debian/changelog

@@ -5,6 +5,10 @@ cdk (2.3-1) UNRELEASED; urgency=medium
   * debhelper-compat 12
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.4.1
+  * Run mh_make to create maven-helper input files
+  * Upstream moved from ant to maven
+  TODO: package uk.ac.ebi.beam:beam-core
+                uk.ac.ebi.beam:beam-func
 
  -- Andreas Tille <tille@debian.org>  Tue, 19 Nov 2019 15:56:16 +0100
 

debian/control

@@ -3,11 +3,11 @@ Maintainer: Debian Java Maintainers <pkg-java-maintainers@lists.alioth.debian.or
 Uploaders: Onkar Shinde <onkarshinde@ubuntu.com>
 Section: java
 Priority: optional
-Build-Depends: ant-contrib,
-               ant-optional,
-               antlr,
-               debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 12),
                default-jdk,
+               javahelper,
+               maven-debian-helper,
+               libmaven-install-plugin-java,
                docbook-xsl,
                javacc,
                javahelper,
@@ -19,7 +19,8 @@ Build-Depends: ant-contrib,
                libxerces2-java,
                libxom-java,
                libxpp3-java,
-               r-cran-rjava
+               r-cran-rjava,
+               libmockito-java
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/java-team/cdk
 Vcs-Git: https://salsa.debian.org/java-team/cdk.git

debian/libcdk-java.poms

+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]*
+# where option can be:
+#   --ignore: ignore this POM and its artifact if any
+#   --ignore-pom: don't install the POM. To use on POM files that are created
+#     temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]
+#   --no-parent: remove the <parent> tag from the POM
+#   --package=<package>: an alternative package to use when installing this POM
+#      and its artifact
+#   --has-package-version: to indicate that the original version of the POM is the same as the upstream part
+#      of the version for the package.
+#   --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM
+#      during a clean operation with mh_cleanpom or mh_installpom
+#   --artifact=<path>: path to the build artifact associated with this POM,
+#      it will be installed when using the command mh_install. [mh_install]
+#   --java-lib: install the jar into /usr/share/java to comply with Debian
+#      packaging guidelines
+#   --usj-name=<name>: name to use when installing the library in /usr/share/java
+#   --usj-version=<version>: version to use when installing the library in /usr/share/java
+#   --no-usj-versionless: don't install the versionless link in /usr/share/java
+#   --dest-jar=<path>: the destination for the real jar.
+#     It will be installed with mh_install. [mh_install]
+#   --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.
+#   --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.
+#     Empty by default. [mh_install]
+#
+pom.xml --has-package-version
+bundle/pom.xml --has-package-version
+base/pom.xml --has-package-version
+base/annotation/pom.xml --has-package-version
+base/interfaces/pom.xml --has-package-version
+base/atomtype/pom.xml --has-package-version
+base/core/pom.xml --has-package-version
+base/standard/pom.xml --has-package-version
+base/valencycheck/pom.xml --has-package-version
+base/test-interfaces/pom.xml --has-package-version
+base/test-atomtype/pom.xml --has-package-version
+base/test-core/pom.xml --has-package-version
+base/test-standard/pom.xml --has-package-version
+base/test-valencycheck/pom.xml --has-package-version
+base/data/pom.xml --has-package-version
+base/silent/pom.xml --has-package-version
+base/datadebug/pom.xml --has-package-version
+base/isomorphism/pom.xml --has-package-version
+base/dict/pom.xml --has-package-version
+base/reaction/pom.xml --has-package-version
+base/test/pom.xml --has-package-version
+base/testdata/pom.xml --has-package-version
+descriptor/pom.xml --has-package-version
+descriptor/fingerprint/pom.xml --has-package-version
+descriptor/cip/pom.xml --has-package-version
+descriptor/signature/pom.xml --has-package-version
+descriptor/qsar/pom.xml --has-package-version
+descriptor/ionpot/pom.xml --has-package-version
+descriptor/qsaratomic/pom.xml --has-package-version
+descriptor/qsarbond/pom.xml --has-package-version
+descriptor/qsarcml/pom.xml --has-package-version
+descriptor/qsarionpot/pom.xml --has-package-version
+descriptor/qsarmolecular/pom.xml --has-package-version
+descriptor/qsarprotein/pom.xml --has-package-version
+descriptor/qsarsubstance/pom.xml --has-package-version
+display/pom.xml --has-package-version
+display/render/pom.xml --has-package-version
+display/renderawt/pom.xml --has-package-version
+display/renderbasic/pom.xml --has-package-version
+display/renderextra/pom.xml --has-package-version
+misc/pom.xml --has-package-version
+misc/control/pom.xml --has-package-version
+misc/extra/pom.xml --has-package-version
+misc/test-extra/pom.xml --has-package-version
+misc/diff/pom.xml --has-package-version
+misc/log4j/pom.xml --has-package-version
+misc/qm/pom.xml --has-package-version
+storage/pom.xml --has-package-version
+storage/ctab/pom.xml --has-package-version
+storage/io/pom.xml --has-package-version
+storage/ioformats/pom.xml --has-package-version
+storage/iordf/pom.xml --has-package-version
+storage/libiocml/pom.xml --has-package-version
+storage/libiomd/pom.xml --has-package-version
+storage/pdb/pom.xml --has-package-version
+storage/pdbcml/pom.xml --has-package-version
+storage/inchi/pom.xml --has-package-version
+storage/smiles/pom.xml --has-package-version
+tool/pom.xml --has-package-version
+tool/builder3d/pom.xml --has-package-version
+tool/builder3dtools/pom.xml --has-package-version
+tool/charges/pom.xml --has-package-version
+tool/forcefield/pom.xml --has-package-version
+tool/formula/pom.xml --has-package-version
+tool/fragment/pom.xml --has-package-version
+tool/group/pom.xml --has-package-version
+tool/hash/pom.xml --has-package-version
+tool/pcore/pom.xml --has-package-version
+tool/sdg/pom.xml --has-package-version
+tool/smarts/pom.xml --has-package-version
+tool/smsd/pom.xml --has-package-version
+tool/structgen/pom.xml --has-package-version
+tool/tautomer/pom.xml --has-package-version
+tool/model/pom.xml --has-package-version
+legacy/pom.xml --has-package-version
+app/pom.xml --has-package-version
+app/depict/pom.xml --has-package-version

debian/libcdk-java.substvars

+#List of dependencies for libcdk-java, generated for use by debian/control
+maven.DocOptionalDepends=
+maven.Depends=junit4 (>= 4.12), libcommons-math3-java (>= 3.1.1), libfreehep-graphicsio-pdf-java, libfreehep-graphicsio-ps-java, libfreehep-graphicsio-svg-java, libguava-java, libjama-java, libjaxp1.3-java, liblog4j1.2-java (>= 1.2.17), libvecmath-java (>= 1.5.2), libxom-java
+maven.OptionalDepends=
+maven.CompileDepends=libmaven-compiler-plugin-java (>= 3.8.1), libmaven-jar-plugin-java (>= 3.1.2), libmaven-shade-plugin-java (>= 3.1.1), libsurefire-java (>= 2.22.2)
+maven.DocDepends=default-jdk-doc, junit4-doc, libcommons-math3-java-doc, libguava-java-doc, libjama-java-doc, liblog4j1.2-java-doc, libvecmath-java-doc, libxom-java-doc
+maven.TestDepends=junit4 (>= 4.12), libcdk-java (>= 2.3), libguava-java, libhamcrest-java, libjama-java, libjaxp1.3-java, libjni-inchi-java (>= 0.8), liblog4j1.2-java (>= 1.2.17), libslf4j-java (>= 1.7.10), libvecmath-java (>= 1.5.2), libxom-java, libxpp3-java
+maven.UpstreamPackageVersion=2.3

debian/maven.cleanIgnoreRules

+

debian/maven.ignoreRules

+
+com.github.gilleain.signatures signatures * * * *
+org.apache.jena jena-core * * * *
+org.apache.maven.plugins maven-javadoc-plugin * * * *
+org.apache.maven.plugins maven-pmd-plugin * * * *
+org.codehaus.mojo findbugs-maven-plugin * * * *
+org.codehaus.mojo javacc-maven-plugin * * * *
+org.jacoco jacoco-maven-plugin * * * *
+org.mockito mockito-all * * * *
+org.openscience.cdk cdk-build-utils * * * *
+org.xml-cml cmlxom * * * *
+uk.ac.ebi.beam beam-core * * * *
+uk.ac.ebi.beam beam-func * * * *

debian/maven.publishedRules

+

debian/maven.rules

+
+s/com.google.code.google-collections/com.google.guava/ s/google-collect/guava/ s/jar/bundle/ s/.*/debian/ * *
+s/com.google.collections/com.google.guava/ s/google-collections/guava/ s/jar/bundle/ s/.*/debian/ * *
+com.google.guava guava bundle s/.*/debian/ * *
+com.google.guava guava s/jar/bundle/ s/.*/debian/ * *
+junit junit jar s/4\..*/4.x/ * *
+net.sf.jni-inchi jni-inchi jar s/.*/debian/ * *
+org.openscience.cdk cdk-annotation jar s/.*/debian/ * *
+org.openscience.cdk cdk-app pom s/.*/debian/ * *
+org.openscience.cdk cdk-atomtype jar s/.*/debian/ * *
+org.openscience.cdk cdk-base pom s/.*/debian/ * *
+org.openscience.cdk cdk-builder3d jar s/.*/debian/ * *
+org.openscience.cdk cdk-builder3dtools jar s/.*/debian/ * *
+org.openscience.cdk cdk-bundle jar s/.*/debian/ * *
+org.openscience.cdk cdk-charges jar s/.*/debian/ * *
+org.openscience.cdk cdk-cip jar s/.*/debian/ * *
+org.openscience.cdk cdk-control jar s/.*/debian/ * *
+org.openscience.cdk cdk-core jar s/.*/debian/ * *
+org.openscience.cdk cdk-ctab jar s/.*/debian/ * *
+org.openscience.cdk cdk-data jar s/.*/debian/ * *
+org.openscience.cdk cdk-datadebug jar s/.*/debian/ * *
+org.openscience.cdk cdk-depict jar s/.*/debian/ * *
+org.openscience.cdk cdk-descriptor pom s/.*/debian/ * *
+org.openscience.cdk cdk-dict jar s/.*/debian/ * *
+org.openscience.cdk cdk-diff jar s/.*/debian/ * *
+org.openscience.cdk cdk-display pom s/.*/debian/ * *
+org.openscience.cdk cdk-extra jar s/.*/debian/ * *
+org.openscience.cdk cdk-fingerprint jar s/.*/debian/ * *
+org.openscience.cdk cdk-forcefield jar s/.*/debian/ * *
+org.openscience.cdk cdk-formula jar s/.*/debian/ * *
+org.openscience.cdk cdk-fragment jar s/.*/debian/ * *
+org.openscience.cdk cdk-group jar s/.*/debian/ * *
+org.openscience.cdk cdk-hash jar s/.*/debian/ * *
+org.openscience.cdk cdk-inchi jar s/.*/debian/ * *
+org.openscience.cdk cdk-interfaces jar s/.*/debian/ * *
+org.openscience.cdk cdk-io jar s/.*/debian/ * *
+org.openscience.cdk cdk-ioformats jar s/.*/debian/ * *
+org.openscience.cdk cdk-ionpot jar s/.*/debian/ * *
+org.openscience.cdk cdk-iordf jar s/.*/debian/ * *
+org.openscience.cdk cdk-isomorphism jar s/.*/debian/ * *
+org.openscience.cdk cdk-legacy jar s/.*/debian/ * *
+org.openscience.cdk cdk-libiocml jar s/.*/debian/ * *
+org.openscience.cdk cdk-libiomd jar s/.*/debian/ * *
+org.openscience.cdk cdk-log4j jar s/.*/debian/ * *
+org.openscience.cdk cdk-misc pom s/.*/debian/ * *
+org.openscience.cdk cdk-model jar s/.*/debian/ * *
+org.openscience.cdk cdk-pcore jar s/.*/debian/ * *
+org.openscience.cdk cdk-pdb jar s/.*/debian/ * *
+org.openscience.cdk cdk-pdbcml jar s/.*/debian/ * *
+org.openscience.cdk cdk-qm jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsar jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsaratomic jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarbond jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarcml jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarionpot jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarmolecular jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarprotein jar s/.*/debian/ * *
+org.openscience.cdk cdk-qsarsubstance jar s/.*/debian/ * *
+org.openscience.cdk cdk-reaction jar s/.*/debian/ * *
+org.openscience.cdk cdk-render jar s/.*/debian/ * *
+org.openscience.cdk cdk-renderawt jar s/.*/debian/ * *
+org.openscience.cdk cdk-renderbasic jar s/.*/debian/ * *
+org.openscience.cdk cdk-renderextra jar s/.*/debian/ * *
+org.openscience.cdk cdk-sdg jar s/.*/debian/ * *
+org.openscience.cdk cdk-signature jar s/.*/debian/ * *
+org.openscience.cdk cdk-silent jar s/.*/debian/ * *
+org.openscience.cdk cdk-smarts jar s/.*/debian/ * *
+org.openscience.cdk cdk-smiles jar s/.*/debian/ * *
+org.openscience.cdk cdk-smsd jar s/.*/debian/ * *
+org.openscience.cdk cdk-standard jar s/.*/debian/ * *
+org.openscience.cdk cdk-storage pom s/.*/debian/ * *
+org.openscience.cdk cdk-structgen jar s/.*/debian/ * *
+org.openscience.cdk cdk-tautomer jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-atomtype jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-core jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-extra jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-interfaces jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-standard jar s/.*/debian/ * *
+org.openscience.cdk cdk-test-valencycheck jar s/.*/debian/ * *
+org.openscience.cdk cdk-test jar s/.*/debian/ * *
+org.openscience.cdk cdk-testdata jar s/.*/debian/ * *
+org.openscience.cdk cdk-tool pom s/.*/debian/ * *
+org.openscience.cdk cdk-valencycheck jar s/.*/debian/ * *
+org.openscience.cdk cdk pom s/.*/debian/ * *
+log4j log4j * s/1\.2\..*/1.2.x/ * *
+org.apache.maven.plugins maven-enforcer-plugin * s/.*/debian/ * *
+org.apache.rat apache-rat-plugin * s/.*/debian/ * *

debian/rules

@@ -21,7 +21,7 @@ COMPONENTS := \
 	dh $@ --with javahelper
 
 override_dh_auto_build:
-	dh_auto_build -- -Dlib=/usr/share/java info dist-all
+	dh_auto_build -- -Dlib=/usr/share/java install
 
 override_dh_install:
 	dh_install