Update code coverage documentation

cice.setup

@@ -504,11 +504,18 @@ EOF0
 cat >! ${tsdir}/report_codecov.csh << EOF0
 #!/bin/csh -f
 
-#setenv CODECOV_TOKEN "1d09241f-ed9e-47d8-847c-038bab024b53"   # consortium cice
-#setenv CODECOV_TOKEN "f3236008-0b92-4707-9ad5-ad906f5d2ba7"   # apcraig cice
-setenv CODECOV_TOKEN "0dcc6066-fdce-47b6-b84a-c55e2a0af4c0"   # apcraig test_cice_icepack
-set report_name = "${shhash}:${branch}:${machine} ${testsuite}"
+# define CODECOV_TOKEN env variable
+if !(\$?CODECOV_TOKEN) then
+  if (-e ~/.codecov_cice_token) then
+    source ~/.codecov_cice_token
+  endif
+  if !(\$?CODECOV_TOKEN) then
+    echo "\${0}: ERROR, CODECOV_TOKEN env variable not defined"
+    exit 2
+  endif
+endif
 
+set report_name = "${shhash}:${branch}:${machine} ${testsuite}"
 set use_curl = 1
 
 EOF0

configuration/scripts/tests/cice_test_codecov.csh

@@ -0,0 +1,75 @@
+#!/bin/csh 
+
+# This was a script on gordon
+# This script should only be run on hardware with the gnu compiler with a
+#   modified Macros file to turn on the codecov flags
+# This should be run interactively because git push will require login information
+
+#PBS -N cice_test
+#PBS -q standard
+#PBS -A NRLSS03755018
+#PBS -l application=Regional-Arctic-System-Model
+#PBS -l select=1:ncpus=32:mpiprocs=32
+#PBS -l walltime=24:00:00
+#PBS -j oe
+#PBS -M anthony.p.craig@gmail.com
+#PBS -m be
+
+#set verbose
+module load costinit git
+
+set scrdir = "~"
+set testdir = "~/cice_testing"
+set date0 = `date -u "+%y%m%d"`
+set date = ${date0}cc
+
+mkdir -p ${testdir}
+
+cd ${testdir}
+
+# Check out current cice master
+echo " "
+echo "*** checkout current cice master ***"
+git clone https://github.com/cice-consortium/cice cice.master.${date} --recursive
+cd cice.master.${date}
+set hash = `git rev-parse --short HEAD `
+cd ../
+
+# Check out test_cice_icepack, remove all code and copy from cice master
+# Need to be careful about dot files, particularly .git* files
+# This copies in all files via standard file expansion (except dot files at root)
+# This also copies in all dot file at the root that do not start with .g (ie. .git*)
+echo " "
+echo "*** checkout current test_cice_master ***"
+git clone https://github.com/apcraig/test_cice_icepack test_cice_icepack.${date}
+cd test_cice_icepack.${date}
+echo " "
+echo "*** remove current files and copy in cice master files ***"
+set verbose
+git rm -r *  >& /dev/null
+cp -p -r ../cice.master.${date}/* .
+cp -p    ../cice.master.${date}/.[a-f,h-z]* .
+
+# Clean up icepack .git stuff and commit
+rm -r -f icepack/.git*
+git add .
+unset verbose
+echo " "
+echo "*** git status of changes ***"
+git status
+echo " "
+echo "*** commit changes ***"
+git commit -m "update test_cice_icepack master to ${hash}"
+
+# Push test_cice_icepack 
+echo " "
+echo "*** push changes to test_cice_icepack ***"
+git push origin master
+
+# Run test suite
+echo " "
+echo "*** run test suite ***"
+./cice.setup --suite first_suite,base_suite,travis_suite,decomp_suite,reprosum_suite,quick_suite -m gordon -e gnu --testid T${date} --codecov --queue standard
+
+# The test suite will wait until all jobs are complete then run report_codecov.csh
+# If that fails, you can run report_codecov.csh manually after all jobs are done

doc/source/user_guide/ug_testing.rst

@@ -668,32 +668,25 @@ Code Coverage Testing
 The ``--codecov`` feature in **cice.setup** provides a method to diagnose code coverage.
 This argument turns on special compiler flags including reduced optimization and then
 invokes the gcov tool.
-This option is currently only available with the gnu compiler and on a few systems.
+This option is currently only available with the gnu compiler and on a few systems
+with modified Macros files.
 
 Because codecov.io does not support git submodule analysis right now, a customized
 repository has to be created to test CICE with Icepack integrated directly.  The repository 
 https://github.com/apcraig/Test_CICE_Icepack serves as the current default test repository.
 In general, to setup the code coverage test in CICE, the current CICE master has
-to be copied into the Test_CICE_Icepack repository, then the code coverage tool can
-be run on that repository.  A sample script to do that would be::
+to be copied into the Test_CICE_Icepack repository, then the full test suite
+can be run with the gnu compiler with the ``--codecov`` argument.
 
-  git clone https://github.com/cice-consortium/cice cice.master --recursive
-
-  git clone https://github.com/apcraig/test_cice_icepack
-  cd test_cice_icepack
-  git rm -r *
-  cp -p -r ../cice.master/* .
-  git add .
-  git commit -m "update to current cice master"
-  git push origin master
-
-  ./cice.setup --suite first_suite,base_suite,travis_suite,decomp_suite,reprosum_suite,quick_suite -m gordon -e gnu --codecov --testid cc01
-
-To use, submit a full test suite using an updated Test_CICE_Icepack version
-and the gnu compiler with the ``--codecov`` argument.
 The test suite will run and then a report will be generated and uploaded to 
 the `codecov.io site <https://codecov.io/gh/apcraig/Test_CICE_Icepack>`_ by the 
-**report_codecov.csh** script.  
+**report_codecov.csh** script.  The env variable CODECOV_TOKEN needs to be defined
+either in the environment or in a file named **~/.codecov_cice_token**.  That
+token provides write permission to the Test_CICE_Icepack codecov.io site and is available
+by contacting the Consortium team directly.
+
+A script that carries out the end-to-end testing can be found in 
+**configuration/scripts/tests/cice_test_codecov.csh**
 
 This is a special diagnostic test and does not constitute proper model testing.
 General use is not recommended, this is mainly used as a diagnostic to periodically