[med-svn] [Git][med-team/fastlink][master] 5 commits: Add autopkgtests
Shruti Sridhar
gitlab at salsa.debian.org
Sun Feb 21 20:03:06 GMT 2021
Shruti Sridhar pushed to branch master at Debian Med / fastlink
Commits:
565ffced by Shruti Sridhar at 2021-02-22T01:25:19+05:30
Add autopkgtests
- - - - -
9cd74b54 by Shruti Sridhar at 2021-02-22T01:25:39+05:30
Add docs
- - - - -
195bb66a by Shruti Sridhar at 2021-02-22T01:28:09+05:30
Add data
- - - - -
34552a7a by Shruti Sridhar at 2021-02-22T01:28:19+05:30
Add examples
- - - - -
994afe56 by Shruti Sridhar at 2021-02-22T01:32:25+05:30
Update changelog
- - - - -
8 changed files:
- + debian/README.test
- debian/changelog
- + debian/examples
- debian/fastlink.docs
- + debian/tests/control
- + debian/tests/data/datafile.dat
- + debian/tests/data/pedfile.dat
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,14 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
+
+Notes on the files used for testing
+────────────────────────────────────────
+Files: debian/tests/data/*
+Source: https://watson.hgen.pitt.edu/docs/SLink.html
+
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+fastlink (4.1P-fix100+dfsg-3ubuntu1) UNRELEASED; urgency=medium
+
+ * Add autopkgtests. Closes: #909713
+ * Add docs
+ * Add data
+ * Add examples
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com> Mon, 22 Feb 2021 01:30:24 +0530
+
fastlink (4.1P-fix100+dfsg-3) unstable; urgency=medium
* Add fake watch file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/fastlink.docs
=====================================
@@ -16,3 +16,6 @@ README.trouble
README.unknown
README.updates
debian/fastlink.html
+debian/README*
+debian/tests/run-unit-test
+
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/datafile.dat
=====================================
@@ -0,0 +1,16 @@
+3 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
+ 0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1)
+ 1 3 2
+3 3 << ALLELE NUMBERS, NO. OF ALLELES Locus p105-599Ha/TaqI
+ 0.320000 0.160000 0.520000 << GENE FREQUENCIES
+1 2 << AFFECTION, NO. OF ALLELES Locus Schizophrenia
+ 0.991500 0.008500 << GENE FREQUENCIES
+ 3 << NO. OF LIABILITY CLASSES
+ 1.0000 0.1400 0.0000 Normal
+ 0.0000 0.8600 0.0000 Affected
+ 1.0000 0.0000 0.0000 Married in Normals << PENETRANCES
+3 2 << ALLELE NUMBERS, NO. OF ALLELES Locus p105-153Ra/XbaI
+ 0.330000 0.670000 << GENE FREQUENCIES
+ 0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
+ 0.11970 0.12500 << RECOMBINATION VALUES
+ 2 0.12500 0.38000 << REC VARIED, INCREMENT, FINISHING VALUE
\ No newline at end of file
=====================================
debian/tests/data/pedfile.dat
=====================================
@@ -0,0 +1,31 @@
+1 1 0 0 3 0 0 1 1 1 3 2 3 1 2 2 Linked Mk Avail; Tr orig
+ 1 2 0 0 3 0 0 2 0 0 0 2 2 0 0 0 Linked Mk Unkno; Tr orig
+ 1 3 1 2 0 4 4 2 0 1 3 2 2 1 2 2 Linked Mk Avail; Tr orig
+ 1 4 1 2 0 5 5 2 0 1 3 2 1 1 1 2 Linked Mk Avail; Tr orig
+ 1 5 1 2 0 6 6 1 0 1 3 2 2 1 2 2 Linked Mk Avail; Tr orig
+ 1 6 1 2 0 7 7 2 0 3 3 2 1 2 2 2 Linked Mk Avail; Tr orig
+ 1 7 1 2 0 8 8 1 0 3 3 2 1 2 2 2 Linked Mk Avail; Tr orig
+ 1 8 1 2 0 9 9 1 0 1 1 2 2 1 1 2 Linked Mk Avail; Tr orig
+ 1 9 1 2 0 10 10 1 0 1 3 2 2 1 2 2 Linked Mk Avail; Tr orig
+ 1 10 1 2 14 12 12 2 0 1 1 2 2 1 1 2 Linked Mk Avail; Tr orig
+ 1 11 0 0 14 0 0 1 0 1 3 2 3 2 2 2 Linked Mk Avail; Tr orig
+ 1 12 1 2 0 13 13 1 0 1 1 2 2 2 1 2 Linked Mk Avail; Tr orig
+ 1 13 1 2 0 0 0 2 0 3 3 2 1 1 2 2 Linked Mk Avail; Tr orig
+ 1 14 11 10 0 15 15 2 0 1 3 2 1 1 2 2 Linked Mk Avail; Tr orig
+ 1 15 11 10 0 16 16 1 0 1 1 2 2 2 1 2 Linked Mk Avail; Tr orig
+ 1 16 11 10 0 17 17 1 0 1 3 2 2 1 2 2 Linked Mk Avail; Tr orig
+ 1 17 11 10 0 0 0 2 0 1 3 2 1 1 2 2 Linked Mk Avail; Tr orig
+ 2 1 0 0 3 0 0 1 1 0 0 2 3 0 0 0 Linked Mk Unkno; Tr orig
+ 2 2 0 0 3 0 0 2 0 1 2 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 3 1 2 0 4 4 2 0 1 1 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 4 1 2 0 5 5 1 0 1 1 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 5 1 2 0 6 6 1 0 1 1 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 6 1 2 10 8 8 1 0 1 2 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 7 0 0 10 0 0 2 0 3 3 2 3 1 2 2 Linked Mk Avail; Tr orig
+ 2 8 1 2 13 0 0 2 0 1 2 2 2 2 2 2 Linked Mk Avail; Tr orig
+ 2 9 0 0 13 0 0 1 0 1 3 2 3 2 1 2 Linked Mk Avail; Tr orig
+ 2 10 6 7 0 11 11 1 0 2 3 2 1 2 1 2 Linked Mk Avail; Tr orig
+ 2 11 6 7 0 12 12 1 0 2 3 2 1 2 2 2 Linked Mk Avail; Tr orig
+ 2 12 6 7 0 0 0 1 0 1 3 2 2 2 1 2 Linked Mk Avail; Tr orig
+ 2 13 9 8 0 14 14 1 0 1 2 2 1 2 2 2 Linked Mk Avail; Tr orig
+ 2 14 9 8 0 0 0 1 0 1 1 2 2 2 2 2 Linked Mk Avail; Tr orig
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,33 @@
+#!/bin/bash
+set -e
+
+pkg=fastlink
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+unknown
+echo "95dc2997370f4f76928fd79e09a10a50 ipedfile.dat" >> checksums
+echo "30944ffa33e66c2923c1cd1d78112ec8 loopfile.dat" >> checksums
+echo "d8e8c1a3795eb42b23de343d992b1f7b newspeedfile.dat" >> checksums
+echo "8e461242dc9ebce4ff855790e1b2d349 speedfile.dat" >> checksums
+
+mlink > linkage
+echo "7c26709e720f8232a5e204ff1b97e067 linkage" >> checksums
+
+linkmap > map
+echo "8040c09d668a567ca1bc85ea8f10a67f map" >> checksums
+
+lodscore > score
+sed -i '3,18!d' score
+echo "b20aea5b69fbf609153f1bcf427def36 score" >> checksums
+
+md5sum --check checksums
+
View it on GitLab: https://salsa.debian.org/med-team/fastlink/-/compare/72a91f9f65385ce7c0f45f2834b5b823553e2464...994afe56de484c4c88c672e8fbba20f01e8cce2b
--
View it on GitLab: https://salsa.debian.org/med-team/fastlink/-/compare/72a91f9f65385ce7c0f45f2834b5b823553e2464...994afe56de484c4c88c672e8fbba20f01e8cce2b
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210221/3b69cb12/attachment-0001.htm>
More information about the debian-med-commit
mailing list