From fcc0ac736338dd6f85b8e36d5ad8cb59f2c5d201 Mon Sep 17 00:00:00 2001
From: Shawn Reuland <sreuland@users.noreply.github.com>
Date: Wed, 18 Feb 2026 14:30:32 -0800
Subject: [PATCH 1/3] UD-3169: added gh release workflow

---
 .github/workflows/release.yml | 42 +++++++++++++++++++++++++++++++++++
 Makefile                      |  7 +++++-
 pom.xml                       |  4 +++-
 3 files changed, 51 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/release.yml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 0000000..51a1bae
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,42 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-release:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: 'maven'
+
+    - name: Extract and validate version from tag
+      id: version
+      run: |
+        TAG="${{ github.event.release.tag_name }}"
+        VERSION="${TAG#v}"
+        if ! echo "$VERSION" | grep -qE '^[0-9]+\.[0-9]+\.[0-9]+$'; then
+          echo "Error: version '$VERSION' is not valid semver (expected X.Y.Z)"
+          exit 1
+        fi
+        echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+    - name: Build release JAR
+      run: xvfb-run make install-release VERSION=${{ steps.version.outputs.version }}
+
+    - name: Upload JAR to release
+      run: |
+        gh release upload "${{ github.event.release.tag_name }}" \
+          "target/open-cyweb-${{ steps.version.outputs.version }}.jar" \
+          --clobber
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Makefile b/Makefile
index c46a30f..6d57125 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: clean test coverage install updateversion help
+.PHONY: clean test coverage install install-release updateversion help
 .DEFAULT_GOAL := help
 
 help:
@@ -11,6 +11,7 @@ help:
 	@echo "  lint-fix       auto-fix Spotless formatting"
 	@echo "  coverage       check code coverage with jacoco (report: target/site/jacoco/index.html)"
 	@echo "  install        install the package to local repo"
+	@echo "  install-release  build and install a release jar with VERSION (e.g. make install-release VERSION=1.2.3)"
 	@echo "  updateversion  updates version in pom.xml via maven command"
 
 clean:
@@ -31,5 +32,9 @@ coverage:
 install: clean
 	mvn install
 
+install-release:
+	@if [ -z "$(VERSION)" ]; then echo "Error: VERSION is required. Usage: make install-release VERSION=1.2.3"; exit 1; fi
+	mvn clean install -Drevision=$(VERSION)
+
 updateversion:
 	mvn versions:set
diff --git a/pom.xml b/pom.xml
index 952a5c6..7fa6774 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,6 +4,8 @@
 
 	<properties>
 
+		<revision>1.0.0-SNAPSHOT</revision>
+
 		<bundle.symbolicName>edu.ucsd.idekerlab.opencyweb</bundle.symbolicName>
 		<bundle.namespace>edu.ucsd.idekerlab.opencyweb</bundle.namespace>
 
@@ -21,7 +23,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>edu.ucsd.idekerlab</groupId>
 	<artifactId>open-cyweb</artifactId>
-	<version>1.0.0-SNAPSHOT</version>
+	<version>${revision}</version>
 	<packaging>bundle</packaging>
 	<name>OpenCytoscapeWeb</name>
 

From 33811a02eff9ca45869cd946bdd5a7741a8f06cc Mon Sep 17 00:00:00 2001
From: Shawn Reuland <sreuland@users.noreply.github.com>
Date: Wed, 18 Feb 2026 14:32:40 -0800
Subject: [PATCH 2/3] UD-3169: added changelog

---
 CHANGELOG.md | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 CHANGELOG.md

diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..dcc02c5
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,12 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [1.0.0] - 2026-02-18
+
+### Added
+- Initial release of the OpenCytoscapeWeb Cytoscape app
+- Open the current network in Cytoscape Web directly from the File > Export menu
+- Configurable Cytoscape Web URL via app properties
+- Configurable maximum file size limit for network export
+- Validation of network size before attempting to open, with a user-friendly error dialog when the limit is exceeded

From 9f1b2b696282d01e3df5cd85b0fd205ef92bbe4a Mon Sep 17 00:00:00 2001
From: Shawn Reuland <sreuland@users.noreply.github.com>
Date: Wed, 18 Feb 2026 14:41:18 -0800
Subject: [PATCH 3/3] UD-3169: prefent duplicate test runs on gh ci

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bf13d84..5ea97f9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,10 +3,10 @@ name: Continuous Integration
 on:
   push:
     branches:
-      - '**'  # Run on push to any branch
+      - main  # Run on merge to main
   pull_request:
     branches:
-      - main  # Run on PRs to main
+      - main  # Run on PR updates targeting main
 
 jobs:
   test: