[med-svn] [Git][med-team/canu][master] 3 commits: update cpuid bug forwarding

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / canu


Commits:
819e8fa1 by Michael R. Crusoe at 2023-08-22T16:59:22+02:00
update cpuid bug forwarding

- - - - -
179ab22a by Michael R. Crusoe at 2023-09-29T16:14:57+02:00
d/tests/run-unit-test: entire test suite output is too large for saving

- - - - -
5da39a50 by Michael R. Crusoe at 2023-09-29T18:30:39+02:00
routine-update: Ready to upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/patches/cpuid
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+canu (2.2+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+  * d/tests/run-unit-test: entire test suite output is too large for
+    saving, so only copy over a bit
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Fri, 29 Sep 2023 16:19:22 +0200
+
 canu (2.2+dfsg-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/cpuid
=====================================
@@ -1,10 +1,6 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: enable cpuid on arm64, pcc64el, and other architectures
-Forwarded: https://github.com/marbl/meryl-utility/pull/4
-
-By synchronizing with upstream parasail
-
-https://github.com/jeffdaily/parasail/blob/600fb26151ff19899ee39a214972dcf2b9b11ed7/src/cpuid.c
+Forwarded: https://github.com/jeffdaily/parasail/pull/102
 
 --- canu.orig/src/utility/src/parasail/cpuid.c
 +++ canu/src/utility/src/parasail/cpuid.c


=====================================
debian/tests/run-unit-test
=====================================
@@ -11,10 +11,12 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
 fi
 export TMPDIR="${AUTOPKGTEST_TMP}"
 
-if [ "${AUTOPKGTEST_ARTIFACTS}" = "" ] ; then
-  AUTOPKGTEST_ARTIFACTS=${PWD}
-fi
-cd "${AUTOPKGTEST_ARTIFACTS}"
+#if [ "${AUTOPKGTEST_ARTIFACTS}" = "" ] ; then
+#  AUTOPKGTEST_ARTIFACTS=${PWD}
+#fi
+#cd "${AUTOPKGTEST_ARTIFACTS}"
+# Too big, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1050388
+cd "${AUTOPKGTEST_TMP}"
 
 cores=$(nproc)
 mem=$(free --giga | grep Mem | awk '{ print $7}')
@@ -36,9 +38,16 @@ fi
 
 curl -L -o "${AUTOPKGTEST_TMP}"/pacbio.fastq \
 	http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p6_25x.filtered.fastq
-
+set +e
 # shellcheck disable=SC2086
 canu -p ecoli -d ecoli-pacbio \
 	genomeSize=4.8m \
 	maxThreads="${cores}" ${corThreads} ${oeaMemory} ${redMemory} \
-	-pacbio "${AUTOPKGTEST_TMP}"/pacbio.fastq
+	-pacbio "${AUTOPKGTEST_TMP}"/pacbio.fastq ; result=$?
+
+if [ ! "${AUTOPKGTEST_ARTIFACTS}" = "" ] ; then
+	cp ecoli-pacbio/*.report ecoli-pacbio/*.err "${AUTOPKGTEST_ARTIFACTS}/"
+	cp -r ecoli-pacbio/canu-logs "${AUTOPKGTEST_ARTIFACTS}/"
+fi
+
+exit ${result}



View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/7e63a105092667c59072340a1b04c98e7b3ad2df...5da39a50c2f0f57d1733e93bc1faa07aa722102e

-- 
View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/7e63a105092667c59072340a1b04c98e7b3ad2df...5da39a50c2f0f57d1733e93bc1faa07aa722102e
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