diff --git a/docs/Integrator.md b/docs/Integrator.md
index 6726f35b039868206d1e4f3395b316ac7703e4b7..93c703a3a37b023193599a89a5cff0a1f1a83c9a 100644
--- a/docs/Integrator.md
+++ b/docs/Integrator.md
@@ -102,3 +102,8 @@ The preprocessed versions of the source code are put in branches named \<model\>
The preprocessing tools are described in the [Tools documentation](./Tools.md).
+## Code validation
+
+The testing.h script can be automatically run to help for validation. This script is described
+in the [Tools documentation](./Tools.md).
+
diff --git a/docs/Tools.md b/docs/Tools.md
index 6fb2df1d0478ff442f973a1a2bac3d87926daa9c..aef6814aed5719215c635383ffe3954819230f46 100644
--- a/docs/Tools.md
+++ b/docs/Tools.md
@@ -61,6 +61,12 @@ script with the 'REF' argument), the reference simulation directory (under $TEST
This script is used by the different check\_commit\_\* scripts and can be used directly to pre-process the source code.
The installation is described in the [tools/INSTALL\_mnh\_expand.md file](../tools/INSTALL_mnh_expand.md)
+### testing.sh
+
+This script is designed to be run periodically by cron. It searches for the last commit on a github repository,
+use the different check\_commit\_\* scripts to run the test cases and add a comments attached to the gihub commit
+to report success or unsecess of these tests. In case of an error, the script can also send an email.
+
### others
Other scripts are:
diff --git a/tools/check_commit_ial.sh b/tools/check_commit_ial.sh
index 9539527200a47738ca1239cfd77fc041f372ecfc..e3c05adf428d1a9e0f5174a0c80c2b9d7e8cc90d 100755
--- a/tools/check_commit_ial.sh
+++ b/tools/check_commit_ial.sh
@@ -65,6 +65,7 @@ set -o pipefail #abort if left command on a pipe fails
specialPack="ori split split_48t1 split_48t3 recompil split_49t0"
availTests="small_3D,small_3D_np2,small_3D_alt1,small_3D_alt2,small_3D_alt3,small_3D_alt4,small_3D_alt5,small_3D_alt6,small_3D_alt7"
defaultTest="small_3D"
+allowedTests="small_3D,small_3D_np2,small_3D_alt1,small_3D_alt2,small_3D_alt3,small_3D_alt4,small_3D_alt5,small_3D_alt6,small_3D_alt7,small_3D_alt8,small_3D_alt9,small_3D_alt10,small_3D_alt11,small_3D_alt12,small_3D_lima"
separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allergies (':', '.', '@')
#- seprator must be in sync with prep_code.sh separator
@@ -83,6 +84,7 @@ if [ $(hostname | cut -c 1-7) == 'belenos' -o $(hostname | cut -c 1-7) == 'taran
defaultMainPackVersion=01
defaultRef='split_${cycle}'
availTests="${availTests},big_3D"
+ allowedTests="${allowedTests},big_3D"
else
HPC=0
gmkpack_l[default]=MPIGFORTRAN920DBL
@@ -97,7 +99,7 @@ mainPackVersion=${mainPackVersion:-${defaultMainPackVersion}}
extraCompilationCheck=1
function usage {
- echo "Usage: $0 [-h] [-p] [-c] [-r] [-C] [-s] [-f] [--noexpand] [-t test] [--cycle CYCLE] [--repo-user] [--repo-protocol] commit [reference]"
+ echo "Usage: $0 [-h] [-p] [-c] [-r] [-C] [-s] [-f] [--noexpand] [-t test] [--cycle CYCLE] [--repo-user] [--repo-protocol] [--remove] commit [reference]"
echo "commit commit hash (or a directory, or among $specialPack) to test"
echo "reference commit hash (or a directory, or among $specialPack) REF to use as a reference"
echo "-s suppress compilation pack"
@@ -115,12 +117,17 @@ function usage {
echo " defaults to the env variable PHYEXREOuser (=$PHYEXREOuser)"
echo "--repo-protocol protocol (https or ssh) to reach the PHYEX repository on github,"
echo " defaults to the env variable PHYEXREOprotocol (=$PHYEXREOprotocol)"
+ echo "--remove removes the pack"
echo ""
- echo "If nothing is asked (pack creation, compilation, running, check) everything is done"
+ echo "If nothing is asked (pack creation, compilation, running, check, removing) everything"
+ echo "except the removing is done"
+ echo
echo "If no test is aked for, the default one ($defaultTest) is executed"
echo
echo "With the special reference REF commit, a suitable reference is guessed"
+ echo
echo "The directory (for commit only, not ref) can take the form server:directory"
+ echo
echo "If using a directory (for commit or reference) it must contain at least one '/'"
echo "The commit can be a tag, written with syntagx tags/<TAG>"
echo
@@ -141,6 +148,7 @@ useexpand=1
fullcompilation=0
cycle=""
scripttag=''
+remove=0
while [ -n "$1" ]; do
case "$1" in
@@ -157,6 +165,7 @@ while [ -n "$1" ]; do
'--scripttag') scripttag="$2"; shift;;
'--repo-user') export PHYEXREPOuser=$2; shift;;
'--repo-protocol') export PHYEXREPOprotocol=$2; shift;;
+ '--remove') remove=1;;
#--) shift; break ;;
*) if [ -z "${commit-}" ]; then
commit=$1
@@ -195,7 +204,8 @@ fi
if [ $packcreation -eq 0 -a \
$compilation -eq 0 -a \
$run -eq 0 -a \
- $check -eq 0 ]; then
+ $check -eq 0 -a \
+ $remove -eq 0 ]; then
packcreation=1
compilation=1
run=1
@@ -534,17 +544,18 @@ if [ $compilation -eq 1 ]; then
grep -v "'CPLNG: Error" | \
grep -v '"Error' | \
grep -v "'*** Error" | \
- grep -v "-- Up-to-date:" | wc -l) -ne 0 ]; then
- echo "MASTERODB was produced but errors occured during compilation:"
- grep Error Output_compilation | \
- grep -v TestErrorHandler | \
- grep -v "'Error" | \
- grep -v "'CPLNG: Error" | \
- grep -v '"Error' | \
- grep -v "'*** Error" | \
- grep -v "-- Up-to-date:"
- echo "MASTERODB suppressed!"
- rm -f bin/MASTERODB
+ grep -v "\-\- Up-to-date:" | wc -l) -ne 0 ]; then
+ echo "MASTERODB was produced but errors occured during compilation:"
+ grep Error Output_compilation | \
+ grep -v TestErrorHandler | \
+ grep -v "'Error" | \
+ grep -v "'CPLNG: Error" | \
+ grep -v '"Error' | \
+ grep -v "'*** Error" | \
+ grep -v "\-\- Up-to-date:"
+ echo "MASTERODB suppressed!"
+ rm -f bin/MASTERODB
+ exit 12
fi
fi
@@ -566,10 +577,14 @@ if [ $run -ge 1 ]; then
#Run the tests one after the other
for t in $(echo $tests | sed 's/,/ /g'); do
- cd $HOMEPACK/$name
- mkdir -p conf_tests/$t
- cd conf_tests/$t
- MYLIB=$name TESTDIR=$dirconf/$t exescript Output_run $dirconf/$t/aro${cycle}${scripttag}.sh
+ if echo $allowedTests | grep -w $t; then
+ cd $HOMEPACK/$name
+ mkdir -p conf_tests/$t
+ cd conf_tests/$t
+ MYLIB=$name TESTDIR=$dirconf/$t exescript Output_run $dirconf/$t/aro${cycle}${scripttag}.sh
+ else
+ echo "The test $t is not allowed"
+ fi
done
fi
@@ -580,10 +595,14 @@ if [ $check -eq 1 ]; then
message=""
filestocheck=""
for t in $(echo $tests | sed 's/,/ /g'); do
- if echo $t | grep 'small' > /dev/null; then
- filestocheck="$filestocheck ${t},conf_tests/$t/ICMSHFPOS+0002:00 ${t},conf_tests/$t/DHFDLFPOS+0002"
+ if echo $allowedTests | grep -w $t; then
+ if echo $t | grep 'small' > /dev/null; then
+ filestocheck="$filestocheck ${t},conf_tests/$t/ICMSHFPOS+0002:00 ${t},conf_tests/$t/DHFDLFPOS+0002"
+ else
+ filestocheck="$filestocheck ${t},conf_tests/$t/NODE.001_01"
+ fi
else
- filestocheck="$filestocheck ${t},conf_tests/$t/NODE.001_01"
+ echo "The test $t is not allowed"
fi
done
for tag_file in $filestocheck; do
@@ -656,5 +675,13 @@ if [ $check -eq 1 ]; then
else
echo "*************** Files are different *******************"
echo -e "$message"
+ cmpstatus=50
fi
fi
+
+if [ $remove -eq 1 ]; then
+ echo "### Remove model directory for commit $commit"
+ [ -d $HOMEPACK/$name ] && rm -rf $HOMEPACK/$name
+fi
+
+exit $cmpstatus
diff --git a/tools/check_commit_lmdz.sh b/tools/check_commit_lmdz.sh
index e9b73e6d8655d1afca5edc867273d72db4312a53..b8b1d0af79d3025a17601f9718d27e38231ca821 100755
--- a/tools/check_commit_lmdz.sh
+++ b/tools/check_commit_lmdz.sh
@@ -17,7 +17,7 @@ separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allerg
#- seprator must be in sync with prep_code.sh separator
function usage {
- echo "Usage: $0 [-h] [-p] [-c] [-C] [-r] [-s] [--expand] [-t test] [--version VERSION] [--repo-user] [--repo-protocol] commit [reference]"
+ echo "Usage: $0 [-h] [-p] [-c] [-C] [-r] [-s] [--expand] [-t test] [--version VERSION] [--repo-user] [--repo-protocol] [--remove] commit [reference]"
echo "commit commit hash (or a directory, or among $specialPack) to test"
echo "reference commit hash (or a directory, or among $specialPack) REF to use as a reference"
echo "-s suppress compilation pack"
@@ -34,12 +34,17 @@ function usage {
echo " defaults to the env variable PHYEXREOuser (=$PHYEXREOuser)"
echo "--repo-protocol protocol (https or ssh) to reach the PHYEX repository on github,"
echo " defaults to the env variable PHYEXREOprotocol (=$PHYEXREOprotocol)"
+ echo "--remove removes the pack"
echo ""
- echo "If nothing is asked (pack creation, compilation, running, check) everything is done"
+ echo "If nothing is asked (pack creation, compilation, running, check, removing) everything"
+ echo "except the removing is done"
+ echo
echo "If no test is aked for, the default one ($defaultTest) is executed"
echo
echo "With the special reference REF commit, a suitable reference is guessed"
+ echo
echo "The directory (for commit only, not ref) can take the form server:directory"
+ echo
echo "If using a directory (for commit or reference) it must contain at least one '/'"
echo "The commit can be a tag, written with syntagx tags/<TAG>"
}
@@ -56,6 +61,7 @@ suppress=0
useexpand=0
version=""
link=0 #Not yet put in command line argument becaus this option has not been tested here
+remove=0
while [ -n "$1" ]; do
case "$1" in
@@ -71,6 +77,7 @@ while [ -n "$1" ]; do
'--version') version="$2"; shift;;
'--repo-user') export PHYEXREPOuser=$2; shift;;
'--repo-protocol') export PHYEXREPOprotocol=$2; shift;;
+ '--remove') remove=1;;
#--) shift; break ;;
*) if [ -z "${commit-}" ]; then
commit=$1
@@ -95,7 +102,8 @@ fi
if [ $packcreation -eq 0 -a \
$compilation -eq 0 -a \
$run -eq 0 -a \
- $check -eq 0 ]; then
+ $check -eq 0 -a \
+ $remove -eq 0 ]; then
packcreation=1
compilation=1
run=1
@@ -325,3 +333,7 @@ if [ $check -eq 1 ]; then
exit 6
fi
+if [ $remove -eq 1 ]; then
+ echo "### Remove model directory for commit $commit"
+ [ -d $LMDZPACK/$name ] && rm -rf $LMDZPACK/$name
+fi
diff --git a/tools/check_commit_mesonh.sh b/tools/check_commit_mesonh.sh
index 3c54c7b48eda522f644e904e155ab0604b810f40..b3d2835f5b4f05baa97d2207ef2110feadf57daa 100755
--- a/tools/check_commit_mesonh.sh
+++ b/tools/check_commit_mesonh.sh
@@ -22,7 +22,7 @@ separator='_' #- be carrefull, gmkpack (at least on belenos) has multiple allerg
PHYEXTOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
function usage {
- echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [--expand] [-t test] commit reference"
+ echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [--expand] [-t test] [--remove] commit [reference]"
echo "commit commit hash (or a directory)"
echo "reference commit hash or a directory or nothing for ref"
echo "-s suppress compilation pack"
@@ -36,14 +36,19 @@ function usage {
echo " defaults to the env variable PHYEXREOuser (=$PHYEXREOuser)"
echo "--repo-protocol protocol (https or ssh) to reach the PHYEX repository on github,"
echo " defaults to the env variable PHYEXREOprotocol (=$PHYEXREOprotocol)"
+ echo "--remove removes the pack"
echo ""
- echo "If nothing is asked (compilation, running, check) everything is done"
- echo
- echo "If no test is aked for, the default on ($defaultTest) is executed"
+ echo "If nothing is asked (compilation, running, check, removing) everything"
+ echo "except the removing is done"
+ echo
+ echo "If no test is aked for, the default one ($defaultTest) is executed"
+ echo
+ echo "With the special reference REF commit, a suitable reference is guessed"
echo
echo "The directory (for commit only, not ref) can take the form server:directory"
echo
echo "If using a directory (for commit or reference) it must contain at least one '/'"
+ echo "The commit can be a tag, written with syntagx tags/<TAG>"
}
compilation=0
@@ -54,6 +59,7 @@ reference=""
tests=""
suppress=0
useexpand=0
+remove=0
while [ -n "$1" ]; do
case "$1" in
@@ -66,6 +72,7 @@ while [ -n "$1" ]; do
'--expand') useexpand=1;;
'--repo-user') export PHYEXREPOuser=$2; shift;;
'--repo-protocol') export PHYEXREPOprotocol=$2; shift;;
+ '--remove') remove=1;;
#--) shift; break ;;
*) if [ -z "${commit-}" ]; then
commit=$1
@@ -94,7 +101,8 @@ fi
if [ $compilation -eq 0 -a \
$run -eq 0 -a \
- $check -eq 0 ]; then
+ $check -eq 0 -a \
+ $remove -eq 0 ]; then
compilation=1
run=1
check=1
@@ -546,6 +554,14 @@ if [ $check -eq 1 ]; then
status="OK"
else
status="Files are different"
+ cmpstatus=50
fi
echo "...comparison done: $status"
fi
+
+if [ $remove -eq 1 ]; then
+ echo "### Remove model directory for commit $commit"
+ [ -d $MNHPACK/$name ] && rm -rf $MNHPACK/$name
+fi
+
+exit $cmpstatus
diff --git a/tools/check_commit_testprogs.sh b/tools/check_commit_testprogs.sh
index 71e5974838aa09c1a94301db7fbc9b7550561cd5..3314f89eccc4b2f75912b8982cd102c364ca19bb 100755
--- a/tools/check_commit_testprogs.sh
+++ b/tools/check_commit_testprogs.sh
@@ -46,7 +46,7 @@ fi
defaultRef=ref
function usage {
- echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [-f] [--noexpand] [-t test] [--repo-user user] [--repo-protocol protocol] [-a arch] [-A arch] commit [reference]"
+ echo "Usage: $0 [-h] [-c] [-r] [-C] [-s] [-f] [--noexpand] [-t test] [--repo-user user] [--repo-protocol protocol] [-a arch] [-A arch] [--remove] commit [reference]"
echo "commit commit hash (or a directory, or among $specialName) to test"
echo "reference commit hash (or a directory, or among $specialName) REF to use as a reference"
echo "-s suppress compilation directory"
@@ -60,18 +60,21 @@ function usage {
echo " defaults to the env variable PHYEXREOuser (=$PHYEXREOuser)"
echo "--repo-protocol protocol (https or ssh) to reach the PHYEX repository on github,"
echo " defaults to the env variable PHYEXREOprotocol (=$PHYEXREOprotocol)"
+ echo "--remove removes the pack"
echo "-a arch architecture name to use to build and run the commit (=$defaultarchfile)"
echo "-A arch architecture name to use for the reference simulation (=$defaultarchfile)"
echo ""
- echo "If nothing is asked (compilation, running, check) everything is done"
- echo
- echo "With the special reference REF commit, a suitable reference is guessed"
+ echo "If nothing is asked (compilation, running, check, removing) everything"
+ echo "except the removing is done"
echo
echo "If no test is aked for, the default one ($defaultTest) is executed"
echo
+ echo "With the special reference REF commit, a suitable reference is guessed"
+ echo
echo "The directory (for commit only, not ref) can take the form server:directory"
echo
echo "If using a directory (for commit or reference) it must contain at least one '/'"
+ echo "The commit can be a tag, written with syntagx tags/<TAG>"
}
compilation=0
@@ -84,6 +87,7 @@ suppress=0
useexpand=""
archfile=$defaultarchfile
refarchfile=$defaultarchfile
+remove=0
while [ -n "$1" ]; do
case "$1" in
@@ -96,6 +100,7 @@ while [ -n "$1" ]; do
'--noexpand') useexpand=$1;;
'--repo-user') export PHYEXREPOuser=$2; shift;;
'--repo-protocol') export PHYEXREPOprotocol=$2; shift;;
+ '--remove') remove=1;;
'-a') archfile="$2"; shift;;
'-A') refarchfile="$2"; shift;;
#--) shift; break ;;
@@ -136,7 +141,8 @@ fi
if [ $compilation -eq 0 -a \
$run -eq 0 -a \
- $check -eq 0 ]; then
+ $check -eq 0 -a \
+ $remove -eq 0 ]; then
compilation=1
run=1
check=1
@@ -267,5 +273,13 @@ if [ $check -eq 1 ]; then
else
echo "*************** Files are different *******************"
echo -e "$message"
+ cmpstatus=50
fi
fi
+
+if [ $remove -eq 1 ]; then
+ echo "### Remove model directory for commit $commit"
+ [ -d $TESTDIR/$name ] && rm -rf $TESTDIR/$name
+fi
+
+exit $cmpstatus
diff --git a/tools/compare.py b/tools/compare.py
index 230462e4f16f8e987fb9acf344d5a7076950abc1..16410e00d3faddfd4647bb5f6a8daa7eb0e9a6f1 100755
--- a/tools/compare.py
+++ b/tools/compare.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python3
import xarray as xr
+import sys
avail_groups=['Stations/sta1',
'LES_budgets/Miscellaneous/Cartesian/Not_time_averaged/Not_normalized/cart/',
@@ -119,9 +120,12 @@ if __name__ == "__main__":
parser.add_argument('--f3', metavar='file3', type=str, help=".000 file1 user ")
parser.add_argument('--f4', metavar='file4', type=str, help=".000 file2 reference")
args = parser.parse_args()
+ totalstatus=0
status1=compareBACKUPFiles(args.f1, args.f2)
+ totalstatus += status1
print('status1 = ' + str(status1))
if args.f3:
status2=compareTSERIESFiles(args.f3, args.f4)
+ totalstatus += status2
print('status2 = ' + str(status2))
-
+ sys.exit(totalstatus)
diff --git a/tools/testing.sh b/tools/testing.sh
new file mode 100755
index 0000000000000000000000000000000000000000..391aa9438dbc3d95cfd211af48313433fa37c2d8
--- /dev/null
+++ b/tools/testing.sh
@@ -0,0 +1,354 @@
+#!/bin/bash
+
+set -e
+set -o pipefail #abort if left command on a pipe fails
+
+function usage {
+ echo "Usage: $0 [-h] [--repo-user] [--repo-protocol] [--repo-repo] [--no-update] [--no-compil]"
+ echo " [--no-exec] [--no-comp] [--no-remove] [--commit SHA] [--ref REF] [--force] [MAIL]"
+ echo "--repo-user user hosting the PHYEX repository on github,"
+ echo " defaults to the env variable PHYEXREPOuser (=$PHYEXREPOuser)"
+ echo "--repo-protocol protocol (https or ssh) to reach the PHYEX repository on github,"
+ echo " defaults to the env variable PHYEXREPOprotocol (=$PHYEXREPOprotocol)"
+ echo "--repo-repo repository name"
+ echo " defaults to the env variable PHYEXREPOrepo (=$PHYEXREPOrepo)"
+ echo "--no-update do not update the tools"
+ echo "--no-compil do not compil (only usefull after a first execution with --no-update)"
+ echo "--no-exec do not execute (only usefull after a first execution with --no-update)"
+ echo "--no-comp do not compare (only usefull after a first execution with --no-update)"
+ echo "--no-remove do not remove compilation directory"
+ echo "--force perform the test even if github commit comment already exists"
+ echo "--commit SHA use the commit with sha SHA instead of the last one"
+ echo "--ref REF ref to use (defaults to refs/heads/master)"
+ echo "--only-model MODEL"
+ echo " performs the test only using model MODEL (option can be provided several times)"
+ echo "MAIL comma-separated list of e-mail addresses (no spaces); if not provided, mail is not sent"
+ echo ""
+ echo "This script provides functionality for automated tests."
+ echo "It can be run with cron to periodically test the last commit on the PHYEX repository"
+ echo "(eg '00 22 * * * bash -l -c \"SHELL=/bin/bash PHYEXWORKDIR=~/PHYEXTESTING ~/PHYEXTESTING/PHYEX/tools/testing.sh \\"
+ echo " --repo-user UMR-CNRM --repo-protocol ssh --repo-repo PHYEX user@domain\"')"
+ echo "The repository must be hosted on github as it relies on github commit comments functionnality."
+ echo "A github token must be set in the .netrc file."
+ echo ""
+ echo "All the work is done within the \${PHYEXWORKDIR} directory (it defaults to ~/PHYEXTESTING)."
+ echo "It may be necessary to fill the \${PHYEXWORKDIR}/PHYEX/tools/pack with base source code"
+ echo "(for arome and/or mesonh) or with data (testprogs)."
+ echo ""
+ echo "The script compare the results against reference simulations. These reference simulations must"
+ echo "be available in the different subdirectories in \${WORKDIR}."
+}
+
+MAIL=""
+PHYEXREPOuser=${PHYEXREPOuser:=UMR-CNRM}
+PHYEXREPOrepo=${PHYEXREPOrepo:=PHYEX}
+PHYEXREPOprotocol=${PHYEXREPOprotocol:=ssh}
+REF="refs/heads/master"
+WORKDIR=${PHYEXWORKDIR:=${HOME}/PHYEXTESTING}
+update=1
+compil=1
+execute=1
+comp=1
+remove=1
+commit=""
+SHA=0
+force=0
+models=""
+
+while [ -n "$1" ]; do
+ case "$1" in
+ '-h') usage; exit;;
+ '--repo-user') export PHYEXREPOuser=$2; shift;;
+ '--repo-protocol') export PHYEXREPOprotocol=$2; shift;;
+ '--repo-repo') export PHYEXREPOrepo=$2; shift;;
+ '--no-update') update=0;;
+ '--no-compil') compil=0;;
+ '--no-exec') execute=0;;
+ '--no-comp') comp=0;;
+ '--no-remove') remove=0;;
+ '--force') force=1;;
+ '--commit') SHA=$2; shift;;
+ '--ref') REF=$2; shift;;
+ '--only-model') models="${models} $2"; shift;;
+ #--) shift; break ;;
+ *) if [ -z "${MAIL-}" ]; then
+ MAIL="$1"
+ else
+ echo "Only one email address allowed"
+ exit 1
+ fi;;
+ esac
+ shift
+done
+[ "${models}" == "" ] && models="ial mesonh testprogs lmdz"
+
+[ ! -d ${WORKDIR} ] && mkdir -p ${WORKDIR}
+
+#stdout and stderr redirection
+logfile="${WORKDIR}/logfile"
+exec > "${logfile}" 2>&1
+
+#Title used to identify comments added by this script
+title="__ PHYEX TESTING V1.0 ${HOSTNAME} __"
+
+#Interactions with github
+if [ "${PHYEXREPOprotocol}" == 'ssh' ]; then
+ PHYEXREPOgiturl="git@github.com:${PHYEXREPOuser}/${PHYEXREPOrepo}.git"
+else
+ PHYEXREPOgiturl="https://github.com/${PHYEXREPOuser}/${PHYEXREPOrepo}.git"
+fi
+function get_last_commit {
+ git ls-remote "${PHYEXREPOgiturl}" "${REF}" | cut -f1
+}
+
+function get_comments {
+ SHA="$1"
+ curl -L --netrc \
+ -H "Accept: application/vnd.github+json" \
+ -H "X-GitHub-Api-Version: 2022-11-28" \
+ "https://api.github.com/repos/${PHYEXREPOuser}/${PHYEXREPOrepo}/commits/${SHA}/comments"
+}
+
+function add_comment {
+ SHA="$1"
+ comment="$2"
+
+ #The --netrc option does not seem to be enough, we manually read token from the .netrc file
+ TOKEN=$(python3 -c "import netrc, socket; print(netrc.netrc().authenticators('github.com')[2])")
+ curl -L --netrc \
+ -X POST \
+ -H "Authorization: Bearer $TOKEN"\
+ -H "Accept: application/vnd.github+json" \
+ -H "X-GitHub-Api-Version: 2022-11-28" \
+ "https://api.github.com/repos/${PHYEXREPOuser}/${PHYEXREPOrepo}/commits/${SHA}/comments" \
+ -d "{\"body\":\"${comment}\"}"
+}
+
+function get_cases {
+ SHA="$1"
+ file="$2"
+
+ url="https://raw.githubusercontent.com/${PHYEXREPOuser}/${PHYEXREPOrepo}/${SHA}/${file}"
+ content=$(wget --no-check-certificate "${url}" -O - 2>/dev/null)
+ if [ "${content}" != "" ]; then
+ content="${content}" python3 -c "import json, os; print(' '.join([k+':'+v for k, v in json.loads(os.environ['content']).get('testing', {}).items()]))"
+ fi
+}
+
+#reporting
+function send_mail {
+ message="$1"
+ if [ "$MAIL" != "" ]; then
+ mail -s "$title" "$MAIL" <<EOF
+$(echo -e ${message})
+EOF
+ fi
+}
+
+header="${title}\n\n$(date)"
+message=""
+function report {
+ ret=$1
+ if [ ${ret} -eq 0 ]; then
+ error_msg=""
+ else
+ error_msg="XXXXXXXXXXXXXXXXXXXX ERROR ${ret} XXXXXXXXXXXXXXXXXXXX"
+ error_msg="${error_msg}\n\n"
+ fi
+ message="${header}\n${message}\n\n${error_msg}$(date)"
+ if [ ${ret} -ne 0 ]; then
+ send_mail "${message}"
+ fi
+ if [ "${SHA}" != 0 ]; then
+ add_comment "${SHA}" "${message}"
+ fi
+}
+
+log_message=""
+function exit_error {
+ ret=$1
+ if [ ${ret} -ne 0 ]; then
+ message="__ ABNORMAL EXIT ${ret} __\n${log_message}\n${message}"
+ message="${message}\n\nMore information can be found in ${HOSTNAME}:${logfile}"
+ report ${ret}
+ fi
+}
+trap 'exit_error $?' EXIT
+
+function log {
+ level=$1; shift
+ echo "$@"
+ if [ ${level} -eq 0 ]; then
+ message="${message}\n$@"
+ fi
+ log_message="${log_message}\n$@"
+}
+
+#Test
+if [ "${SHA}" -eq 0 ]; then
+ log 1 "Getting last commit hash"
+ SHA=$(get_last_commit)
+ log 1 "Commit hash is ${SHA}"
+fi
+if [ ${force} -eq 1 -o $(get_comments "${SHA}" | grep "${title}" | wc -l) -eq 0 ]; then
+ log 1 "This commit has not been tested (or --force id provided)"
+ ret=0
+
+ export TESTPROGSDIR="${WORKDIR}/TESTPROGS"
+ export HOMEPACK="${WORKDIR}/pack"
+ export MNHPACK="${WORKDIR}/MesoNH"
+ export LMDZPACK="${WORKDIR}/LMDZ"
+ for d in "${TESTPROGSDIR}" "${HOMEPACK}" "${MNHPACK}" "${LMDZPACK}"; do
+ if [ ! -d "${d}" ]; then
+ log 1 "Creating directory ${d}"
+ mkdir -p "${d}"
+ fi
+ done
+
+ #Checkout tools, set PATH and use the last version of the testing script
+ currentdir="${PWD}"
+ if [ ${update} -eq 1 ]; then
+ currentMD5=$(md5sum "${BASH_SOURCE[0]}" | cut -d\ -f1)
+ if [ ! -d "${WORKDIR}/PHYEX" ]; then
+ log 1 "Clonig PHYEX in ${WORKDIR}/PHYEX"
+ git clone "${PHYEXREPOgiturl}" "${WORKDIR}/PHYEX"
+
+ log 1 "Installing filepp"
+ cd tools/mnh_expand
+ wget https://www-users.york.ac.uk/~dm26/filepp/filepp-1.8.0.tar.gz
+ tar xvf filepp-1.8.0.tar.gz
+ cd filepp-1.8.0
+ ./configure --prefix="${PWD}"
+ make install
+ cd ..
+ ln -s filepp-1.8.0 filepp
+
+ log 1 "Installing MNH_Expand_Array"
+ git clone https://github.com/JuanEscobarMunoz/MNH_Expand_Array.git
+ fi
+ log 1 "Checkout commit ${SHA}"
+ cd "${WORKDIR}/PHYEX"
+ git fetch "${PHYEXREPOgiturl}"
+ git checkout "${SHA}"
+ cd "${currentdir}"
+ . "${WORKDIR}/PHYEX/tools/env.sh"
+ if [ -f "${WORKDIR}/PHYEX/tools/testing.sh" ]; then
+ if [ "${currentMD5}" != $(md5sum "${WORKDIR}/PHYEX/tools/testing.sh" | cut -d\ -f1) ]; then
+ log 1 "Script has changed, running the new version" #This log and the preivous ones are lost
+ exec "${WORKDIR}/PHYEX/tools/testing.sh" $@
+ fi
+ fi
+ fi
+
+ for model in $models; do
+ log 1 "Starting tests for model ${model}"
+ #Model specific configuration
+ if [ "${model}" == 'ial' ]; then
+ compilation='-p -c'
+ execution='-r'
+ jsonfile="src/arome/ial_version.json"
+ docmp=1
+ elif [ "${model}" == 'lmdz' ]; then
+ compilation='-p -c --nofcm'
+ execution='-r --nofcm'
+ jsonfile="src/${model}/${model}_version.json"
+ docmp=0
+ else
+ compilation='-c'
+ execution='-r'
+ jsonfile="src/${model}/${model}_version.json"
+ docmp=1
+ fi
+
+ #Commande
+ cmd="check_commit_${model}.sh --repo-user ${PHYEXREPOuser} --repo-protocol ${PHYEXREPOprotocol} ${SHA}"
+
+ #Compilation
+ result=0
+ if [ ${compil} -eq 1 ]; then
+ compilecmd="$cmd ${compilation}"
+ log 1 "Compilation with ${compilecmd}"
+ set +e
+ ${compilecmd}
+ result=$?
+ set -e
+ if [ ${result} -ne 0 ]; then
+ ret=1
+ log 0 "${model} compilation: error"
+ else
+ log 0 "${model} compilation: OK"
+ fi
+ fi
+
+ #Execution and comparison
+ if [ ${result} -eq 0 ]; then
+ #Get the list of cases with associated references
+ cases=$(get_cases "${SHA}" "${jsonfile}")
+ [ "${cases}" == "" ] && cases="DEF:DEF"
+ for case_ref in ${cases}; do
+ case=$(echo "${case_ref}" | cut -d: -f1)
+ ref=$(echo "${case_ref}" | cut -d: -f2)
+ if [ "${case}" == "DEF" -a "${ref}" == "DEF" ]; then
+ casearg=""
+ refarg="REF"
+ casedescr="default case(s)"
+ log 1 "No cases found in ${jsonfile}, we only test the default cases"
+ else
+ casearg="-t ${case}"
+ refarg="${ref}"
+ casedescr="${case} (ref=${ref})"
+ log 1 "Testing case ${case} against reference ${ref}"
+ fi
+
+ result=0
+ if [ ${execute} -eq 1 ]; then
+ execcmd="$cmd ${execution} ${casearg}"
+ log 1 "Excution with ${execcmd}"
+ set +e
+ ${execcmd}
+ result=$?
+ set -e
+ if [ ${result} -ne 0 ]; then
+ ret=1
+ log 0 " ${model} ${casedescr}: execution error"
+ else
+ log 0 " ${model} ${casedescr}: execution OK (but status not reliable)"
+ fi
+ fi
+ if [ ${result} -eq 0 -a ${docmp} -eq 1 -a ${comp} -eq 1 ]; then
+ compcmd="$cmd -C ${casearg} ${refarg}"
+ log 1 "Comparison with ${compcmd}"
+ set +e
+ ${compcmd}
+ result=$?
+ set -e
+ if [ ${result} -ne 0 ]; then
+ ret=1
+ log 0 " ${model} ${casedescr}: comparison error"
+ else
+ log 0 " ${model} ${casedescr}: comparison OK"
+ fi
+ fi
+ done
+
+ #Cleaning
+ if [ ${remove} -eq 1 ]; then
+ cleancmd="${cmd} --remove"
+ log 1 "Cleaning with ${cleancmd}"
+ set +e
+ ${cleancmd}
+ result=$?
+ set -e
+ if [ ${result} -ne 0 ]; then
+ ret=1
+ log 0 " ${model}: cleaning error"
+ else
+ log 0 " ${model}: cleaning OK"
+ fi
+ fi
+ fi
+ done
+
+ #Report result
+ report ${ret}
+fi