml
/Users/jmapel/ISIS3/build/bin/xml/cubediff.xml       /Users/jmapel/ISIS3/build/bin/xml/pca.xml
/Users/jmapel/ISIS3/build/bin/xml/cubefunc.xml       /Users/jmapel/ISIS3/build/bin/xml/pds2hideal.xml
/Users/jmapel/ISIS3/build/bin/xml/cubeit.xml         /Users/jmapel/ISIS3/build/bin/xml/pds2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/cubenorm.xml       /Users/jmapel/ISIS3/build/bin/xml/percent.xml
/Users/jmapel/ISIS3/build/bin/xml/dawnfc2isis.xml    /Users/jmapel/ISIS3/build/bin/xml/phocube.xml
/Users/jmapel/ISIS3/build/bin/xml/dawnvir2isis.xml   /Users/jmapel/ISIS3/build/bin/xml/phoempglobal.xml
/Users/jmapel/ISIS3/build/bin/xml/ddd2isis.xml       /Users/jmapel/ISIS3/build/bin/xml/phoemplocal.xml
/Users/jmapel/ISIS3/build/bin/xml/decorstretch.xml   /Users/jmapel/ISIS3/build/bin/xml/phohillier.xml
/Users/jmapel/ISIS3/build/bin/xml/deltack.xml        /Users/jmapel/ISIS3/build/bin/xml/photemplate.xml
/Users/jmapel/ISIS3/build/bin/xml/dempack.xml        /Users/jmapel/ISIS3/build/bin/xml/photomet.xml
/Users/jmapel/ISIS3/build/bin/xml/demprep.xml        /Users/jmapel/ISIS3/build/bin/xml/photrim.xml
/Users/jmapel/ISIS3/build/bin/xml/deriv.xml      /Users/jmapel/ISIS3/build/bin/xml/pixel2map.xml
/Users/jmapel/ISIS3/build/bin/xml/desmear.xml        /Users/jmapel/ISIS3/build/bin/xml/pointreg.xml
/Users/jmapel/ISIS3/build/bin/xml/desmile.xml        /Users/jmapel/ISIS3/build/bin/xml/poly.xml
/Users/jmapel/ISIS3/build/bin/xml/divfilter.xml      /Users/jmapel/ISIS3/build/bin/xml/prtloganalyzer.xml
/Users/jmapel/ISIS3/build/bin/xml/dsk2isis.xml       /Users/jmapel/ISIS3/build/bin/xml/pvldiff.xml
/Users/jmapel/ISIS3/build/bin/xml/dstripe.xml        /Users/jmapel/ISIS3/build/bin/xml/qmos.xml
/Users/jmapel/ISIS3/build/bin/xml/editlab.xml        /Users/jmapel/ISIS3/build/bin/xml/qnet.xml
/Users/jmapel/ISIS3/build/bin/xml/edrget.xml         /Users/jmapel/ISIS3/build/bin/xml/qtie.xml
/Users/jmapel/ISIS3/build/bin/xml/enlarge.xml        /Users/jmapel/ISIS3/build/bin/xml/qview.xml
/Users/jmapel/ISIS3/build/bin/xml/equalizer.xml      /Users/jmapel/ISIS3/build/bin/xml/ratio.xml
/Users/jmapel/ISIS3/build/bin/xml/errors.xml         /Users/jmapel/ISIS3/build/bin/xml/raw2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/explode.xml        /Users/jmapel/ISIS3/build/bin/xml/reduce.xml
/Users/jmapel/ISIS3/build/bin/xml/fakecube.xml       /Users/jmapel/ISIS3/build/bin/xml/remrx.xml
/Users/jmapel/ISIS3/build/bin/xml/fft.xml        /Users/jmapel/ISIS3/build/bin/xml/rgb2hsv.xml
/Users/jmapel/ISIS3/build/bin/xml/fillgap.xml        /Users/jmapel/ISIS3/build/bin/xml/ringsautomos.xml
/Users/jmapel/ISIS3/build/bin/xml/findfeatures.xml   /Users/jmapel/ISIS3/build/bin/xml/ringscam2map.xml
/Users/jmapel/ISIS3/build/bin/xml/findgaps.xml       /Users/jmapel/ISIS3/build/bin/xml/ringsmappt.xml
/Users/jmapel/ISIS3/build/bin/xml/findimageoverlaps.xml  /Users/jmapel/ISIS3/build/bin/xml/ringspt.xml
/Users/jmapel/ISIS3/build/bin/xml/findrx.xml         /Users/jmapel/ISIS3/build/bin/xml/rolo2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/fits2isis.xml      /Users/jmapel/ISIS3/build/bin/xml/rososiris2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/flip.xml       /Users/jmapel/ISIS3/build/bin/xml/rosvirtis2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/footprintinit.xml  /Users/jmapel/ISIS3/build/bin/xml/rotate.xml
/Users/jmapel/ISIS3/build/bin/xml/footprintmerge.xml     /Users/jmapel/ISIS3/build/bin/xml/seedgrid.xml
/Users/jmapel/ISIS3/build/bin/xml/fplanemap.xml      /Users/jmapel/ISIS3/build/bin/xml/segment.xml
/Users/jmapel/ISIS3/build/bin/xml/fx.xml         /Users/jmapel/ISIS3/build/bin/xml/shade.xml
/Users/jmapel/ISIS3/build/bin/xml/gauss.xml      /Users/jmapel/ISIS3/build/bin/xml/shadow.xml
/Users/jmapel/ISIS3/build/bin/xml/gaussstretch.xml   /Users/jmapel/ISIS3/build/bin/xml/shadowtau.xml
/Users/jmapel/ISIS3/build/bin/xml/getkey.xml         /Users/jmapel/ISIS3/build/bin/xml/sharpen.xml
/Users/jmapel/ISIS3/build/bin/xml/getsn.xml      /Users/jmapel/ISIS3/build/bin/xml/sigmastretch.xml
/Users/jmapel/ISIS3/build/bin/xml/gllnims2isis.xml   /Users/jmapel/ISIS3/build/bin/xml/skymap.xml
/Users/jmapel/ISIS3/build/bin/xml/gllssi2isis.xml    /Users/jmapel/ISIS3/build/bin/xml/skypt.xml
/Users/jmapel/ISIS3/build/bin/xml/gllssical.xml      /Users/jmapel/ISIS3/build/bin/xml/skyrange.xml
/Users/jmapel/ISIS3/build/bin/xml/gradient.xml       /Users/jmapel/ISIS3/build/bin/xml/slither.xml
/Users/jmapel/ISIS3/build/bin/xml/greyscale.xml      /Users/jmapel/ISIS3/build/bin/xml/slpmap.xml
/Users/jmapel/ISIS3/build/bin/xml/grid.xml       /Users/jmapel/ISIS3/build/bin/xml/smtk.xml
/Users/jmapel/ISIS3/build/bin/xml/handmos.xml        /Users/jmapel/ISIS3/build/bin/xml/socetframesettings.xml
/Users/jmapel/ISIS3/build/bin/xml/hi2isis.xml        /Users/jmapel/ISIS3/build/bin/xml/socetlinescankeywords.xml
/Users/jmapel/ISIS3/build/bin/xml/hical.xml      /Users/jmapel/ISIS3/build/bin/xml/specadd.xml
/Users/jmapel/ISIS3/build/bin/xml/hicalbeta.xml      /Users/jmapel/ISIS3/build/bin/xml/specdivfilter.xml
/Users/jmapel/ISIS3/build/bin/xml/hicalproc.xml      /Users/jmapel/ISIS3/build/bin/xml/spechighpass.xml
/Users/jmapel/ISIS3/build/bin/xml/hiccdstitch.xml    /Users/jmapel/ISIS3/build/bin/xml/speclowpass.xml
/Users/jmapel/ISIS3/build/bin/xml/hicolormos.xml     /Users/jmapel/ISIS3/build/bin/xml/specpix.xml
/Users/jmapel/ISIS3/build/bin/xml/hicrop.xml         /Users/jmapel/ISIS3/build/bin/xml/spicefit.xml
/Users/jmapel/ISIS3/build/bin/xml/hicubeit.xml       /Users/jmapel/ISIS3/build/bin/xml/spiceinit.xml
/Users/jmapel/ISIS3/build/bin/xml/hicubenorm.xml     /Users/jmapel/ISIS3/build/bin/xml/spiceserver.xml
/Users/jmapel/ISIS3/build/bin/xml/hideal2pds.xml     /Users/jmapel/ISIS3/build/bin/xml/spkwriter.xml
/Users/jmapel/ISIS3/build/bin/xml/hidestripe.xml     /Users/jmapel/ISIS3/build/bin/xml/stats.xml
/Users/jmapel/ISIS3/build/bin/xml/hidtmgen.xml       /Users/jmapel/ISIS3/build/bin/xml/std2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/hiequal.xml        /Users/jmapel/ISIS3/build/bin/xml/stretch.xml
/Users/jmapel/ISIS3/build/bin/xml/hifringe.xml       /Users/jmapel/ISIS3/build/bin/xml/sumspice.xml
/Users/jmapel/ISIS3/build/bin/xml/hifurrows.xml      /Users/jmapel/ISIS3/build/bin/xml/svfilter.xml
/Users/jmapel/ISIS3/build/bin/xml/highpass.xml       /Users/jmapel/ISIS3/build/bin/xml/table2cube.xml
/Users/jmapel/ISIS3/build/bin/xml/higlob.xml         /Users/jmapel/ISIS3/build/bin/xml/tabledump.xml
/Users/jmapel/ISIS3/build/bin/xml/hijitreg.xml       /Users/jmapel/ISIS3/build/bin/xml/tgocassis2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/hijitter.xml       /Users/jmapel/ISIS3/build/bin/xml/tgocassismos.xml
/Users/jmapel/ISIS3/build/bin/xml/himos.xml      /Users/jmapel/ISIS3/build/bin/xml/tgocassisrdrgen.xml
/Users/jmapel/ISIS3/build/bin/xml/hinoise.xml        /Users/jmapel/ISIS3/build/bin/xml/tgocassisstitch.xml
/Users/jmapel/ISIS3/build/bin/xml/hirdr2isis.xml     /Users/jmapel/ISIS3/build/bin/xml/tgocassisunstitch.xml
/Users/jmapel/ISIS3/build/bin/xml/hirdrgen.xml       /Users/jmapel/ISIS3/build/bin/xml/thm2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/hisharpen.xml      /Users/jmapel/ISIS3/build/bin/xml/thmbasemap1.xml
/Users/jmapel/ISIS3/build/bin/xml/hist.xml       /Users/jmapel/ISIS3/build/bin/xml/thmdriftcor.xml
/Users/jmapel/ISIS3/build/bin/xml/histat.xml         /Users/jmapel/ISIS3/build/bin/xml/thmnoseam.xml
/Users/jmapel/ISIS3/build/bin/xml/histeq.xml         /Users/jmapel/ISIS3/build/bin/xml/thmproc.xml
/Users/jmapel/ISIS3/build/bin/xml/histitch.xml       /Users/jmapel/ISIS3/build/bin/xml/thmvisflat.xml
/Users/jmapel/ISIS3/build/bin/xml/histmatch.xml      /Users/jmapel/ISIS3/build/bin/xml/thmvistrim.xml
/Users/jmapel/ISIS3/build/bin/xml/hrsc2isis.xml      /Users/jmapel/ISIS3/build/bin/xml/tonematch.xml
/Users/jmapel/ISIS3/build/bin/xml/hsv2rgb.xml        /Users/jmapel/ISIS3/build/bin/xml/trackextract.xml
/Users/jmapel/ISIS3/build/bin/xml/hyb1pds4gen.xml    /Users/jmapel/ISIS3/build/bin/xml/translate.xml
/Users/jmapel/ISIS3/build/bin/xml/hyb2onc2isis.xml   /Users/jmapel/ISIS3/build/bin/xml/trim.xml
/Users/jmapel/ISIS3/build/bin/xml/hyb2onccal.xml     /Users/jmapel/ISIS3/build/bin/xml/trimfilter.xml
/Users/jmapel/ISIS3/build/bin/xml/ifft.xml       /Users/jmapel/ISIS3/build/bin/xml/uncrop.xml
/Users/jmapel/ISIS3/build/bin/xml/interestcube.xml   /Users/jmapel/ISIS3/build/bin/xml/vdcomp.xml
/Users/jmapel/ISIS3/build/bin/xml/ipce.xml       /Users/jmapel/ISIS3/build/bin/xml/vicar2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2ascii.xml     /Users/jmapel/ISIS3/build/bin/xml/vik2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2fits.xml      /Users/jmapel/ISIS3/build/bin/xml/vikcal.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2gml.xml       /Users/jmapel/ISIS3/build/bin/xml/vikclean.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2pds.xml       /Users/jmapel/ISIS3/build/bin/xml/vikfixtrx.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2raw.xml       /Users/jmapel/ISIS3/build/bin/xml/viknobutter.xml
/Users/jmapel/ISIS3/build/bin/xml/isis2std.xml       /Users/jmapel/ISIS3/build/bin/xml/viknonoodle.xml
/Users/jmapel/ISIS3/build/bin/xml/isiscomplete.xml   /Users/jmapel/ISIS3/build/bin/xml/viknopepper.xml
/Users/jmapel/ISIS3/build/bin/xml/isisminer.xml      /Users/jmapel/ISIS3/build/bin/xml/viknosalt.xml
/Users/jmapel/ISIS3/build/bin/xml/isisui.xml         /Users/jmapel/ISIS3/build/bin/xml/vims2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/jigsaw.xml         /Users/jmapel/ISIS3/build/bin/xml/vimscal.xml
/Users/jmapel/ISIS3/build/bin/xml/junocam2isis.xml   /Users/jmapel/ISIS3/build/bin/xml/voy2isis.xml
/Users/jmapel/ISIS3/build/bin/xml/kaguyami2isis.xml  /Users/jmapel/ISIS3/build/bin/xml/voycal.xml
/Users/jmapel/ISIS3/build/bin/xml/kaguyasp2ascii.xml     /Users/jmapel/ISIS3/build/bin/xml/voyramp.xml
/Users/jmapel/ISIS3/build/bin/xml/kaguyasp2isis.xml  /Users/jmapel/ISIS3/build/bin/xml/warp.xml
/Users/jmapel/ISIS3/build/bin/xml/kaguyatc2isis.xml
jessemapel commented 5 years ago

I think there's a problem with the checks run on the xml file. Specifically,

        if(entry.is_file() and
           os.access(entry, os.X_OK) and
           not entry.name.startswith('.')):

The check if the xml is executable fails on most apps when working with a build (not install) version of ISIS3. The xml files are symlinks into the source tree.

lrwxr-xr-x 1 jmapel domainusers 48 Feb 21 11:16 /Users/jmapel/ISIS3/build/bin/xml/fx.xml -> /Users/jmapel/ISIS3/isis/src/base/apps/fx/fx.xml

99% of the app xmls in the source tree have permissions like this

-rw-r--r-- 1 jmapel domainusers 40872 Nov 12 19:35 /Users/jmapel/ISIS3/isis/src/base/apps/fx/fx.xml

Same with installed xmls

-rw-r--r-- 1 jmapel domainusers 40872 Nov 12 19:35 /Users/jmapel/ISIS3/install/bin/xml/fx.xml
jessemapel commented 5 years ago

Commenting out the executable check solves the issue. It should probably be changed to a check that the app is executable, though.