Cleanup of the cdk/base modules - using dependency analzye to ensure …

…all used undelcared dependencies are included and unused declared are removed.
cdk · Dec 22, 2021 · 869bfce · 869bfce
1 parent a207f62
commit 869bfce
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Showing 21 changed files with 90 additions and 46 deletions.
diff --git a/base/annotation/pom.xml b/base/annotation/pom.xml
@@ -13,13 +13,6 @@
     <artifactId>cdk-annotation</artifactId>
 
     <name>cdk-annotation</name>
-    <dependencies>
-    	<dependency>
-        	<groupId>junit</groupId>
-        	<artifactId>junit</artifactId>
-        	<scope>test</scope>
-        </dependency>
-    </dependencies>
 	<build>
     	<plugins>
         	<plugin>

diff --git a/base/atomtype/pom.xml b/base/atomtype/pom.xml
@@ -29,11 +29,6 @@
             <artifactId>cdk-standard</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
-        <dependency>
-        	<groupId>junit</groupId>
-        	<artifactId>junit</artifactId>
-        	<scope>test</scope>
-        </dependency>
     </dependencies>
 	<build>
     	<plugins>

diff --git a/base/core/pom.xml b/base/core/pom.xml
@@ -14,6 +14,10 @@
 
     <name>cdk-core</name>
     <dependencies>
+        <dependency>
+            <groupId>javax.vecmath</groupId>
+            <artifactId>vecmath</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
@@ -23,11 +27,6 @@
             <artifactId>cdk-interfaces</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
-        <dependency>
-        	<groupId>junit</groupId>
-        	<artifactId>junit</artifactId>
-        	<scope>test</scope>
-        </dependency>
     </dependencies>
 
     <build>

diff --git a/base/data/pom.xml b/base/data/pom.xml
@@ -29,7 +29,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

diff --git a/base/datadebug/pom.xml b/base/datadebug/pom.xml
@@ -25,7 +25,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

diff --git a/base/dict/pom.xml b/base/dict/pom.xml
@@ -19,19 +19,26 @@
             <artifactId>xom</artifactId>
         </dependency>
         <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
+            <groupId>xml-apis</groupId>
+            <artifactId>xml-apis</artifactId>
+            <version>1.3.03</version>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
         <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <!-- Only used for CDK logging in tests-->
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-core</artifactId>
             <version>${project.parent.version}</version>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>

diff --git a/base/isomorphism/pom.xml b/base/isomorphism/pom.xml
@@ -29,7 +29,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

diff --git a/base/reaction/pom.xml b/base/reaction/pom.xml
@@ -19,6 +19,11 @@
             <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/base/silent/pom.xml b/base/silent/pom.xml
@@ -29,7 +29,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>

diff --git a/base/test-atomtype/pom.xml b/base/test-atomtype/pom.xml
@@ -25,6 +25,11 @@
             <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-interfaces</artifactId>

diff --git a/base/test-core/pom.xml b/base/test-core/pom.xml
@@ -127,6 +127,18 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-ioformats</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-ctab</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/base/test-interfaces/pom.xml b/base/test-interfaces/pom.xml
@@ -30,6 +30,11 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>

diff --git a/base/test-standard/pom.xml b/base/test-standard/pom.xml
@@ -15,14 +15,14 @@
     <name>cdk-test-standard</name>
     <dependencies>
         <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>cdk-standard</artifactId>
-            <version>${project.parent.version}</version>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-standard</artifactId>
+            <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -144,6 +144,18 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-atomtype</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-formula</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/base/test-valencycheck/pom.xml b/base/test-valencycheck/pom.xml
@@ -20,6 +20,11 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
@@ -91,6 +96,12 @@
             <version>${project.parent.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>cdk-ctab</artifactId>
+            <version>${project.parent.version}</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>cdk-testdata</artifactId>

diff --git a/base/test/pom.xml b/base/test/pom.xml
@@ -19,6 +19,11 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>

diff --git a/base/testdata/pom.xml b/base/testdata/pom.xml
@@ -3,21 +3,18 @@
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
-
     <parent>
         <artifactId>cdk-base</artifactId>
         <groupId>org.openscience.cdk</groupId>
         <version>2.7-SNAPSHOT</version>
     </parent>
-
     <artifactId>cdk-testdata</artifactId>
-
     <name>cdk-testdata</name>
     <dependencies>
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
+            <scope>test</scope>
         </dependency>
     </dependencies>
-
 </project>
diff --git a/descriptor/fingerprint/pom.xml b/descriptor/fingerprint/pom.xml
@@ -35,7 +35,7 @@
             <groupId>uk.ac.ebi.beam</groupId>
             <artifactId>beam-func</artifactId>
         </dependency>
-            <dependency>
+        <dependency>
             <groupId>org.hamcrest</groupId>
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>

diff --git a/pom.xml b/pom.xml
@@ -894,11 +894,4 @@
             </build>
         </profile>
     </profiles>
-    <dependencies>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
 </project>
diff --git a/storage/ctab/pom.xml b/storage/ctab/pom.xml
@@ -42,11 +42,6 @@
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
             <artifactId>hamcrest</artifactId>

diff --git a/tool/model/pom.xml b/tool/model/pom.xml
@@ -13,6 +13,11 @@
     <name>cdk-model</name>
 
     <dependencies>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.openscience.cdk</groupId>
             <artifactId>cdk-fingerprint</artifactId>

diff --git a/tool/smarts/pom.xml b/tool/smarts/pom.xml
@@ -34,6 +34,11 @@
             <artifactId>hamcrest</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.mockito</groupId>
             <artifactId>mockito-core</artifactId>