Index: create_tarball.sh
===================================================================
--- create_tarball.sh	(revision e4925fb7d17ac01f0e5fca31aa981ea9f2d507f2)
+++ create_tarball.sh	(revision 577bd0450ed0e9ad4e71090356e160fa175af415)
@@ -1,4 +1,5 @@
 #!/bin/bash
 # Ignacio Pisso, May 2017 
+# Changes 2018-2019
 
 echo CREATE A NEW FLEXPART DISTRIBUTION
@@ -43,6 +44,4 @@
 
 # start packing
-
-
 ## needs in addition to the git repo ANCILLARY git repos
 # VERIFY THESE RESOURCES EXIST BEFORE PACKING DISTRIBUTION
@@ -51,7 +50,5 @@
 #3 flex_read_fortran from ../flex_read_matlab/export_basic  TODO: add functions to ../flex_read_matlab/export/ 
 #  flex_read_matlab_src=../flex_read_matlab/export_basic
-#4 tests/examples ../flex_tests_examples/examples3/*
-#5  
-#6
+#4 tests/examples ../flex_tests_examples/examples/*
 
 
@@ -69,5 +66,4 @@
 echo ---------------------------------------------------------
 echo ')' copy pathnames 
-#cp pathnames_distribution $tarball_tmp/pathnames
 cp pathnames $tarball_tmp/pathnames
 echo ---------------------------------------------------------
@@ -81,7 +77,5 @@
 cp src/*.f90 $tarball_tmp/src
 cp -r src/gributils $tarball_tmp/src 
-# echo '3)' copy makefile
 cp src/makefile $tarball_tmp/src
-#cp src/makefile.gfs $tarball_tmp/src
 echo ---------------------------------------------------------
 
@@ -92,6 +86,4 @@
 echo ')' copy options/ 
 echo ---------------------------------------------------------
-# (for the distribution they work with the defult flex_ecmwf test winds)
-#cp -r options_flex_ecmwf_EA $tarball_tmp/options
 mkdir $tarball_tmp/options
 user_input_files="AGECLASSES     COMMAND        IGBP_int1.dat  OUTGRID        OUTGRID_NEST   RECEPTORS      RELEASES       surfdata.t     surfdepo.t"
@@ -100,5 +92,4 @@
   echo $i
   cp -r options/$i $tarball_tmp/options
-  #echo copy $i to $tarball_tmp/options
 done
 mkdir $tarball_tmp/options/SPECIES
@@ -123,5 +114,4 @@
 echo ---------------------------------------------------------
 echo ')' copy AVAILABLE
-#cp AVAILABLE_flex_ecmwf_EA $tarball_tmp/AVAILABLE
 cp AVAILABLE $tarball_tmp/AVAILABLE
 echo ---------------------------------------------------------
@@ -144,14 +134,5 @@
 mkdir $tarball_tmp/preprocess
 echo -----------------flex_extract-------------------
-#echo '6)'  mkdir $tarball_tmp/flex_extract [a separate repository]
-#mkdir $tarball_tmp/preprocess
-#mkdir $tarball_tmp/preprocess/flex_ecmwf
 mkdir $tarball_tmp/preprocess/flex_extract
-#echo '7)  add ECMWF retrieve routines (change EA wind files for latest source code)'
-#mkdir $tarball_tmp/preprocess/flex_extract
-#mkdir $tarball_tmp/preprocess/flex_extract/work
-#cp -r flex_ecmwf_src/* $tarball_tmp/preprocess/flex_ecmwf/
-#cp -r flex_ecmwf_src/* $tarball_tmp/preprocess/flex_extract/
-## cp -r flex_extract/work/EA* $tarball_tmp/preprocess/flex_extract/work   
 flex_extract=../flex_extract_v7.0.4/
 echo include flex_extract v7.0.4 b7c1c04a204c91e53759ef590504bf52dfaece64
@@ -167,10 +148,4 @@
 echo ---------------------------------------------------------
 
-#echo '10)' cp example generating scripts [a separate repository]
-#echo moved below
-#mkdir $tarball_tmp/examples
-#cp -r examples/*.sh $tarball_tmp/examples/ 
-#cp -r examples/Makefile $tarball_tmp/examples/ 
-
 echo 
 
@@ -183,6 +158,4 @@
 echo -----------------flex_read_fortran-------------------
 flex_read_fortran_src=$postprocess/flex_read_fortran/
-#echo ')'  directory for reading routines
-#echo '12)'  add fortran reading routines [a separate repository]
 mkdir $tarball_tmp/$postprocess/flex_read_fortran
 cp $postprocess/flex_read_fortran/*.f $tarball_tmp/$postprocess/flex_read_fortran
@@ -196,7 +169,4 @@
 cp -r $flex_read_matlab_src/* $tarball_tmp/$postprocess/flex_read_matlab
 echo flex_read_fortran from $flex_read_matlab_src  # NOT copied
-# add matlab reading routines
-#mkdir $tarball_tmp/postprocess/flex_read_matlab
-#cp postprocess/flex_read_matlab/*.m $tarball_tmp/postprocess/flex_read_matlab
 echo ---------------------------------------------------------
 
@@ -205,24 +175,9 @@
 echo ---------------------------------------------------------
 echo ')' tests/
-###############################################################
 #echo '13) tests' 
 mkdir $tarball_tmp/tests
-#echo -----------------flex_read_fortran-------------------
-#echo 'b) ./tests/flex_read_fortran/' 
-#echo fixme
-#mkdir $tarball_tmp/tests/flex_read_fortran
-#cp tests/flex_read_fortran/test_read_default.sh  $tarball_tmp/tests/flex_read_fortran
-
-
-###############################################################
 echo ----------------- examples -------------------
 
-#echo ') ./tests/examples/' 
 mkdir $tarball_tmp/tests/examples
-#echo ') scripts' 
-#cp -r ./tests/examples/*.sh $tarball_tmp/tests/examples/ 
-#echo ') makefile' 
-#cp -r ./tests/examples/Makefile $tarball_tmp/tests/examples/ 
-# echo USAGE: ~/repos/flexpart/tests/examples'$' make run
 cp -r ../flex_tests_examples/examples3/* $tarball_tmp/tests/examples/
 
@@ -230,11 +185,6 @@
 cp -r ./tests/examples_reference $tarball_tmp/tests/
 
-
-
-###############################################################
-# echo -----------------postprocess examples-------------------
 echo -----------------read examples-------------------
 
-#echo '13 c) ./tests/read_examples/' 
 mkdir $tarball_tmp/tests/read_examples
 
@@ -249,41 +199,16 @@
 cp tests/read_examples/read_headers.sh $tarball_tmp/tests/read_examples/
 cp tests/read_examples/read_examples_output.txt $tarball_tmp/tests/ #read_examples/
-# echo USAGE ~/repos/flexpart/tests/read_examples'$'./read_grids.sh
-
-###############################################################
+
 echo ------------compare examples-------------------
-#echo tests/compare_examples.sh
 mkdir $tarball_tmp/tests/compare_examples
 
 
-#mkdir $tarball_tmp/tests/compare_examples
-#cp tests/compare_examples/compare_grids.sh $tarball_tmp/tests/compare_examples
-#cp tests/compare_grids.sh $tarball_tmp/tests/
 cp tests/compare_examples/*.sh $tarball_tmp/tests/compare_examples
 cp tests/compare_examples/compare_grids_output.txt $tarball_tmp/tests/ #compare_examples
-# list of examples with units
-#cp tests/declare_examples $tarball_tmp/tests/
-
-echo 
-
-# ~/repos/flexpart/tests$./compare_grids.sh 
-
-#echo mkdir $tarball_tmp/tests/examples2/
-#echo cp tests/examples2/setup.sh $tarball_tmp/tests/examples2/
-# echo --repeat examples-------------------
-# echo FIXME 
-
-###############################################################
-#echo -----------------ctbto-------------------
-# mkdir $tarball_tmp/tests/ctbto
-
-# cp -r tests/NILU/test_1 $tarball_tmp/tests/
-# cp -r tests/default_cases $tarball_tmp/tests/
+
+echo 
 
 echo ---------------------------------------------------------
 echo create tarball
-#tar cvf $tarball  $tarball_tmp  
-#tar cf $tarball  $tarball_tmp  
-#cd 
 
 cd $targetdir
@@ -292,8 +217,8 @@
 pwd
 
-
 echo  tarball $tarball complete
 echo exported untarred files in $tarball_tmp 
 
+echo verify:
 echo cp -r preprocess/flex_extract/work $tarball_tmp/preprocess/flex_extract/ 
 echo cd $tarball_tmp/src
@@ -302,8 +227,6 @@
 echo cd postprocess/flex_read_fortran
 echo make test
-echo  max:  0.115784094     mean:   4.70877676E-05
-#echo cd $tarball_tmp/tests/examples ';'   make run
+echo e.g.: max:  0.115784094     mean:   4.70877676E-05
 echo cd ../../tests/examples ';'   make run
-#echo cd $tarball_tmp/tests/read_examples
 echo cd ../read_examples
 echo ./read_examples.sh
@@ -315,68 +238,2 @@
 echo e.g. tar --append --file=$tarball_tmp/ ../compare_grids_output.txt ../read_examples_output.txt
  
- 
-
-
-exit
-#return
-###############################################################
-
-# obtain $FLEXHOME (and set)
-#1 cd $FLEXHOME/src 
-
-#2 compile
-#
-#[laptop] source /Users/ignacio/repos/flexpart/src/make_in_laptop.sh 
-# [njord] make
-# ->created executable (FLEXPART)
-
-#3 execute in src (absolute paths)
-#
-#[laptop] cp  /Users/ignacio/repos/flexpart/src/pathnames .
-#[njord] FIXME
-#
-# mkdir output
-# ./FLEXPART
-# ->created output in output/
-
-#4 read output
-# cd  $FLEXHOME/postprocess/flex_read_fortran/
-# make
-# -> printheader* printgrid* flex_read_compare2*
-#/postprocess/flex_read_fortran$./printheader ../../src/output/
-#/postprocess/flex_read_fortran$./printgrid ../../src/output/ conc
-# -> output in stdout (max:   11122924.0     sum:   90330784.0)
-
-#5 execute in $FLEXHOME
-# cd $FLEXHOME
-# get winds
-#[laptop] cp -r ~/repos/flex_winds/work/ ./preprocess/flex_extract/ 
-#[njord] curl https://folk.nilu.no/~ignacio/FLEXPART/EA120101.tar --output EA120101.tar ; tar -xvf EA120101.tar ; mv flex_extract/work preprocess/flex_extract/ ; rmdir flex_extract
-
-# src/FLEXPART
-# -> output in $FLEXHOME/output/
-
-#6 read output
-# postprocess/flex_read_fortran/printheader output/
-# postprocess/flex_read_fortran/printgrid output/ conc
-# -> output in stdout ( max:   11578738.0     sum:   104058720.)
-
-#7 gnererate examples
-# cd $FLEXHOME/tests/examples
-
-#make run
-
-#make examples
-#make batch
-#./run_batch_cl.sh
-
-#make (set_default_example.sh)
-#tests/examples$../../src/FLEXPART
-#output
-
-#8 read examples:
-#cd $FLEXHOME/tests/read_examples  
-# ./read_headers.sh
-# ./read_grids.sh 
-
-#9 compare examples with reference
