[med-svn] [Git][med-team/quicktree][master] 3 commits: Add autopkgtests

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / quicktree


Commits:
cb1c6212 by Nilesh Patra at 2020-08-07T16:37:05+05:30
Add autopkgtests

- - - - -
157b6736 by Nilesh Patra at 2020-08-07T16:37:25+05:30
Install relevant examples

- - - - -
f341e758 by Nilesh Patra at 2020-08-07T16:37:48+05:30
Fix spellings

- - - - -


6 changed files:

- + debian/examples
- debian/rules
- + debian/tests/README
- + debian/tests/control
- + debian/tests/data/cysprot.stockholm
- + debian/tests/run-unit-test


Changes:

=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/cysprot.stockholm


=====================================
debian/rules
=====================================
@@ -8,6 +8,8 @@ export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
 	dh $@
 
 override_dh_auto_build:
+	sed -i 's/expexted/expected/' src/tree.c
+	sed -i 's/optio\\n/option/' src/quicktree.c	
 	dh_auto_build
 	help2man -i debian/quicktree.htm --no-discard-stderr ./quicktree > quicktree.1
 


=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for quicktree
+===================
+
+The data for tests has been referenced from:
+	https://salsa.debian.org/med-team/bioperl-run/-/blob/master/t/data/cysprot.stockholm


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+


=====================================
debian/tests/data/cysprot.stockholm
=====================================
@@ -0,0 +1,12 @@
+# STOCKHOLM 1.0
+
+#=GF ID   NoName
+
+CATH_HUMAN/1-335      ....MWATLPLLCAGAWLLGVPVCGAAELSVN..........................SLEKFHFKSWMSKHRKTYS.TEEYHHRLQTFASNWRKINAHN....NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDF........NNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY.CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT.QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNG.....IPYWIVKNSWGPQWGMNGYFLIERGK....NMCGLAACASYPIPLV
+CATH_RAT/1-333        ....MWTALPLLCAGAWLLSAGAT..AELTVN..........................AIEKFHFTSWMKQHQKTYS.SREYSHRLQVFANNWRKIQAHN....QRNHTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNF........NNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNGQ.CKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVT.EDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNG.....LLYWIVKNSWGSNWGNNGYFLIERGK....NMCGLAACASYPIPQV
+ALEU_HORVU/1-362      ....MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN....RKGLPYRLGINRFSDMSWEEFQATRLG.AAQTCSATLAGNHLMRDAA..ALPETKDWREDG.IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGF........NNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV.CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI.DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENG.....VPYWLIKNSWGADWGDNGYFKMEMGK....NMCAIATCASYPVVAA
+PAPA_CARPA/1-345      MAMIPSISKLLFVAICLFVYMGLSFGDFSIVG.................YSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETN....KKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKG.AVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDR..........RSYGCNGGYPWSALQLVAQYG.IHYRNTYPYEGVQRY.CRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVG....PCGNKVDHAVAAVGYGPN.........YILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN.
+CATL_HUMAN/1-333      ......MNPTLILAAFCLGIASATLTFDHSLE..............................AQWTKWKAMHNRLYG.MNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ....NRKPRKGKVFQEPLFYEAPRSVDWREKG.YVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGP....QG....NEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES.CKYNPKYSVANDTGFVDIPK.QEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPD..CSSEDMDHGVLVVGYGFESTESDNNK.YWLVKNSWGEEWGMGGYVKMAKDRR...NHCGIASAASYPTV..
+CATL_RAT/1-334        ......MTPLLLLAVLCLGTALATPKFDQTFN..............................AQWHQWKSTHRRLYG.TNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYR....HQKHKKGRLFQEPLMLQIPKTVDWREKG.CVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHD....QG....NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS.CKYRAEYAVANDTGFVDIPQ.QEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPN..CSSKDLDHGVLVVGYGYEGTDSNKDK.YWLVKNSWGKEWGMDGYIKIAKDRN...NHCGLATAASYPIVN.
+CYS1_DICDI/1-343      ......MKVILLFVLAVFTVFVSSRGIPPEEQ..............................SQFLEFQDKFNKKYS.HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG.AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK.NETVMAGYIVSTGPLAIAADA..VEWQFYIGGVFDIP...CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK....NTCGVSNFVSTSII..
+//


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=quicktree
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+echo 'Test Basic functionality'
+quicktree -upgma -boot 0 cysprot.stockholm 
+echo 'PASS'
+



View it on GitLab: https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d

-- 
View it on GitLab: https://salsa.debian.org/med-team/quicktree/-/compare/b809b19533a9b9947b23ff8a4a434010984d3563...f341e75896107d2b49991561c78446d09e71a46d
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