[med-svn] [Git][med-team/probabel][master] 4 commits: Patch executables path in examples
Pranav Ballaney
gitlab at salsa.debian.org
Mon Aug 3 16:22:19 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / probabel
Commits:
984c965c by Pranav Ballaney at 2020-08-03T20:45:43+05:30
Patch executables path in examples
- - - - -
4a905312 by Pranav Ballaney at 2020-08-03T20:46:04+05:30
Add autopkgtests
- - - - -
742b5953 by Pranav Ballaney at 2020-08-03T20:47:57+05:30
Install docs
- - - - -
f3346ba2 by Pranav Ballaney at 2020-08-03T20:49:19+05:30
Add Pranav Ballaney to Uploaders
- - - - -
8 changed files:
- + debian/README.test
- debian/changelog
- debian/control
- + debian/docs
- + debian/patches/examples.patch
- debian/patches/series
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+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.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+probabel (0.5.0+dfsg-4) UNRELEASED; urgency=medium
+
+ * Patch executables path in examples
+ * Add autopkgtests
+ * Install docs
+ * Add Pranav Ballaney to Uploaders
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Mon, 03 Aug 2020 20:49:03 +0530
+
probabel (0.5.0+dfsg-3) unstable; urgency=medium
* Add ppc64el to architectures where test result is ignored due to
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: probabel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- L.C. Karssen <lennart at karssen.org>
+ L.C. Karssen <lennart at karssen.org>,
+ Pranav Ballaney <ballaneypranav at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
=====================================
debian/docs
=====================================
@@ -0,0 +1,4 @@
+README*
+doc/QuickStart.txt
+doc/README*
+debian/README*
\ No newline at end of file
=====================================
debian/patches/examples.patch
=====================================
@@ -0,0 +1,44 @@
+--- a/examples/example_bt.sh
++++ b/examples/example_bt.sh
+@@ -9,7 +9,7 @@ gtdatadir="gtdata"
+ # installed ProbABEL according to the instructions in the doc/INSTALL
+ # file, or installed it via your Linux distribution's package manager,
+ # you can leave this variable empty.
+-padir="../src/"
++padir=""
+
+
+ # Using text-based dosage genotype files as input
+--- a/examples/example_cox.sh
++++ b/examples/example_cox.sh
+@@ -8,7 +8,7 @@ gtdatadir="gtdata"
+ # installed ProbABEL according to the instructions in the doc/INSTALL
+ # file, or installed it via your Linux distribution's package manager,
+ # you can leave this variable empty.
+-padir="../src/"
++padir=""
+
+
+ # Using text-based dosage genotype files as input
+--- a/examples/example_mmscore.sh
++++ b/examples/example_mmscore.sh
+@@ -11,7 +11,7 @@ gtdatadir="gtdata"
+ # installed ProbABEL according to the instructions in the doc/INSTALL
+ # file, or installed it via your Linux distribution's package manager,
+ # you can leave this variable empty.
+-padir="../src/"
++padir=""
+
+
+ # Using text-based dosage genotype files as input
+--- a/examples/example_qt.sh
++++ b/examples/example_qt.sh
+@@ -10,7 +10,7 @@ gtdatadir="gtdata"
+ # installed ProbABEL according to the instructions in the doc/INSTALL
+ # file, or installed it via your Linux distribution's package manager,
+ # you can leave this variable empty.
+-padir="${padir}"
++padir=""
+
+ # Using text-based dosage genotype files as input
+ echo "basic analysis"
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
+examples.patch
c++11.patch
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,137 @@
+#!/bin/bash
+set -e
+
+pkg=probabel
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+
+gunzip -r *
+ls -R
+#do_stuff_to_test_package#
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+
+./example_bt.sh
+
+echo "68c03a199e054d2571a962d5e023945c logist_add.out.txt" >> checksums
+echo "68c03a199e054d2571a962d5e023945c logist_fv_add.out.txt" >> checksums
+echo "ed3e18330990192e764646f9b47a76d3 logist_prob_2df.out.txt" >> checksums
+echo "68c03a199e054d2571a962d5e023945c logist_prob_add.out.txt" >> checksums
+echo "18272da9ee07c7306a8658fb8683a644 logist_prob_domin.out.txt" >> checksums
+echo "ed3e18330990192e764646f9b47a76d3 logist_prob_fv_2df.out.txt" >> checksums
+echo "68c03a199e054d2571a962d5e023945c logist_prob_fv_add.out.txt" >> checksums
+echo "18272da9ee07c7306a8658fb8683a644 logist_prob_fv_domin.out.txt" >> checksums
+echo "886faec17489000e013e0beeb0b2634d logist_prob_fv_over_domin.out.txt" >> checksums
+echo "85197b01f372230ec136a89df248ca7e logist_prob_fv_recess.out.txt" >> checksums
+echo "886faec17489000e013e0beeb0b2634d logist_prob_over_domin.out.txt" >> checksums
+echo "85197b01f372230ec136a89df248ca7e logist_prob_recess.out.txt" >> checksums
+
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+
+./example_cox.sh
+
+rm checksums
+echo "e265eec53382ad7b049275649742f564 coxph_dose_add.out.txt" >> checksums
+echo "e265eec53382ad7b049275649742f564 coxph_dose_fv_add.out.txt" >> checksums
+echo "439b1f56bf76917d9f73ea04fbf12e10 coxph_prob_2df.out.txt" >> checksums
+echo "e265eec53382ad7b049275649742f564 coxph_prob_add.out.txt" >> checksums
+echo "2bfb396e615585e36647f3fd0e3a7475 coxph_prob_domin.out.txt" >> checksums
+echo "439b1f56bf76917d9f73ea04fbf12e10 coxph_prob_fv_2df.out.txt" >> checksums
+echo "e265eec53382ad7b049275649742f564 coxph_prob_fv_add.out.txt" >> checksums
+echo "2bfb396e615585e36647f3fd0e3a7475 coxph_prob_fv_domin.out.txt" >> checksums
+echo "757fa3187a3fdef308ac31b7d3416614 coxph_prob_fv_over_domin.out.txt" >> checksums
+echo "7a81d14bcf571c3dc456abd90254deb9 coxph_prob_fv_recess.out.txt" >> checksums
+echo "757fa3187a3fdef308ac31b7d3416614 coxph_prob_over_domin.out.txt" >> checksums
+echo "7a81d14bcf571c3dc456abd90254deb9 coxph_prob_recess.out.txt" >> checksums
+
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+
+./example_mmscore.sh
+
+rm checksums
+echo "791929049d1c7950ecab01cc6450e71a mmscore_dose_add.out.txt" >> checksums
+echo "791929049d1c7950ecab01cc6450e71a mmscore_dose_fv_add.out.txt" >> checksums
+echo "b8a3e34a6398f64d1df4dd164cc0b39c mmscore_prob_2df.out.txt" >> checksums
+echo "791929049d1c7950ecab01cc6450e71a mmscore_prob_add.out.txt" >> checksums
+echo "ee050519b0612a83f9612f85d4cfaa52 mmscore_prob_domin.out.txt" >> checksums
+echo "b8a3e34a6398f64d1df4dd164cc0b39c mmscore_prob_fv_2df.out.txt" >> checksums
+echo "791929049d1c7950ecab01cc6450e71a mmscore_prob_fv_add.out.txt" >> checksums
+echo "ee050519b0612a83f9612f85d4cfaa52 mmscore_prob_fv_domin.out.txt" >> checksums
+echo "8dcba7570c9000230bdcad862a5fb0fd mmscore_prob_fv_over_domin.out.txt" >> checksums
+echo "dbb8fd46b55b7b391d73d059f7eccbac mmscore_prob_fv_recess.out.txt" >> checksums
+echo "8dcba7570c9000230bdcad862a5fb0fd mmscore_prob_over_domin.out.txt" >> checksums
+echo "dbb8fd46b55b7b391d73d059f7eccbac mmscore_prob_recess.out.txt" >> checksums
+
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+
+./example_qt.sh
+
+rm checksums
+echo "28793bacdc6669f72aab25569f8ec009 height_allcov_fv_add.out.txt" >> checksums
+echo "2fd1eb068363f83a5965f07f37570f87 height_base_add.out.txt" >> checksums
+echo "2fd1eb068363f83a5965f07f37570f87 height_base_fv_add.out.txt" >> checksums
+echo "899928574b0313b09dccba699cdd9d94 height_int1_fv_add.out.txt" >> checksums
+echo "f22db745b47e9975b000c272f45c433a height_ngp2_2df.out.txt" >> checksums
+echo "2fd1eb068363f83a5965f07f37570f87 height_ngp2_add.out.txt" >> checksums
+echo "53ebb5400919cbce3459b60b0490a1b9 height_ngp2_allcov_fv_2df.out.txt" >> checksums
+echo "28793bacdc6669f72aab25569f8ec009 height_ngp2_allcov_fv_add.out.txt" >> checksums
+echo "71246344e2f2b59dea547c301f45c180 height_ngp2_allcov_fv_domin.out.txt" >> checksums
+echo "9fa7a891fd59b8cb9c99bec5ce4a881a height_ngp2_allcov_fv_over_domin.out.txt" >> checksums
+echo "b09bf47ef40977a91d6298624f8d9cc1 height_ngp2_allcov_fv_recess.out.txt" >> checksums
+echo "6b2bd9c9068bbd93ae028fc967899464 height_ngp2_domin.out.txt" >> checksums
+echo "f22db745b47e9975b000c272f45c433a height_ngp2_fv_2df.out.txt" >> checksums
+echo "2fd1eb068363f83a5965f07f37570f87 height_ngp2_fv_add.out.txt" >> checksums
+echo "6b2bd9c9068bbd93ae028fc967899464 height_ngp2_fv_domin.out.txt" >> checksums
+echo "1c4c9e0a1573be84392e75ec80f48048 height_ngp2_fv_over_domin.out.txt" >> checksums
+echo "9c01531e3c01013308f2a9ab693227ed height_ngp2_fv_recess.out.txt" >> checksums
+echo "516b6052d30df298ae5d4507e50cfaae height_ngp2_int1_fv_2df.out.txt" >> checksums
+echo "899928574b0313b09dccba699cdd9d94 height_ngp2_int1_fv_add.out.txt" >> checksums
+echo "83bfad80d7077ade08497453e444c7e4 height_ngp2_int1_fv_domin.out.txt" >> checksums
+echo "7d5b0288ced3b044930d0d59573fd8d8 height_ngp2_int1_fv_over_domin.out.txt" >> checksums
+echo "e69263eba3939d87572a76c4ec5749bb height_ngp2_int1_fv_recess.out.txt" >> checksums
+echo "1c4c9e0a1573be84392e75ec80f48048 height_ngp2_over_domin.out.txt" >> checksums
+echo "9c01531e3c01013308f2a9ab693227ed height_ngp2_recess.out.txt" >> checksums
+echo "b88b24ec1f197cad0d7ee1642375f0f8 height_ngp2_robust_fv_2df.out.txt" >> checksums
+echo "770ae8c5d4c5950af5cca28ea8c3be03 height_ngp2_robust_fv_add.out.txt" >> checksums
+echo "0946a8b6f3193c1e5a6994e6771fc4a9 height_ngp2_robust_fv_domin.out.txt" >> checksums
+echo "f4111f088959d5ae7421d990581f7506 height_ngp2_robust_fv_over_domin.out.txt" >> checksums
+echo "cc30f61baf5c8eacfa2c876d1ee23a81 height_ngp2_robust_fv_recess.out.txt" >> checksums
+echo "a13b9398bb6f9f4d362310508b65efe7 height_ngp2_robust_int1_fv_2df.out.txt" >> checksums
+echo "bda239a9ab25d53b415575d70c0219be height_ngp2_robust_int1_fv_add.out.txt" >> checksums
+echo "c1396b25602cfabf657e66314df150b4 height_ngp2_robust_int1_fv_domin.out.txt" >> checksums
+echo "780951e73361135649fa8e9a0b362c0a height_ngp2_robust_int1_fv_over_domin.out.txt" >> checksums
+echo "d605c4b52658eadd5efbfed35f17e6f4 height_ngp2_robust_int1_fv_recess.out.txt" >> checksums
+echo "770ae8c5d4c5950af5cca28ea8c3be03 height_robust_fv_add.out.txt" >> checksums
+echo "bda239a9ab25d53b415575d70c0219be height_robust_int1_fv_add.out.txt" >> checksums
+
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/probabel/-/compare/0390ea6b503a30e731c3f8a3b385c207d96e6d88...f3346ba2f12201ad7a6dd07f9bd6854579154c69
--
View it on GitLab: https://salsa.debian.org/med-team/probabel/-/compare/0390ea6b503a30e731c3f8a3b385c207d96e6d88...f3346ba2f12201ad7a6dd07f9bd6854579154c69
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