[Git][java-team/jalview][master] 8 commits: Putting example files in the working directory of the autopkgtest

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Sun Oct 6 17:08:48 BST 2024



Pierre Gruet pushed to branch master at Debian Java Maintainers / jalview


Commits:
dead56e1 by Pierre Gruet at 2024-10-04T16:15:05+02:00
Putting example files in the working directory of the autopkgtest

- - - - -
35a540ac by Pierre Gruet at 2024-10-04T16:15:24+02:00
Disabling unneeded Java version checks at startup

- - - - -
2e74e9c1 by Pierre Gruet at 2024-10-04T16:16:00+02:00
Upload to experimental

- - - - -
7b9e8f11 by Pierre Gruet at 2024-10-05T23:47:35+02:00
Waiting a bit for the launcher to start

- - - - -
df497ffd by Pierre Gruet at 2024-10-05T23:48:40+02:00
Launcher autopkgtest with xvfb-run to avoid errors due to headless environment

- - - - -
6f87a62c by Pierre Gruet at 2024-10-05T23:49:19+02:00
Upload to experimental

- - - - -
ceae80fc by Pierre Gruet at 2024-10-06T09:40:50+02:00
waiting_launcher patch is Debian-specific

- - - - -
f16bdd97 by Pierre Gruet at 2024-10-06T09:41:28+02:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/patches/series
- + debian/patches/unneeded_checks_when_launching.patch
- + debian/patches/waiting_launcher.patch
- debian/tests/control
- debian/tests/someCommandLineInvocations


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,24 @@
+jalview (2.11.4.0+dfsg-3) unstable; urgency=medium
+
+  * Upload to unstable after fixes in experimental
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 06 Oct 2024 09:40:55 +0200
+
+jalview (2.11.4.0+dfsg-3~exp1) experimental; urgency=medium
+
+  * Waiting a bit for the launcher to start
+  * Launching autopkgtest with xvfb-run to avoid errors due to headless
+    environment
+
+ -- Pierre Gruet <pgt at debian.org>  Sat, 05 Oct 2024 23:48:52 +0200
+
+jalview (2.11.4.0+dfsg-3~exp0) experimental; urgency=medium
+
+  * Putting example files in the working directory of the autopkgtest
+  * Disabling unneeded Java version checks at startup
+
+ -- Pierre Gruet <pgt at debian.org>  Fri, 04 Oct 2024 16:15:33 +0200
+
 jalview (2.11.4.0+dfsg-2) unstable; urgency=medium
 
   * Restoring jalview invocation in the wrapper, with no HOME overriding


=====================================
debian/patches/series
=====================================
@@ -12,3 +12,5 @@ no_applet.patch
 timestamp_from_changelog.patch
 groovy_syntax.patch
 deactivate_flatlaf.patch
+unneeded_checks_when_launching.patch
+waiting_launcher.patch


=====================================
debian/patches/unneeded_checks_when_launching.patch
=====================================
@@ -0,0 +1,61 @@
+Description: disabling Java version checks, which cause trouble with our 
+ home-made build_properties file.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-10-04
+
+--- a/src/jalview/bin/Jalview.java
++++ b/src/jalview/bin/Jalview.java
+@@ -680,7 +680,7 @@
+          * Check to see that the JVM version being run is suitable for the Java
+          * version this Jalview was compiled for. Popup a warning if not.
+          */
+-        if (!LaunchUtils.checkJavaVersion())
++        /*if (!LaunchUtils.checkJavaVersion())
+         {
+           Console.warn("The Java version being used (Java "
+                   + LaunchUtils.getJavaVersion()
+@@ -703,7 +703,7 @@
+                     JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+                     null, options, options[0]);
+           }
+-        }
++        }*/
+ 
+         /**
+          * Check to see if we've been launched from the installer volume
+@@ -853,13 +853,13 @@
+ 
+     // Check if JVM and compile version might cause problems and log if it
+     // might.
+-    if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
++    /*if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
+     {
+       Console.warn("The Java version being used (Java "
+               + LaunchUtils.getJavaVersion()
+               + ") may lead to problems. This installation of Jalview should be used with Java "
+               + LaunchUtils.getJavaCompileVersion() + ".");
+-    }
++    }*/
+ 
+     String file = null, data = null;
+ 
+--- a/src/jalview/bin/Launcher.java
++++ b/src/jalview/bin/Launcher.java
+@@ -69,14 +69,14 @@
+    */
+   public static void main(String[] args)
+   {
+-    if (!LaunchUtils.checkJavaVersion())
++    /*if (!LaunchUtils.checkJavaVersion())
+     {
+       jalview.bin.Console
+               .errPrintln("WARNING - The Java version being used (Java "
+                       + LaunchUtils.getJavaVersion()
+                       + ") may lead to problems. This installation of Jalview should be used with Java "
+                       + LaunchUtils.getJavaCompileVersion() + ".");
+-    }
++    }*/
+ 
+     ErrorLog.setPrefix("LAUNCHER - ");
+ 


=====================================
debian/patches/waiting_launcher.patch
=====================================
@@ -0,0 +1,17 @@
+Description: wiaint a bit for the launcher to start instead of failing at
+ startup. This seems to be problematic only with the Debian packaging.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-10-05
+
+--- a/src/jalview/bin/Launcher.java
++++ b/src/jalview/bin/Launcher.java
+@@ -93,7 +93,7 @@
+     // must set --debug before --launcher...
+     boolean launcherstop = false;
+     boolean launcherprint = false;
+-    boolean launcherwait = false;
++    boolean launcherwait = true;
+     ArrayList<String> arguments = new ArrayList<>();
+     String previousArg = null;
+     // set debug first


=====================================
debian/tests/control
=====================================
@@ -1,5 +1,5 @@
 Tests: someCommandLineInvocations
-Depends: @
+Depends: @, xauth, xvfb
 Restrictions: allow-stderr
 
 Tests: run-unit-test


=====================================
debian/tests/someCommandLineInvocations
=====================================
@@ -10,13 +10,14 @@ SOURCEDIR=$(pwd)
 WORKDIR=$(mktemp -d)
 TEMP_HOME=$(mktemp -d)
 trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cp -r examples $WORKDIR
 cd $WORKDIR
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -blc uniref50_out.blc
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -fasta uniref50_out.mfa
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pfam uniref50_out.pfam
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pir uniref50_out.pir
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -clustal uniref50_out1.aln
-HOME="${TEMP_HOME}" jalview -nodisplay -jvmmemmax=512m -open $SOURCEDIR/examples/uniref50.fa -pileup uniref50_out2.aln
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -blc uniref50_out.blc
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -fasta uniref50_out.mfa
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -pfam uniref50_out.pfam
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -pir uniref50_out.pir
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -clustal uniref50_out1.aln
+HOME="${TEMP_HOME}" xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" jalview -nodisplay -jvmmemmax=512m -open examples/uniref50.fa -pileup uniref50_out2.aln
 
 diff uniref50_out.blc $SOURCEDIR/debian/tests/expectedOutputs/test_uniref50_out.blc
 



View it on GitLab: https://salsa.debian.org/java-team/jalview/-/compare/70dd3f6790de2c044680d8d47488bb33bfcfa6b3...f16bdd97737c11c94601a7e20b2bfa90a5f8f53f

-- 
View it on GitLab: https://salsa.debian.org/java-team/jalview/-/compare/70dd3f6790de2c044680d8d47488bb33bfcfa6b3...f16bdd97737c11c94601a7e20b2bfa90a5f8f53f
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