[med-svn] [iqtree] 05/05: Create flexible test script usable at build time and in autopkgtest
Andreas Tille
tille at debian.org
Tue Sep 8 20:41:54 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository iqtree.
commit d24c98f8368608c0f4c928d128972dce4d303699
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 8 22:06:26 2015 +0200
Create flexible test script usable at build time and in autopkgtest
---
debian/Documents_source/create_example_script | 33 ++++++++++--
debian/Documents_source/example.sh | 72 +++++++++++++++++----------
debian/control | 3 +-
debian/rules | 10 +++-
4 files changed, 86 insertions(+), 32 deletions(-)
diff --git a/debian/Documents_source/create_example_script b/debian/Documents_source/create_example_script
index 4e70f62..abd0e1c 100755
--- a/debian/Documents_source/create_example_script
+++ b/debian/Documents_source/create_example_script
@@ -1,6 +1,31 @@
#!/bin/sh
+OUT=example.sh
+cat > $OUT <<EOT
+#!/bin/sh -e
+CURDIR=\`pwd\`
+if [ -d /usr/share/doc/iqtree/examples ] ; then
+ EXAMPLEDIR=/usr/share/doc/iqtree/examples
+else
+ EXAMPLEFILE=\`find \$CURDIR -name example.phy | head -n 1\`
+ EXAMPLEDIR=\`dirname \$EXAMPLEFILE\`
+fi
+
+pkg=iqtree
+if [ "\$ADTTMP" = "" ] ; then
+ ADTTMP=\`mktemp -d /tmp/\${pkg}-test.XXXXXX\`
+fi
+cd \$ADTTMP
+cp -a \$EXAMPLEDIR/example.phy* \$EXAMPLEDIR/example.nex* .
+find . -name "*.gz" -exec gunzip \{\} \;
+
+PATHTOEXE=\`which iqtree\`
+if [ "\$PATHTOEXE" = "" ] ; then
+ PATHTOEXE=\`find \$CURDIR -name iqtree -type f -executable\`
+fi
+echo "Executing tests using \$PATHTOEXE ..."
+EOT
+
grep example.phy iqtree-manual-1.0.tex | \
- grep "^ *iqtree" | \
- sed -e 's?example.phy?/usr/share/doc/iqtree/examples/&?' \
- -e 's?example.nex?/usr/share/doc/iqtree/examples/&?' \
- > example.sh
+ grep '^ *iqtree' | \
+ sed "s?^ *iqtree?time \$PATHTOEXE?" \
+ >> ${OUT}
diff --git a/debian/Documents_source/example.sh b/debian/Documents_source/example.sh
index 3458968..9bf139c 100644
--- a/debian/Documents_source/example.sh
+++ b/debian/Documents_source/example.sh
@@ -1,25 +1,47 @@
- iqtree -s /usr/share/doc/iqtree/examples/example.phy
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -pre myprefix
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -nni1
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TEST
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TESTONLY
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -pll -m GTR+G
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -bb 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -b 100
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -alrt 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -lbp 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -alrt 1000 -lbp 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m TIM+I+G -bb 1000 -alrt 1000 -lbp 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -sp /usr/share/doc/iqtree/examples/example.nex
- iqtree-omp -s /usr/share/doc/iqtree/examples/example.phy
- iqtree-omp -s /usr/share/doc/iqtree/examples/example.phy -omp 2
- iqtree-omp -s /usr/share/doc/iqtree/examples/example.phy -omp 3
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -z example.treels
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -z example.treels -n 1
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -z example.treels -n 1 -zb 1000
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -z example.treels -n 1 -zb 1000 -zw
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m 010010+G
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m mymodel+G
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m 'TN{2.0,3.0}+G8{0.5}+I{0.15}'
- iqtree -s /usr/share/doc/iqtree/examples/example.phy -m GTR+G+Fo
+#!/bin/sh -e
+CURDIR=`pwd`
+if [ -d /usr/share/doc/iqtree/examples ] ; then
+ EXAMPLEDIR=/usr/share/doc/iqtree/examples
+else
+ EXAMPLEFILE=`find $CURDIR -name example.phy | head -n 1`
+ EXAMPLEDIR=`dirname $EXAMPLEFILE`
+fi
+
+pkg=iqtree
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a $EXAMPLEDIR/example.phy* $EXAMPLEDIR/example.nex* .
+find . -name "*.gz" -exec gunzip \{\} \;
+
+PATHTOEXE=`which iqtree`
+if [ "$PATHTOEXE" = "" ] ; then
+ PATHTOEXE=`find $CURDIR -name iqtree -type f -executable`
+fi
+echo "Executing tests using $PATHTOEXE ..."
+time $PATHTOEXE -s example.phy
+time $PATHTOEXE -s example.phy -pre myprefix
+time $PATHTOEXE -s example.phy -nni1
+time $PATHTOEXE -s example.phy -m TEST
+time $PATHTOEXE -s example.phy -m TIM+I+G
+time $PATHTOEXE -s example.phy -m TESTONLY
+time $PATHTOEXE -s example.phy -pll -m GTR+G
+time $PATHTOEXE -s example.phy -m TIM+I+G -bb 1000
+time $PATHTOEXE -s example.phy -m TIM+I+G -b 100
+time $PATHTOEXE -s example.phy -m TIM+I+G -alrt 1000
+time $PATHTOEXE -s example.phy -m TIM+I+G -lbp 1000
+time $PATHTOEXE -s example.phy -m TIM+I+G -alrt 1000 -lbp 1000
+time $PATHTOEXE -s example.phy -m TIM+I+G -bb 1000 -alrt 1000 -lbp 1000
+time $PATHTOEXE -s example.phy -sp example.nex
+time $PATHTOEXE-omp -s example.phy
+time $PATHTOEXE-omp -s example.phy -omp 2
+time $PATHTOEXE-omp -s example.phy -omp 3
+time $PATHTOEXE -s example.phy -z example.treels
+time $PATHTOEXE -s example.phy -z example.treels -n 1
+time $PATHTOEXE -s example.phy -z example.treels -n 1 -zb 1000
+time $PATHTOEXE -s example.phy -z example.treels -n 1 -zb 1000 -zw
+time $PATHTOEXE -s example.phy -m 010010+G
+time $PATHTOEXE -s example.phy -m mymodel+G
+time $PATHTOEXE -s example.phy -m 'TN{2.0,3.0}+G8{0.5}+I{0.15}'
+time $PATHTOEXE -s example.phy -m GTR+G+Fo
diff --git a/debian/control b/debian/control
index 3ba4c8a..9ec8622 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,8 @@ Build-Depends: debhelper (>= 9),
libeigen3-dev,
libsprng2-dev,
zlib1g-dev,
- help2man
+ help2man,
+ time
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/iqtree.git
Vcs-Git: git://anonscm.debian.org/debian-med/iqtree.git
diff --git a/debian/rules b/debian/rules
index a80ae3a..2aa2fff 100755
--- a/debian/rules
+++ b/debian/rules
@@ -25,8 +25,14 @@ override_dh_installman:
--name='efficient phylogenetic software by maximum likelihood' \
--version-string="$(version)" $(CURDIR)/debian/$(pkg)/usr/bin/iqtree > $(mandir)/iqtree.1
-override_dh_compress:
- dh_compress --exclude=.phy --exclude=.nex
+override_dh_auto_test:
+ # use only the first example for build time test to save time on autobuilders
+ sed '/ myprefix/,$$d' debian/Documents_source/example.sh > example.short
+ time sh example.short
+ rm example.short
+
+#override_dh_compress:
+# dh_compress --exclude=.phy --exclude=.nex
get-orig-source:
uscan --verbose --force-download --repack --compression xz
--
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