[med-svn] [Git][med-team/blasr][master] 4 commits: Fix test file substitution regex

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / blasr


Commits:
b59a1aeb by Nilesh Patra at 2022-09-29T15:12:24+00:00
Fix test file substitution regex

- - - - -
8306dd3d by Nilesh Patra at 2022-09-29T20:51:05+05:30
Cat the files for future output ref/md5sum mismatch

- - - - -
f131b550 by Nilesh Patra at 2022-09-29T20:51:42+05:30
Update overrides

- - - - -
b3f49187 by Nilesh Patra at 2022-09-29T20:52:21+05:30
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/source/lintian-overrides
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+blasr (5.3.5+dfsg-5) unstable; urgency=medium
+
+  * Team Upload.
+  * Update lintian overrides
+  * Fix test file substitution regex in autopkgtest (Closes: #1018972)
+
+ -- Nilesh Patra <nilesh at debian.org>  Thu, 29 Sep 2022 20:51:45 +0530
+
 blasr (5.3.5+dfsg-4) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/source/lintian-overrides
=====================================
@@ -1,3 +1,3 @@
 # False Positives
-source: very-long-line-length-in-source-file README.md *
-source: very-long-line-length-in-source-file ctest/pgc-fasta.t *
+blasr source: very-long-line-length-in-source-file 701 > 512 [README.md:21]
+blasr source: very-long-line-length-in-source-file 9883 > 512 [ctest/pgc-fasta.t:28]


=====================================
debian/tests/run-unit-test
=====================================
@@ -18,12 +18,20 @@ blasr query.fasta ref.fa --minMatch 1 --maxMatch 10 > output
 if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
 then
 	echo "8db2f4d5737a90d087da90a6779c8d7b  output" >> checksums
-	sed 's/\(PN:BLASR[[:space:]]\+VN:\)5.3.5\([[:space:]]\+CL:blasr\)/\1VERSION\2/' alignment.sam > alignment.sam.check
+	sed 's/\(PN:BLASR.*VN:\).*5.3.5\(.*\+CL:blasr\)/\1VERSION\2/' alignment.sam > alignment.sam.check
+
+	# Cat orig file for future ref/regressions
+	echo "alignment.sam"
+	cat alignment.sam
+
+	# Cat expected file for future ref/regressions
+	echo "alignment.sam.check:"
+	cat alignment.sam.check
+
 	echo "4ff931c75012f8c2e02c75120351e217  alignment.sam.check" >> checksums
-	
-  md5sum --check checksums
+	md5sum --check checksums
 	echo "Expected output and generated output are same: PASS Test"
 else
 	[ -s "output" ] && [ -s "alignment.sam" ] || exit 1
 	echo "PASS Test"
-fi
\ No newline at end of file
+fi



View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/a516ef9d7c22f7f26b520f1ce199b3a187a40083...b3f49187493ebb64cd84abd406f962d9840f6342

-- 
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/a516ef9d7c22f7f26b520f1ce199b3a187a40083...b3f49187493ebb64cd84abd406f962d9840f6342
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