[med-svn] [Git][med-team/libgoby-java][master] 3 commits: Raising Standards version to 4.6.1 (no change)
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Jul 3 18:07:03 BST 2022
Pierre Gruet pushed to branch master at Debian Med / libgoby-java
Commits:
0992a9a8 by Pierre Gruet at 2022-07-03T07:27:51+02:00
Raising Standards version to 4.6.1 (no change)
- - - - -
ea40cb0a by Pierre Gruet at 2022-07-03T14:51:39+02:00
Omitting more tests failing randomly
- - - - -
9d7e40de by Pierre Gruet at 2022-07-03T19:06:48+02:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/patches/omit_test_failing_randomly.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libgoby-java (3.3.1+dfsg2-8) unstable; urgency=medium
+
+ * Raising Standards version to 4.6.1 (no change)
+ * Omitting more flaky tests (Closes: #1013664)
+
+ -- Pierre Gruet <pgt at debian.org> Sun, 03 Jul 2022 14:51:44 +0200
+
libgoby-java (3.3.1+dfsg2-7) unstable; urgency=medium
* Creating the test-results directory before running the tests
=====================================
debian/control
=====================================
@@ -45,7 +45,7 @@ Build-Depends: debhelper-compat (= 13),
junit4 <!nocheck>,
testng <!nocheck>,
libpicard-java <!nocheck>
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/
Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git
Homepage: http://campagnelab.org/software/goby/
=====================================
debian/patches/omit_test_failing_randomly.patch
=====================================
@@ -1,8 +1,7 @@
-Description: omit a test that fails randomly, as QualityTestFilter uses the
- output of a random number generator
+Description: omit tests that fail randomly
Author: Pierre Gruet <pgt at debian.org>
Forwarded: https://github.com/CampagneLaboratory/goby3/issues/11
-Last-Update: 2021-11-28
+Last-Update: 2022-07-03
--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java
+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java
@@ -14,3 +13,127 @@ Last-Update: 2021-11-28
@Test
public void testRemoveThresholdingEffectArtifact() {
QualityScoreFilter qualityScoreFilter = new QualityScoreFilter();
+--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReadQualityStatsMode.java
++++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReadQualityStatsMode.java
+@@ -19,6 +19,7 @@
+ package org.campagnelab.goby.modes;
+
+ import org.apache.commons.io.FileUtils;
++import org.junit.Ignore;
+ import org.junit.Test;
+
+ import java.io.File;
+@@ -32,6 +33,7 @@
+ * Make sure read-quality-stats is returning stats if the file has quality scores.
+ */
+ public class TestReadQualityStatsMode {
++ @Ignore
+ @Test
+ public void testHasStats() throws IOException {
+ final ReadQualityStatsMode readQuality = new ReadQualityStatsMode();
+@@ -46,6 +48,7 @@
+ assertEquals("Wrong number of stats lines in output file", 39, lines.size());
+ }
+
++ @Ignore
+ @Test
+ public void testHasStatsWithSampling() throws IOException {
+ final ReadQualityStatsMode readQuality = new ReadQualityStatsMode();
+--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java
++++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java
+@@ -43,6 +43,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void noChange() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -63,6 +64,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void startAndEndAtExtremes() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -84,6 +86,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void startAndEndAtExactLength() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -104,6 +107,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void zeroEntries() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -130,6 +134,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void reformatChunkSize() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -170,6 +175,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void reformatStartOfCompactFile() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -203,6 +209,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void reformatSubsetOfCompactFile() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -239,6 +246,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void excludeReadLengthsOf23() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -269,6 +277,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void trimPairedReadsAt10() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -304,6 +313,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void excludeReadLengthsAt35() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -326,6 +336,7 @@
+ *
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void trimReadLengthsAt35() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
+@@ -433,6 +444,7 @@
+ * Validates that reformating does not change quality score length by default.
+ * @throws IOException if there is a problem reading or writing to the files
+ */
++ @Ignore
+ @Test
+ public void reformatQualityScoreLength() throws IOException {
+ final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/d92f4b17f979b9fe3f0c43b38eb63a57db14327e...9d7e40ded98a9eae26e01a7abdc255b308ade804
--
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/d92f4b17f979b9fe3f0c43b38eb63a57db14327e...9d7e40ded98a9eae26e01a7abdc255b308ade804
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