Merge pull request #966 from egonw/devel/moreDepUpdates

Updates of code and build dependencies
cdk · Apr 12, 2023 · cc8e9f8 · cc8e9f8
2 parents 0f581a8 + 1d33c2c
commit cc8e9f8
Show file tree

Hide file tree

Showing 18 changed files with 30 additions and 28 deletions.
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -29,7 +29,9 @@ jobs:
     - name: Build with Maven
       run: mvn clean install -q -Pjacoco
     - name: push JaCoCo stats to codecov.io
-      run: bash <(curl -s https://codecov.io/bash)
+      uses: codecov/codecov-action@v3
+      env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   build-sonarcloud:
     name: Build sonarcloud

diff --git a/base/annotation/pom.xml b/base/annotation/pom.xml
@@ -18,7 +18,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/base/atomtype/pom.xml b/base/atomtype/pom.xml
@@ -35,7 +35,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/base/core/pom.xml b/base/core/pom.xml
@@ -46,7 +46,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/base/data/pom.xml b/base/data/pom.xml
@@ -74,7 +74,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-pmd-plugin</artifactId>
-                <version>3.1</version>
+                <version>3.20.0</version>
                 <configuration>
                     <rulesets>
                         <ruleset>/pmd/custom-data.xml</ruleset>

diff --git a/base/datadebug/pom.xml b/base/datadebug/pom.xml
@@ -79,7 +79,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-pmd-plugin</artifactId>
-                <version>3.1</version>
+                <version>3.20.0</version>
                 <configuration>
                     <rulesets>
                         <ruleset>/pmd/custom-data.xml</ruleset>

diff --git a/base/interfaces/pom.xml b/base/interfaces/pom.xml
@@ -34,7 +34,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/base/silent/pom.xml b/base/silent/pom.xml
@@ -74,7 +74,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-pmd-plugin</artifactId>
-                <version>3.1</version>
+                <version>3.20.0</version>
                 <configuration>
                     <rulesets>
                         <ruleset>/pmd/custom-data.xml</ruleset>

diff --git a/base/standard/pom.xml b/base/standard/pom.xml
@@ -34,7 +34,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/base/test/pom.xml b/base/test/pom.xml
@@ -76,7 +76,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.2</version>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <goals>

diff --git a/base/valencycheck/pom.xml b/base/valencycheck/pom.xml
@@ -35,7 +35,7 @@
         	<plugin>
         		<groupId>org.apache.maven.plugins</groupId>
         		<artifactId>maven-surefire-plugin</artifactId>
-        		<version>2.16</version>
+        		<version>3.0.0-M7</version>
         		<configuration>
           			<skipTests>true</skipTests>
         		</configuration>

diff --git a/bundle/pom.xml b/bundle/pom.xml
@@ -299,7 +299,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
+                <version>3.10.0</version>
                 <configuration>
                     <source>1.6</source>
                     <target>1.6</target>

diff --git a/descriptor/qsarcml/pom.xml b/descriptor/qsarcml/pom.xml
@@ -31,7 +31,7 @@
         <dependency>
             <groupId>org.blueobelisk</groupId>
             <artifactId>cmlxom</artifactId>
-            <version>4.4</version>
+            <version>4.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

diff --git a/pom.xml b/pom.xml
@@ -528,17 +528,17 @@
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
                 <artifactId>log4j-api</artifactId>
-                <version>2.19.0</version>
+                <version>2.20.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
                 <artifactId>log4j-core</artifactId>
-                <version>2.19.0</version>
+                <version>2.20.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.logging.log4j</groupId>
                 <artifactId>log4j-1.2-api</artifactId>
-                <version>2.19.0</version>
+                <version>2.20.0</version>
             </dependency>
             <dependency>
                 <groupId>xerces</groupId>
@@ -548,7 +548,7 @@
             <dependency>
                 <groupId>xml-apis</groupId>
                 <artifactId>xml-apis</artifactId>
-                <version>1.4.01</version>
+                <version>2.0.2</version>
             </dependency>
         </dependencies>
     </dependencyManagement>
@@ -566,7 +566,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.8.1</version>
+                <version>3.10.1</version>
                 <configuration>
                     <source>1.8</source>
                     <target>1.8</target>
@@ -594,7 +594,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.3.0</version>
                 <inherited>true</inherited>
                 <configuration>
                     <archive>
@@ -609,7 +609,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.4.1</version>
                 <configuration>
                     <tags>
                         <!--cdk.depends and cdk.builddepends no longer used-->
@@ -723,7 +723,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-pmd-plugin</artifactId>
-                <version>3.6</version>
+                <version>3.20.0</version>
                 <configuration>
                     <rulesets>
                         <ruleset>/pmd/custom.xml</ruleset>
@@ -762,12 +762,12 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
-                <version>3.1.2</version>
+                <version>3.5.0</version>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-checkstyle-plugin</artifactId>
-                <version>2.17</version>
+                <version>3.2.1</version>
                 <configuration>
                     <configLocation>checkstyle.xml</configLocation>
                     <linkXRef>false</linkXRef>
@@ -781,7 +781,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.3.1</version>
+                <version>3.4.1</version>
                 <reportSets>
                     <reportSet>
                         <id>default</id>

diff --git a/storage/inchi/pom.xml b/storage/inchi/pom.xml
@@ -13,7 +13,7 @@
     <artifactId>cdk-inchi</artifactId>
 
     <properties>
-        <jna-inchi.version>1.1</jna-inchi.version>
+        <jna-inchi.version>1.2</jna-inchi.version>
     </properties>
 
     <name>cdk-inchi</name>

diff --git a/storage/libiocml/pom.xml b/storage/libiocml/pom.xml
@@ -21,7 +21,7 @@
         <dependency>
             <groupId>org.blueobelisk</groupId>
             <artifactId>cmlxom</artifactId>
-            <version>4.4</version>
+            <version>4.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

diff --git a/storage/libiomd/pom.xml b/storage/libiomd/pom.xml
@@ -17,7 +17,7 @@
         <dependency>
             <groupId>org.blueobelisk</groupId>
             <artifactId>cmlxom</artifactId>
-            <version>4.4</version>
+            <version>4.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>

diff --git a/storage/pdbcml/pom.xml b/storage/pdbcml/pom.xml
@@ -31,7 +31,7 @@
         <dependency>
             <groupId>org.blueobelisk</groupId>
             <artifactId>cmlxom</artifactId>
-            <version>4.4</version>
+            <version>4.5</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.apache.logging.log4j</groupId>