From 8f2c6a1d8657a85f3578f4955b67a212b0e3c969 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 28 Dec 2025 07:25:32 +0100
Subject: [PATCH 1/3] Open for development

---
 org.pathvisio.lib/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/org.pathvisio.lib/pom.xml b/org.pathvisio.lib/pom.xml
index 5a6cc78..3256fd7 100644
--- a/org.pathvisio.lib/pom.xml
+++ b/org.pathvisio.lib/pom.xml
@@ -2,7 +2,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.pathvisio</groupId>
 	<artifactId>org.pathvisio.libgpml</artifactId>
-	<version>4.0.4</version>
+	<version>4.0.5-SNAPSHOT</version>
 	<packaging>jar</packaging>
 	<name>libGPML</name>
 	<description>libGPML is a library for reading, writing, manipulation, and conversion of files and data streams in the GPML (Graphical Pathway Markup Language) format.</description>

From 9d5cb14b84f854c15bcc038a8fbff19e7fd352cd Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Fri, 10 Jul 2026 18:35:48 +0200
Subject: [PATCH 2/3] Updated BridgeDb Java to 3.0.30

---
 org.pathvisio.lib/pom.xml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/org.pathvisio.lib/pom.xml b/org.pathvisio.lib/pom.xml
index 3256fd7..4f3bb57 100644
--- a/org.pathvisio.lib/pom.xml
+++ b/org.pathvisio.lib/pom.xml
@@ -13,6 +13,8 @@
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<maven.compiler.source>11</maven.compiler.source>
 		<maven.compiler.target>11</maven.compiler.target>
+
+		<bridgedb.version>3.0.30</bridgedb.version>
 	</properties>
 
 	<licenses>
@@ -77,9 +79,9 @@
 						</Import-Package>
 						<Require-Bundle>
 							org.apache.servicemix.bundles.jdom;bundle-version="2.0.6",
- 							org.bridgedb;bundle-version="3.0.29",
-						 	org.bridgedb.bio;bundle-version="3.0.29",
-						 	org.bridgedb.rdb;bundle-version="3.0.29",
+ 							org.bridgedb;bundle-version="${bridgedb.version}",
+						 	org.bridgedb.bio;bundle-version="${bridgedb.version}",
+						 	org.bridgedb.rdb;bundle-version="${bridgedb.version}",
 							org.apache.commons.commons-collections4;bundle-version="4.5.0"
 						</Require-Bundle>
 					</instructions>
@@ -198,17 +200,17 @@
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb</artifactId>
-			<version>3.0.29</version>
+			<version>${bridgedb.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb.bio</artifactId>
-			<version>3.0.29</version>
+			<version>${bridgedb.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb.rdb</artifactId>
-			<version>3.0.29</version>
+			<version>${bridgedb.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>

From aeaf87a1a670c8d2df5c2dddd15135d7033f2bf7 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 18 Jul 2026 11:30:15 +0200
Subject: [PATCH 3/3] New method of the token

---
 .github/workflows/maven.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
index 14c0971..165a024 100644
--- a/.github/workflows/maven.yml
+++ b/.github/workflows/maven.yml
@@ -41,8 +41,9 @@ jobs:
       run: cd org.pathvisio.lib; mvn clean install -Dgpg.skip -Pjacoco
     - name: push JaCoCo stats to codecov.io
       uses: codecov/codecov-action@v5
+      env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
         directory: 'org.pathvisio.lib'
         verbose: true
-        token: ${{ secrets.CODECOV_TOKEN }}
         slug: PathVisio/libGPML