[Git][java-team/cdk][master] 8 commits: Preparing to build with InChI.

[Andrius Merkys]

Andrius Merkys pushed to branch master at Debian Java Maintainers / cdk


Commits:
eea1c987 by Andrius Merkys at 2019-11-13T10:25:42Z
Preparing to build with InChI.

- - - - -
2e26cefc by Andrius Merkys at 2019-11-13T10:54:07Z
Refreshing java8-compatibility.patch.

- - - - -
0eb43952 by Andrius Merkys at 2019-11-13T10:55:56Z
Adding a patch fixing the dependency on jni-inchi.

- - - - -
b6c138d8 by Andrius Merkys at 2019-11-13T11:10:34Z
Patching a renamed method in jni-inchi.

- - - - -
3ef02775 by Andrius Merkys at 2019-11-13T11:23:44Z
Adding description for inchi.patch.

- - - - -
ac69b2d0 by Andrius Merkys at 2019-11-13T11:25:39Z
Updating Vcs-* fields.

- - - - -
7300d52c by Andrius Merkys at 2019-11-13T11:28:35Z
Updating debian/watch to point to the GitHub site.

- - - - -
7de3e25c by Andrius Merkys at 2019-11-13T11:31:14Z
Updating the changelog.

- - - - -


8 changed files:

- debian/README.Debian
- debian/changelog
- debian/compile.excludes
- debian/control
- + debian/patches/inchi.patch
- debian/patches/java8-compatibility.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/README.Debian
=====================================
@@ -2,9 +2,6 @@ Some modules are built partially because the required build dependencies
 are not yet in archives. Following is the list of files excluded from
 compilation.
 
-org/openscience/cdk/inchi/InChIGeneratorFactory.java
-org/openscience/cdk/inchi/InChIGenerator.java
-org/openscience/cdk/inchi/InChIToStructure.java
 org/openscience/cdk/libio/cml/Convertor.java
 org/openscience/cdk/io/CMLWriter.java
 org/openscience/cdk/io/RssWriter.java


=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+cdk (1:1.2.10-8) UNRELEASED; urgency=medium
+
+  [ Egon Willighagen ]
+  * Update the homepage URL
+
+  [ Andrius Merkys ]
+  * Team upload.
+  * Build with InChI support (Closes: #627523)
+  * Refreshing java8-compatibility.patch.
+  * Updating Vcs-* fields.
+  * Updating debian/watch to point to the GitHub site.
+
+ -- Andrius Merkys <merkys at debian.org>  Wed, 13 Nov 2019 06:29:17 -0500
+
 cdk (1:1.2.10-7) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/compile.excludes
=====================================
@@ -1,6 +1,3 @@
-**/InChIGeneratorFactory.java
-**/InChIGenerator.java
-**/InChIToStructure.java
 **/Convertor.java
 **/CMLWriter.java
 **/RssWriter.java


=====================================
debian/control
=====================================
@@ -14,6 +14,7 @@ Build-Depends:
  javahelper,
  libjama-java (>= 1.0.3),
  libjgrapht0.6-java,
+ libjni-inchi-java,
  liblog4j1.2-java,
  libvecmath-java,
  libxerces2-java,
@@ -21,8 +22,8 @@ Build-Depends:
  libxpp3-java,
  r-cran-rjava
 Standards-Version: 4.1.3
-Vcs-Git: https://anonscm.debian.org/git/pkg-java/cdk.git
-Vcs-Browser: https://anonscm.debian.org/cgit/pkg-java/cdk.git
+Vcs-Git: https://salsa.debian.org/java-team/cdk.git
+Vcs-Browser: https://salsa.debian.org/java-team/cdk
 Homepage: https://cdk.github.io/
 
 Package: libcdk-java


=====================================
debian/patches/inchi.patch
=====================================
@@ -0,0 +1,30 @@
+Description: Enabling build with jni-inchi v0.8.
+Author: Andrius Merkys <merkys at debian.org>
+--- a/src/META-INF/inchi.libdepends
++++ b/src/META-INF/inchi.libdepends
+@@ -1,4 +1,4 @@
+ vecmath*.jar
+ xom*.jar
+-jniinchi-0.5.jar
++jni-inchi.jar
+ cmlxom-2.5-b1.jar
+--- a/src/META-INF/test-inchi.libdepends
++++ b/src/META-INF/test-inchi.libdepends
+@@ -1,5 +1,5 @@
+ vecmath*.jar
+ xom*.jar
+-jniinchi-0.5.jar
++jni-inchi.jar
+ cmlxom-2.5-b1.jar
+ log4j*.jar
+--- a/src/main/org/openscience/cdk/inchi/InChIGenerator.java
++++ b/src/main/org/openscience/cdk/inchi/InChIGenerator.java
+@@ -383,7 +383,7 @@
+     public String getInchiKey() throws CDKException {
+         JniInchiOutputKey key;
+         try {
+-            key = JniInchiWrapper.getInChIKey(output.getInchi());
++            key = JniInchiWrapper.getInchiKey(output.getInchi());
+             if (key.getReturnStatus() == INCHI_KEY.OK) {
+                 return key.getKey();
+             } else {


=====================================
debian/patches/java8-compatibility.patch
=====================================
@@ -3,7 +3,7 @@ Author: Emmanuel Bourg <ebourg at apache.org>
 Forwarded: no
 --- a/build.xml
 +++ b/build.xml
-@@ -193,13 +193,11 @@
+@@ -187,13 +187,11 @@
                  </or>
              </condition>
              <condition property="isNotJava15+">


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@
 ant19.patch
 jama-1.0.3.patch
 java8-compatibility.patch
+inchi.patch


=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
-version=3
-http://sf.net/cdk/ cdk-(1\.[2468]\.[\d\.]+)\.tar\.gz debian uupdate
+version=4
+https://github.com/cdk/cdk/releases (?:.*?/)?cdk-(\d[\d.]*)\.tar\.gz



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