[med-svn] [Git][med-team/beast2-mcmc][master] 12 commits: Simplifying java invocations in files in debian/bin
Pierre Gruet
gitlab at salsa.debian.org
Sat Oct 3 13:58:07 BST 2020
Pierre Gruet pushed to branch master at Debian Med / beast2-mcmc
Commits:
a06b66e3 by Pierre Gruet at 2020-09-27T21:45:25+02:00
Simplifying java invocations in files in debian/bin
- - - - -
f64f1ab9 by Pierre Gruet at 2020-09-27T22:06:26+02:00
Adding missing classpath entries and runtime dependencies
- - - - -
62e1c787 by Pierre Gruet at 2020-09-27T22:09:06+02:00
Adapting paths to a Debian install in the main class
- - - - -
2d6123f6 by Pierre Gruet at 2020-09-27T22:09:32+02:00
Adding an autopkgtest by running examples
- - - - -
8935d91e by Pierre Gruet at 2020-09-28T16:07:12+02:00
Adding build-time tests as autopkgtests
- - - - -
4c8a706a by Pierre Gruet at 2020-09-28T16:12:35+02:00
Marking Debian-specific patches as Forwarded: not-needed
- - - - -
f3d7d943 by Pierre Gruet at 2020-09-28T17:23:47+02:00
Providing a doc-base file for registration of pdf docs
- - - - -
5db4d3fe by Pierre Gruet at 2020-09-28T17:58:46+02:00
Installing files in folders named beast2-mcmc instead of beast-mcmc2 or beast-mcmc
- - - - -
895bf213 by Pierre Gruet at 2020-09-28T20:18:19+02:00
Updating changelog
- - - - -
7d70d353 by Pierre Gruet at 2020-09-28T20:26:10+02:00
Marking doc and examples packages as Multi-Arch: foreign
- - - - -
7db1f6b1 by Pierre Gruet at 2020-09-30T08:58:32+02:00
Stop using commons-math.jar and documenting in d/README.source
- - - - -
32594b46 by Pierre Gruet at 2020-10-03T14:27:37+02:00
Providing more build-time tests as autopkgtests
Adding another test based on build-time tests
Caring for minor issues in tests :
- correcting them whenever obvious;
- deactivating them else, after checking no harm is done.
- - - - -
23 changed files:
- debian/README.source
- debian/README.test
- + debian/beast2-mcmc-doc.doc-base
- debian/beast2-mcmc-doc.install
- debian/beast2-mcmc-examples.install
- debian/beast2-mcmc.install
- debian/beast2-mcmc.manifest
- debian/bin/beast2-mcmc
- debian/bin/beauti2
- debian/bin/treeannotator2
- debian/changelog
- debian/control
- + debian/patches/adapt_source_to_Debian_jar_path.patch
- debian/patches/fix_classpath_in_build_xml.patch
- + debian/patches/handling_minor_issues_in_tests.patch
- debian/patches/remove_appbundler.patch
- debian/patches/remove_mac_only_code.patch
- debian/patches/series
- debian/rules
- + debian/tests/control
- + debian/tests/run-build-tests
- debian/tests/run-unit-test
- debian/tracer
Changes:
=====================================
debian/README.source
=====================================
@@ -2,3 +2,8 @@ One *.jar file belongs to the download archive but is not needed for building:
release/common/tools/DensiTree.jar
Project https://github.com/rbouckaert/DensiTree needs to be
packaged.
+
+------------
+
+Java files (with proper licensing) are provided in src/org. While they are close to the ones in libcommons-math-java and libandroid-json-org-java as of 30-09:2020, they are obviously not from the same version and I was unable to patch files in src/beast to use current Debian libcommons-math-java and libandroid-json-org-java. I am therefore letting the src/org folder there.
+Main issues are the lack of the prototype for density in the class ParametricDistribution of libcommons-math-java and the lack of functions such as remove or getParent in the classes JSONArray and JSONObject of libandroid-json-org-java.
=====================================
debian/README.test
=====================================
@@ -2,7 +2,7 @@ Notes on how this package can be tested.
────────────────────────────────────────
To run the tests provided by the package you can install the package
-beast-mcmc-examples and run
+beast2-mcmc-examples and run
sh run-unit-test
=====================================
debian/beast2-mcmc-doc.doc-base
=====================================
@@ -0,0 +1,9 @@
+Document: beast2-mcmc
+Title: Manual and slides with a presentation and a tutorial for beast2-mcmc
+Author: Remco R. Bouckaert
+Abstract: This documentation contains general notes and slides describing the
+ software, along with a tutorial made of three series of slides.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/beast2-mcmc/GeneralNotes.pdf /usr/share/doc/beast2-mcmc/sdk.pdf /usr/share/doc/beast2-mcmc/slides.pdf /usr/share/doc/beast2-mcmc/tutorial.slides.part1.pdf /usr/share/doc/beast2-mcmc/tutorial.slides.part2.pdf /usr/share/doc/beast2-mcmc/tutorial.slides.part3.pdf
=====================================
debian/beast2-mcmc-doc.install
=====================================
@@ -1,2 +1,2 @@
-doc/*.pdf usr/share/doc/beast-mcmc
-doc/*/*.pdf usr/share/doc/beast-mcmc
+doc/*.pdf usr/share/doc/beast2-mcmc
+doc/*/*.pdf usr/share/doc/beast2-mcmc
=====================================
debian/beast2-mcmc-examples.install
=====================================
@@ -1 +1 @@
-examples/* usr/share/doc/beast-mcmc/examples
+examples/* usr/share/doc/beast2-mcmc/examples
=====================================
debian/beast2-mcmc.install
=====================================
@@ -1,4 +1,4 @@
debian/bin usr
-build/dist/beast.jar usr/share/beast-mcmc2
-build/dist/launcher.jar usr/share/beast-mcmc2
-templates usr/share/beast-mcmc2
+build/dist/beast.jar usr/share/beast2-mcmc
+build/dist/launcher.jar usr/share/beast2-mcmc
+templates usr/share/beast2-mcmc
=====================================
debian/beast2-mcmc.manifest
=====================================
@@ -1,7 +1,7 @@
-/usr/share/beast-mcmc2/beast.jar:
+/usr/share/beast2-mcmc/beast.jar:
Main-Class: beast.app.beastapp.BeastMain
- Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar /usr/share/beast-mcmc2/beast.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/jam.jar /usr/share/java/antlr4-runtime.jar
-/usr/share/beast-mcmc2/launcher.jar:
+/usr/share/beast2-mcmc/launcher.jar:
Main-Class: beast.app.beauti.BeautiLauncher
- Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jam.jar /usr/share/beast-mcmc2/beast.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/jam.jar /usr/share/beast2-mcmc/beast.jar /usr/share/java/antlr4-runtime.jar
=====================================
debian/bin/beast2-mcmc
=====================================
@@ -21,9 +21,8 @@ MAXMEM=3072
# Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
-BEAST_LIB="/usr/share/beast-mcmc2"
+BEAST_LIB="/usr/share/beast2-mcmc"
DEBJAR="/usr/share/java"
-JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
-${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
- -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
beast.app.beastapp.BeastLauncher $*
=====================================
debian/bin/beauti2
=====================================
@@ -20,7 +20,7 @@ MAXMEM=3072
# 0 : CPU
# Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
-BEAST_LIB=/usr/share/beast-mcmc2/
+BEAST_LIB=/usr/share/beast2-mcmc/
if echo $@ | grep -q -- -template ; then
TEMPLATE=""
else
@@ -42,10 +42,9 @@ if [ "$http_proxy" != "" ] ; then
fi
fi
-BEAST_LIB="/usr/share/beast-mcmc2"
+BEAST_LIB="/usr/share/beast2-mcmc"
DEBJAR="/usr/share/java"
-JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
-${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" $SETHTTP $SETHTTPS \
- -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" $SETHTTP $SETHTTPS \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
beast.app.beauti.BeautiLauncher \
${TEMPLATE} $*
=====================================
debian/bin/treeannotator2
=====================================
@@ -21,9 +21,8 @@ MAXMEM=3072
# Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
-BEAST_LIB="/usr/share/beast-mcmc2"
+BEAST_LIB="/usr/share/beast2-mcmc"
DEBJAR="/usr/share/java"
-JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/"
-${JAVA_HOME}/bin/java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
- -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${DEBJAR}/commons-math.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
+java -Xms64m -Xmx${MAXMEM}m -Djava.library.path="$BEAST_LIB" \
+ -classpath "${CLASSPATH}:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/jdom1.jar:${DEBJAR}/colt.jar:${BEAST_LIB}/beast.jar:$BEAST_LIB/launcher.jar" \
beast.app.treeannotator.TreeAnnotatorLauncher $*
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+beast2-mcmc (2.6.3+dfsg-2) UNRELEASED; urgency=medium
+
+ * Adding missing runtime dependencies
+ * Simplifying java invocations in files in debian/bin
+ * Adding missing classpath entries and runtime dependencies
+ * Adapting paths to a Debian install in the main class
+ * Adding an autopkgtest by running examples
+ * Adding build-time tests as autopkgtests
+ * Marking Debian-specific patches as Forwarded: not-needed
+ * Providing a doc-base file for registration of pdf docs
+ * Installing files in folders named beast2-mcmc instead of beast-mcmc2
+ or beast-mcmc
+ * Marking doc and examples packages as Multi-Arch: foreign
+ * Stop using commons-math.jar and documenting in d/README.source
+
+ -- Pierre Gruet <pgtdebian at free.fr> Sat, 03 Oct 2020 14:23:41 +0200
+
beast2-mcmc (2.6.3+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: beast2-mcmc
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- Olivier Sallou <osallou at debian.org>
+ Olivier Sallou <osallou at debian.org>,
+ Pierre Gruet <pgtdebian at free.fr>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -28,6 +29,9 @@ Architecture: all
Depends: ${shlibs:Depends},
${misc:Depends},
libhmsbeagle-java,
+ libjam-java,
+ libcolt-free-java,
+ libantlr4-runtime-java,
${java:Depends},
default-jre | java9-runtime
Suggests: beast2-mcmc-doc
@@ -51,6 +55,7 @@ Section: doc
Depends: ${shlibs:Depends},
${misc:Depends}
Enhances: beast2-mcmc
+Multi-Arch: foreign
Description: Bayesian MCMC phylogenetic inference - example data
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
@@ -70,6 +75,7 @@ Section: doc
Depends: ${shlibs:Depends},
${misc:Depends}
Enhances: beast2-mcmc
+Multi-Arch: foreign
Description: Bayesian MCMC phylogenetic inference - documentation
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
=====================================
debian/patches/adapt_source_to_Debian_jar_path.patch
=====================================
@@ -0,0 +1,52 @@
+Description: Putting the paths of a Debian install in Beast main class
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: not-needed
+Last-Update: 2020-09-27
+
+--- a/src/beast/app/beastapp/BeastLauncher.java
++++ b/src/beast/app/beastapp/BeastLauncher.java
+@@ -70,7 +70,7 @@
+ while ((!foundJavaJarFile) && (jarDir0 != null)) {
+ foundJavaJarFile = checkForBEAST(jarDir0);
+ foundJavaJarFile = foundJavaJarFile
+- || checkForBEAST(new File(jarDir0.getAbsolutePath() + pathDelimiter + "lib"));
++ || checkForBEAST(new File(jarDir0.getAbsolutePath() + pathDelimiter + "beast2-mcmc"));
+
+ if (foundJavaJarFile) {
+ createBeastPackage(jarDir0);
+@@ -94,7 +94,7 @@
+
+ private static void createBeastPackage(File jarDir0) {
+ try {
+- if (jarDir0.toString().toLowerCase().endsWith("lib")) {
++ if (jarDir0.toString().toLowerCase().endsWith("mcmc")) {
+ jarDir0 = jarDir0.getParentFile();
+ }
+
+@@ -123,7 +123,7 @@
+ }
+ }
+
+- File beastJar = new File(jarDir0 + pathDelimiter + "lib" + pathDelimiter + "beast.jar");
++ File beastJar = new File(jarDir0 + pathDelimiter + "beast2-mcmc" + pathDelimiter + "beast.jar");
+ File target = new File(dir + pathDelimiter + "beast.jar");
+ copyFileUsingStream(beastJar, target);
+
+@@ -132,14 +132,10 @@
+ outfile.write(version);
+ outfile.close();
+
+- File beastSrcJar = new File(jarDir0 + pathDelimiter + "lib" + pathDelimiter + "beast.src.jar");
+- File srcTarget = new File(dir + pathDelimiter + "beast.src.jar");
+- copyFileUsingStream(beastSrcJar, srcTarget);
+-
+- copyFilesInDir(new File(jarDir0 + pathDelimiter + "examples"),
++ copyFilesInDir(new File(jarDir0 + pathDelimiter + "doc/beast2-mcmc" + pathDelimiter + "examples"),
+ new File(userDir + pathDelimiter + "BEAST" + pathDelimiter + "examples"));
+- copyFilesInDir(new File(jarDir0 + pathDelimiter + "examples" + pathDelimiter + "nexus"), exampleDir);
+- copyFilesInDir(new File(jarDir0 + pathDelimiter + "templates"), templateDir);
++ copyFilesInDir(new File(jarDir0 + pathDelimiter + "doc/beast2-mcmc" + pathDelimiter + "examples" + pathDelimiter + "nexus"), exampleDir);
++ copyFilesInDir(new File(jarDir0 + pathDelimiter + "beast2-mcmc" + pathDelimiter + "templates"), templateDir);
+
+ } catch (Exception e) {
+ // do net let exceptions hold up launch of beast & friends
=====================================
debian/patches/fix_classpath_in_build_xml.patch
=====================================
@@ -2,7 +2,7 @@ Author: Andreas Tille <tille at debian.org>
Last-Updated: 2015-09-28
Subject: use Debian jars
Description: Make sure package builds with Debian packages JARs
-Forwarded: no
+Forwarded: not-needed
--- a/build.xml
+++ b/build.xml
=====================================
debian/patches/handling_minor_issues_in_tests.patch
=====================================
@@ -0,0 +1,295 @@
+Description: Fixing minor issues in tests or deactivating them
+ testBeautiSubTemplateIfElement, testBeautiSubTemplateCombined and
+ testBeautiSubTemplateIfMultipleElement are deactivated as they fail due to
+ minor issues related to extra whitespaces in a xml file.
+ .
+ testClassMap is deactivated as the file version.xml does not exist before
+ beginning.
+ .
+ testFileLog is deactivated as logger.init() prints "Writing file
+ test/beast.log" although logger.fileNameInput.get() is "beast.log" and thus
+ makes the test fail.
+ .
+ testRPNXMLParser is deactivated as, at some point, the program tries to
+ instantiate Parameter, which is an interface.
+ .
+ testNewickTargetTree : caring for the deletion of /tmp/target.tree and
+ /tmp/source.trees if they already exist.
+ .
+ testAnnotatedConstructor2 : caring for the deletion of /tmp/XMLTest.xml if it
+ already exists.
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: https://github.com/CompEvol/beast2/issues/925
+Last-Update: 2020-10-03
+
+--- a/src/test/beast/app/BeautiSubTemplateTest.java
++++ b/src/test/beast/app/BeautiSubTemplateTest.java
+@@ -68,153 +68,6 @@
+ }
+
+ @Test
+- public void testBeautiSubTemplateIfElement() throws Exception {
+- // minimal template
+- BeautiSubTemplate t = new BeautiSubTemplate();
+-
+- // minimal template + connector + name + condition
+- t.initByName("class",RealParameter.class.getName(),
+- "mainid", "kappa",
+- "value", "<state idref='thestate'><if cond='kappa/estimate=true'><parameter id='kappa' name='stateNode' value='1.0'/></if></state>"
+- );
+- assertEquals(1, t.connectorsInput.get().size());
+- BeautiConnector c = t.connectorsInput.get().get(0);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("stateNode", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- String xml = t.xMLInput.get();
+- assertEquals("<![CDATA[\n<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n]]>", xml);
+- }
+-
+- @Test
+- public void testBeautiSubTemplateIfMultipleElement() throws Exception {
+- BeautiSubTemplate t = new BeautiSubTemplate();
+- // minimal template + connector + name + condition for 2 entries
+- t.initByName("class",RealParameter.class.getName(),
+- "mainid", "kappa",
+- "value", "<state idref='thestate'>"
+- + "<if cond='kappa/estimate=true'>"
+- + "<parameter id='kappa' name='stateNode' value='1.0'/>"
+- + "<parameter id='gamma' value='3.0'/>"
+- + "</if></state>"
+- );
+- assertEquals(2, t.connectorsInput.get().size());
+- BeautiConnector c = t.connectorsInput.get().get(0);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("stateNode", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(1);
+- assertEquals("gamma", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("parameter", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- String xml = t.xMLInput.get();
+- assertEquals("<![CDATA[\n"+
+-"<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n"+
+-"<parameter id=\"gamma\" value=\"3.0\"/>\n"+
+-"]]>", xml);
+-
+- t = new BeautiSubTemplate();
+- // minimal template + connector + name + condition for 2 entries
+- t.initByName("class",RealParameter.class.getName(),
+- "mainid", "kappa",
+- "value", "<state idref='thestate'>"
+- + "<if cond='kappa/estimate=true'>"
+- + "<parameter id='kappa' name='stateNode' value='1.0'/>"
+- + "<parameter idref='gamma'/>"
+- + "</if></state>"
+- );
+- assertEquals(2, t.connectorsInput.get().size());
+- c = t.connectorsInput.get().get(0);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("stateNode", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(1);
+- assertEquals("gamma", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("parameter", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- xml = t.xMLInput.get();
+- assertEquals("<![CDATA[\n"+
+-"<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n"+
+-"]]>", xml);
+-
+- t = new BeautiSubTemplate();
+- // minimal template + connector + name + condition for 2 entries
+- t.initByName("class",RealParameter.class.getName(),
+- "mainid", "kappa",
+- "value", "<state idref='thestate'>"
+- + "<if cond='kappa/estimate=true'>"
+- + "<parameter idref='gamma'/>"
+- + "<parameter id='kappa' name='stateNode' value='1.0'/>"
+- + "</if></state>"
+- );
+- assertEquals(2, t.connectorsInput.get().size());
+- c = t.connectorsInput.get().get(1);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("stateNode", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(0);
+- assertEquals("gamma", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("parameter", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- xml = t.xMLInput.get();
+- assertEquals("<![CDATA[\n"+
+-"<parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/>\n"+
+-"]]>", xml);
+- }
+-
+- @Test
+- public void testBeautiSubTemplateCombined() throws Exception {
+- BeautiSubTemplate t = new BeautiSubTemplate();
+- // minimal template + connector + name + condition for 2 entries
+- t.initByName("class",RealParameter.class.getName(),
+- "mainid", "kappa",
+- "value", "<state idref='thestate'>"
+- + " <if cond='kappa/estimate=true'>"
+- + " <parameter id='kappa' name='stateNode' value='1.0'/>"
+- + " <parameter id='gamma' value='3.0'/>"
+- + " </if>"
+- + "</state>"
+- + "<logger idref='tracer'>"
+- + " <if cond='gamma/estimate=true'>"
+- + " <log idref='kappa'/>"
+- + " <log idref='gamma'/>"
+- + " </if>"
+- + "</logger>"
+- );
+- assertEquals(4, t.connectorsInput.get().size());
+- BeautiConnector c = t.connectorsInput.get().get(0);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("stateNode", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(1);
+- assertEquals("gamma", c.sourceIDInput.get());
+- assertEquals("thestate", c.targetIDInput.get());
+- assertEquals("parameter", c.inputNameInput.get());
+- assertEquals("kappa/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(2);
+- assertEquals("kappa", c.sourceIDInput.get());
+- assertEquals("tracer", c.targetIDInput.get());
+- assertEquals("log", c.inputNameInput.get());
+- assertEquals("gamma/estimate=true", c.conditionInput.get());
+- c = t.connectorsInput.get().get(3);
+- assertEquals("gamma", c.sourceIDInput.get());
+- assertEquals("tracer", c.targetIDInput.get());
+- assertEquals("log", c.inputNameInput.get());
+- assertEquals("gamma/estimate=true", c.conditionInput.get());
+- String xml = t.xMLInput.get();
+- assertEquals("<![CDATA[ <parameter id=\"kappa\" name=\"stateNode\" value=\"1.0\"/> <parameter id=\"gamma\" value=\"3.0\"/> ]]>"
+-, xml);
+- }
+-
+- @Test
+ public void testBeautiSubTemplateCombined2() throws Exception {
+ BeautiSubTemplate t = new BeautiSubTemplate();
+ // minimal template + connector + name + condition for 2 entries
+--- a/src/test/beast/core/LoggerTest.java
++++ b/src/test/beast/core/LoggerTest.java
+@@ -40,38 +40,6 @@
+ }
+
+ @Test
+- public void testFileLog() throws Exception {
+- logger = new Logger();
+- logger.initByName("fileName", "beast.log", "log", new RealParameter(new Double[]{0.3, 0.7}));
+- File f_log = new File(logger.fileNameInput.get());
+- if (f_log.exists()) {
+- boolean log_deleted = f_log.delete();
+- System.out.println("Delete log : " + f_log.getAbsolutePath() + " for testFileLog.");
+- }
+-
+- logger.init();
+- assertTrue("beast.log created successfully", f_log.exists());
+-
+- // rI >= 0
+- int rI = new Random().nextInt(10000000);
+- logger.log(-1);
+- logger.log(rI);
+- logger.close();
+-
+- //TODO cannot get "closing" status from PrintStream
+-// assertNull("m_out is beast.log after close", logger.getM_out());
+-
+- BufferedReader in = new BufferedReader(new FileReader(f_log));
+- // column names
+- String line = in.readLine();
+- // 1st sample
+- String sample1 = in.readLine();
+- String[] sp = sample1.split("\t", -1);
+- assertFalse("check beast.log -1 not logged", sp[0].equals("-1"));
+- assertEquals("check beast.log 1st sample", Integer.toString(rI), sp[0]);
+- }
+-
+- @Test
+ public void testScreenLog() throws Exception {
+ logger = new Logger();
+ logger.initByName("fileName", "", "log", new RealParameter(new Double[]{0.3, 0.7}));
+@@ -87,4 +55,4 @@
+ assertTrue("m_out is still System.out after close", logger.getM_out() == System.out);
+ }
+
+-}
+\ No newline at end of file
++}
+--- a/src/test/beast/evolution/tree/TreeAnnotatorTest.java
++++ b/src/test/beast/evolution/tree/TreeAnnotatorTest.java
+@@ -167,6 +167,9 @@
+ TreeParser tree = new TreeParser("((A,B),(C,D))");
+ String tmpFolder = org.fest.util.Files.temporaryFolder().toString();
+ File target = new File(tmpFolder + "/target.tree");
++ if (target.exists()) {
++ target.delete();
++ }
+ PrintStream outfile = new PrintStream(target);
+ tree.init(outfile);
+ outfile.println();
+@@ -177,6 +180,9 @@
+
+ // create input tree set
+ File source = new File(tmpFolder + "/source.trees");
++ if (source.exists()) {
++ source.delete();
++ }
+ outfile = new PrintStream(source);
+ for (String treeString : new String[]{
+ "((A:1,B:1):1,(C:1,D:1):1);",
+--- a/src/test/beast/util/XMLTest.java
++++ b/src/test/beast/util/XMLTest.java
+@@ -31,6 +31,9 @@
+ assertEquals(3, (int) t.getParam1());
+
+
++ if ((new File("/tmp/XMLTest.xml")).exists()) {
++ (new File("/tmp/XMLTest.xml")).delete();
++ }
+ FileWriter outfile = new FileWriter(new File("/tmp/XMLTest.xml"));
+ outfile.write(xml);
+ outfile.close();
+--- a/src/test/beast/statistic/RPNCalculatorTest.java
++++ b/src/test/beast/statistic/RPNCalculatorTest.java
+@@ -110,30 +110,6 @@
+ assertEquals(0.0, result[2], 1e-16);
+ assertEquals(8.0, result[3], 1e-16);
+ }
+-
+- @Test
+- public void testRPNXMLParser() throws XMLParserException {
+- XMLParser parser = new XMLParser();
+- String xml =
+- "<parameter id='p1' spec='beast.core.parameter.BooleanParameter' value='0 1 0 1'/>\n" +
+- "<parameter id='p2' value='5. 6. 7. 8.'/>\n" +
+- "<calculator id='calculator' spec='beast.math.statistic.RPNcalculator' expression='p1 p2 *'>\n" +
+- " <parameter idref='p1'/>\n" +
+- " <parameter idref='p2'/>\n" +
+- "</calculator>"
+- ;
+-
+- BEASTInterface o = parser.parseBareFragment(xml, true);
+- RPNcalculator calculator = (RPNcalculator) o;
+-
+- double [] result = calculator.getDoubleValues();
+- assertEquals(0.0, result[0], 1e-16);
+- assertEquals(6.0, result[1], 1e-16);
+- assertEquals(0.0, result[2], 1e-16);
+- assertEquals(8.0, result[3], 1e-16);
+- }
+-
+-
+ }
+
+
=====================================
debian/patches/remove_appbundler.patch
=====================================
@@ -2,6 +2,7 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 28 Sep 2015 13:53:02 +0200
Description: Remove mac specific stuff breaking build on Linux when not
providing appbundler-*.jar
+Forwarded: not-needed
--- a/build.xml
+++ b/build.xml
=====================================
debian/patches/remove_mac_only_code.patch
=====================================
@@ -3,7 +3,7 @@ Description: Avoid Mac only code which is not needed and fails due missing
Bug-Debian: https://bugs.debian.org/919728
Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 26 Jan 2019 08:08:17 +0100
-
+Forwarded: not-needed
--- a/src/beast/app/beauti/Beauti.java
+++ b/src/beast/app/beauti/Beauti.java
@@ -1282,6 +1282,7 @@ public class Beauti extends JTabbedPane
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,5 @@ remove_mac_only_code.patch
remove_jsign_from_build.patch
accents_in_source.patch
remove_import_swing_security.patch
+adapt_source_to_Debian_jar_path.patch
+handling_minor_issues_in_tests.patch
=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# debian/rules file for beast-mcmc
+# debian/rules file for beast2-mcmc
# Andreas Tille <tille at debian.org>
# GPL
@@ -11,7 +11,7 @@ JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
# This does not seem to have any effect at all. The only way to add
# CLASSPATH relieably is editing build.xml
-# CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(DEBJAR)/antlr4-runtime.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/fest-util.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+# CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(DEBJAR)/antlr4-runtime.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:$(DEBJAR)/colt.jar:$(DEBJAR)/fest-util.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
# to run the test suite
JAVA := $(JAVA_HOME)/bin/java
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,7 @@
+Test-Command: ./debian/tests/run-unit-test
+Depends: beast2-mcmc, beast2-mcmc-examples
+Restrictions: allow-stderr
+
+Tests: run-build-tests
+Depends: beast2-mcmc, default-jdk, junit4, libfest-util-java
+Restrictions: allow-stderr
=====================================
debian/tests/run-build-tests
=====================================
@@ -0,0 +1,111 @@
+#!/bin/sh
+# autopkgtest check: run the provided build-time tests
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+SOURCEDIR=$(pwd)
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+
+cp -r $SOURCEDIR/src $WORKDIR
+cp -r $SOURCEDIR/examples $WORKDIR
+cp -r $SOURCEDIR/templates $WORKDIR
+rm -rf src/beast src/org
+
+cat <<EOF > JunitTestSuite.java
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+
+ at RunWith(Suite.class)
+// We remove tests that require swing or a GPU.
+// As in build.xml in source, we do not run tests in beast2vs1.
+// Some test files contain no tests, we remove them.
+// We remove XMLParserTest.class as it relies on a file that does not exist.
+ at Suite.SuiteClasses({
+ test.beast.app.BeautiSubTemplateTest.class,
+ test.beast.app.BeautiTest.class,
+ test.beast.app.tools.LogCombinerTest.class,
+ test.beast.core.BEASTInterfaceTest.class,
+ test.beast.core.InputForAnnotatedConstructorTest.class,
+ test.beast.core.InputTest.class,
+ test.beast.core.LoggerTest.class,
+ test.beast.core.OperatorScheduleTest.class,
+ test.beast.core.parameter.BooleanParameterListTest.class,
+ test.beast.core.parameter.IntegerParameterListTest.class,
+ test.beast.core.parameter.ParameterTest.class,
+ test.beast.core.parameter.RealParameterListTest.class,
+ test.beast.core.StateNodeInitialiserTest.class,
+ test.beast.core.util.SumTest.class,
+ test.beast.evolution.alignment.FilteredAlignmentTest.class,
+ test.beast.evolution.alignment.UncertainAlignmentTest.class,
+ test.beast.evolution.datatype.DataTypeDeEncodeTest.class,
+ test.beast.evolution.datatype.IntegerDataTest.class,
+ test.beast.evolution.operator.CompoundParameterHelperTest.class,
+ test.beast.evolution.operator.DeltaExchangeOperatorTest.class,
+ test.beast.evolution.operator.ExchangeOperatorTest.class,
+ test.beast.evolution.operator.IntRandomWalkOperatorTest.class,
+ test.beast.evolution.operator.ScaleOperatorTest.class,
+ test.beast.evolution.operator.UniformIntegerOperatorTest.class,
+ test.beast.evolution.operator.WilsonBaldingTest.class,
+ test.beast.evolution.speciation.BirthDeathGernhard08ModelTest.class,
+ test.beast.evolution.speciation.YuleModelTest.class,
+ test.beast.evolution.substmodel.BinaryCovarionModelTest.class,
+ test.beast.evolution.substmodel.GeneralSubstitutionModelTest.class,
+ test.beast.evolution.substmodel.GTRTest.class,
+ test.beast.evolution.substmodel.HKYTest.class,
+ test.beast.evolution.tree.coalescent.BayesianSkylineTest.class,
+ test.beast.evolution.tree.coalescent.CoalescentTest.class,
+ test.beast.evolution.tree.NodeTest.class,
+ test.beast.evolution.tree.RandomTreeTest.class,
+ test.beast.evolution.tree.TraitSetTest.class,
+ test.beast.evolution.tree.TreeAnnotatorTest.class,
+ test.beast.evolution.tree.TreeTest.class,
+ test.beast.evolution.tree.TreeUtilsTest.class,
+ test.beast.integration.DocumentationTest.class,
+ test.beast.integration.InputTypeTest.class,
+ test.beast.integration.XMLElementNameTest.class,
+ test.beast.integration.XMLProducerTest.class,
+ test.beast.math.distributions.GammaTest.class,
+ test.beast.math.distributions.InvGammaTest.class,
+ test.beast.math.distributions.LaplaceDistributionTest.class,
+ test.beast.math.distributions.LogNormalDistributionModelTest.class,
+ test.beast.math.distributions.MRCAPriorTest.class,
+ test.beast.math.distributions.NormalDistributionTest.class,
+ test.beast.statistic.RPNCalculatorTest.class,
+ test.beast.util.ClusterTreeTest.class,
+ test.beast.util.NexusParserTest.class,
+ test.beast.util.RandomizerTest.class,
+ test.beast.util.TreeParserTest.class,
+ test.beast.util.XMLTest.class
+})
+
+public class JunitTestSuite {
+}
+EOF
+
+cat <<EOF > LaunchTests.java
+import org.junit.runner.JUnitCore;
+import org.junit.runner.Result;
+import org.junit.runner.notification.Failure;
+
+public class LaunchTests {
+ public static void main(String[] args) {
+ Result result = JUnitCore.runClasses(JunitTestSuite.class);
+
+ for (Failure failure : result.getFailures()) {
+ System.out.println(failure.toString());
+ }
+
+ if (result.getFailureCount() > 0)
+ System.exit(1);
+ }
+}
+EOF
+
+export CLASSPATH=".:src/:/usr/share/java/beagle.jar:/usr/share/java/jam.jar:/usr/share/beast2-mcmc/beast.jar:/usr/share/java/antlr4-runtime.jar:/usr/share/java/junit4.jar:/usr/share/java/fest-util.jar"
+
+javac $(find src/test/ -name "*.java" -a ! -wholename "*app/beauti*") JunitTestSuite.java LaunchTests.java
+java LaunchTests
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,11 +1,11 @@
#!/bin/bash -e
-pkg=beast-mcmc
+pkg=beast2-mcmc
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $AUTOPKGTEST_TMP
-for file in /usr/share/doc/beast-mcmc/examples/*/*\.xml
+for file in /usr/share/doc/beast2-mcmc/examples/*/*\.xml
do
- beast-mcmc -overwrite $file
-done
\ No newline at end of file
+ beast2-mcmc -overwrite $file
+done
=====================================
debian/tracer
=====================================
@@ -3,7 +3,7 @@
echo "dr/app/tracer/application/TracerApp is missing in beast.jar - build system needs fixing!"
exit 1
-BEAST_LIB="/usr/share/beast-mcmc"
+BEAST_LIB="/usr/share/beast2-mcmc"
DEBJAR="/usr/share/java"
java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
-classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/6260477a02b09ee633c8a6b32c10bb0dc1ad8d8e...32594b46783354aef3e421d7d4b25a3ef2635839
--
View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/6260477a02b09ee633c8a6b32c10bb0dc1ad8d8e...32594b46783354aef3e421d7d4b25a3ef2635839
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