Add GitHub actions

.github/PULL_REQUEST_TEMPLATE.md

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+## Summary
+
+<!-- Provide a brief 1-2 sentence summary of what this PR does -->
+
+
+
+---
+
+## Features
+
+<!-- 
+  List new features or enhancements added in this PR.
+  Delete this section if not applicable.
+
+  Format:
+  - Brief description of the feature
+  - Another feature added
+-->
+
+- 
+
+---
+
+## Bug Fixes
+
+<!-- 
+  List bugs that are fixed by this PR.
+  Delete this section if not applicable.
+
+  Format:
+  - Fixed issue where X happened when Y
+  - Resolved crash when doing Z
+-->
+
+- 
+
+---
+
+## Breaking Changes
+
+<!-- 
+  List any changes that break backwards compatibility.
+  Delete this section if not applicable.
+
+  Format:
+  - Changed `--old-flag` to `--new-flag`
+  - Removed deprecated function `oldFunction()`
+  - Changed output format from X to Y
+-->
+
+- 
+
+---
+
+## Checklist
+
+- [ ] I have updated the `version` in `build.gradle.kts` (REQUIRED - see below)
+- [ ] I have tested these changes locally
+- [ ] I have added/updated tests for new functionality
+- [ ] I have updated documentation (if applicable)
+- [ ] Breaking changes are clearly documented above
+
+---
+
+<!--
+
+==== IMPORTANT: VERSION UPDATE REQUIRED
+
+Before this PR can be merged, you MUST update the version in
+build.gradle.kts to be HIGHER than the current released version.
+
+The PR will fail the version check if you don't update it!
+
+Example in build.gradle.kts:
+  version = "0.2.0"  // Update this to be higher than current release
+
+Semantic Versioning Guide:
+  - MAJOR version: Breaking changes (e.g., 1.0.0 -> 2.0.0)
+  - MINOR version: New features, backwards compatible (e.g., 1.0.0 -> 1.1.0)
+  - PATCH version: Bug fixes (e.g., 1.0.0 -> 1.0.1)
+
+
+==== PR DESCRIPTION GUIDELINES
+
+1. SUMMARY
+   - Keep it concise (1-2 sentences)
+   - Focus on WHAT changed and WHY, not HOW
+
+2. FEATURES / BUG FIXES / BREAKING CHANGES
+   - Use bullet points for each item
+   - Start with a verb: "Add", "Fix", "Remove", "Change", "Update"
+   - Be specific: "Fix crash when input file is empty" not "Fix bug"
+   - Delete sections that don't apply to your PR
+
+3. EXAMPLES
+
+   Good:
+   - Add `--threads` flag for parallel sequence alignment
+   - Fix memory leak when processing large FASTA files
+   - Change `--output` to `--output-dir` for clarity
+
+   Bad:
+   - Added new feature
+   - Fixed bug
+   - Updated code
+
+-->

.github/RELEASE_TEMPLATE.md

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+## What's New
+
+${SUMMARY}
+
+## Features
+
+${FEATURES}
+
+## Bug Fixes
+
+${BUG_FIXES}
+
+## Breaking Changes
+
+${BREAKING_CHANGES}
+
+## Installation
+
+Download the appropriate archive for your system:
+- `seq_sim-${VERSION}.tar` - Unix/Linux/macOS
+- `seq_sim-${VERSION}.zip` - Windows
+
+### Quick Start
+
+```bash
+# Extract the archive
+tar -xf seq_sim-${VERSION}.tar
+# or
+unzip seq_sim-${VERSION}.zip
+
+# Run the application
+./seq_sim-${VERSION}/bin/seq_sim --help
+```
+
+## Requirements
+
+- Java 21 or higher
+
+## Full Changelog
+
+**Full Changelog**: https://github.com/${REPO}/compare/${PREVIOUS_TAG}...${VERSION}

.github/workflows/pr-check.yml

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+name: PR Version Check
+
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+
+jobs:
+  version-check:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get version from build.gradle.kts
+        id: get_version
+        run: |
+          VERSION=$(grep -oP 'version\s*=\s*"\K[^"]+' build.gradle.kts)
+          echo "version=v$VERSION" >> $GITHUB_OUTPUT
+          echo "PR version: v$VERSION"
+
+      - name: Get current latest tag
+        id: get_current_tag
+        run: |
+          CURRENT_TAG=$(git describe --tags --abbrev=0 origin/main 2>/dev/null || git describe --tags --abbrev=0 origin/master 2>/dev/null || echo "v0.0.0")
+          echo "current_tag=$CURRENT_TAG" >> $GITHUB_OUTPUT
+          echo "Current released version: $CURRENT_TAG"
+
+      - name: Validate version is higher than current release
+        run: |
+          CURRENT="${{ steps.get_current_tag.outputs.current_tag }}"
+          NEW="${{ steps.get_version.outputs.version }}"
+
+          # Function to convert version to comparable number
+          version_to_num() {
+            local version=$1
+            # Remove 'v' prefix if present
+            version=${version#v}
+            # Split into parts and pad (handles 2 or 3 part versions)
+            echo "$version" | awk -F. '{ printf "%d%03d%03d", $1, ($2 ? $2 : 0), ($3 ? $3 : 0) }'
+          }
+
+          CURRENT_NUM=$(version_to_num "$CURRENT")
+          NEW_NUM=$(version_to_num "$NEW")
+
+          echo "Comparing versions:"
+          echo "  Current release: $CURRENT ($CURRENT_NUM)"
+          echo "  PR version:      $NEW ($NEW_NUM)"
+
+          if [ "$NEW_NUM" -le "$CURRENT_NUM" ]; then
+            echo ""
+            echo "::error::Version must be updated before merging!"
+            echo "::error::Current released version is $CURRENT"
+            echo "::error::Please update the 'version' in build.gradle.kts to be higher than $CURRENT"
+            echo ""
+            echo "To fix this, update build.gradle.kts:"
+            echo '  version = "X.Y.Z"  // Must be higher than current'
+            echo ""
+            echo "Version guidelines (semantic versioning):"
+            echo "  - MAJOR (X): Breaking changes"
+            echo "  - MINOR (Y): New features (backwards compatible)"
+            echo "  - PATCH (Z): Bug fixes"
+            exit 1
+          fi
+
+          echo ""
+          echo "Version check passed: $NEW > $CURRENT"