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Release Surge 2.0 (#17)
Release Surge 2.0
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‎.github/workflows/build.yml‎

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name: Build and Test
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on:
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push:
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branches: [ main, 'release/**' ]
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pull_request:
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branches: [ main ]
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jobs:
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build-linux:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Install dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y gcc make zlib1g-dev
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- name: Build nauty
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run: |
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curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
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tar xzf nauty2_9_3.tar.gz
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cd nauty2_9_3
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./configure && make
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- name: Build surge
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working-directory: src
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run: |
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make surge \
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NAUTY=${{ github.workspace }}/nauty2_9_3 \
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NAUTYLIB=${{ github.workspace }}/nauty2_9_3 \
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CCOPT="-O3"
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- name: Test surge
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working-directory: src
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run: |
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./surge -help 2>&1 | head -3
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./surge -u C6H6
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./surge -u C4H10
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- name: Build canonsdf
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working-directory: src
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run: |
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make canonsdf \
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NAUTY=${{ github.workspace }}/nauty2_9_3 \
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NAUTYLIB=${{ github.workspace }}/nauty2_9_3 \
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CCOPT="-O3"
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- name: Upload Linux binary
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uses: actions/upload-artifact@v4
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with:
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name: surge-linux-x86_64
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path: src/surge
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build-macos:
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strategy:
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matrix:
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include:
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- os: macos-14
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arch: arm64
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- os: macos-15
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arch: arm64-m15
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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- name: Install nauty
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run: brew install nauty
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- name: Create nauty library symlink
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run: |
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NAUTY_LIB=$(brew --prefix nauty)/lib
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ln -sf "$NAUTY_LIB/libnautyL1.a" "$NAUTY_LIB/nautyL1.a"
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- name: Build surge
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working-directory: src
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run: |
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make surge \
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NAUTY=$(brew --prefix nauty)/include/nauty \
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NAUTYLIB=$(brew --prefix nauty)/lib \
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CCOPT="-O3"
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- name: Test surge
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working-directory: src
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run: |
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./surge -help 2>&1 | head -3
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./surge -u C6H6
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./surge -u C4H10
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- name: Upload macOS binary
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uses: actions/upload-artifact@v4
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with:
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name: surge-macos-${{ matrix.arch }}
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path: src/surge
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build-windows:
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runs-on: windows-latest
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defaults:
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run:
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shell: msys2 {0}
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steps:
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- uses: actions/checkout@v4
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- uses: msys2/setup-msys2@v2
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with:
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msystem: UCRT64
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install: >-
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mingw-w64-ucrt-x86_64-gcc
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make
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mingw-w64-ucrt-x86_64-zlib
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curl
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tar
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- name: Build nauty
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run: |
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curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
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tar xzf nauty2_9_3.tar.gz
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cd nauty2_9_3
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./configure && make
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- name: Build surge
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working-directory: src
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run: |
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make surge \
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NAUTY=$(cygpath -u "$GITHUB_WORKSPACE")/nauty2_9_3 \
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NAUTYLIB=$(cygpath -u "$GITHUB_WORKSPACE")/nauty2_9_3 \
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CCOPT="-O3"
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- name: Test surge
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working-directory: src
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run: |
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./surge.exe -help 2>&1 | head -3
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./surge.exe -u C6H6
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./surge.exe -u C4H10
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- name: Upload Windows binary
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uses: actions/upload-artifact@v4
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with:
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name: surge-windows-x86_64
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path: src/surge.exe

‎.github/workflows/release.yml‎

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name: Release
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on:
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push:
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tags:
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- 'v*'
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jobs:
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build-release:
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strategy:
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matrix:
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include:
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- os: ubuntu-latest
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artifact: surge-linux-x86_64
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binary: surge
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- os: macos-14
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artifact: surge-macos-arm64
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binary: surge
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- os: windows-latest
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artifact: surge-windows-x86_64
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binary: surge.exe
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: ${{ matrix.os == 'windows-latest' && 'msys2 {0}' || 'bash' }}
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steps:
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- uses: actions/checkout@v4
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- name: Setup MSYS2 (Windows only)
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if: matrix.os == 'windows-latest'
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uses: msys2/setup-msys2@v2
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with:
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msystem: UCRT64
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install: >-
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mingw-w64-ucrt-x86_64-gcc
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make
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mingw-w64-ucrt-x86_64-zlib
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curl
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tar
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- name: Install dependencies (Linux)
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get update
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sudo apt-get install -y gcc make zlib1g-dev
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- name: Install nauty (macOS)
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if: startsWith(matrix.os, 'macos')
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run: |
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brew install nauty
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NAUTY_LIB=$(brew --prefix nauty)/lib
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ln -sf "$NAUTY_LIB/libnautyL1.a" "$NAUTY_LIB/nautyL1.a"
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- name: Build nauty from source (Linux/Windows)
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if: matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
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run: |
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curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
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tar xzf nauty2_9_3.tar.gz
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cd nauty2_9_3
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./configure && make
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- name: Build surge (Linux/Windows)
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if: matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
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working-directory: src
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run: |
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make surge \
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NAUTY=$(cygpath -u "$GITHUB_WORKSPACE" 2>/dev/null || echo "$GITHUB_WORKSPACE")/nauty2_9_3 \
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NAUTYLIB=$(cygpath -u "$GITHUB_WORKSPACE" 2>/dev/null || echo "$GITHUB_WORKSPACE")/nauty2_9_3 \
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CCOPT="-O3"
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- name: Build surge (macOS)
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if: startsWith(matrix.os, 'macos')
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working-directory: src
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run: |
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make surge \
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NAUTY=$(brew --prefix nauty)/include/nauty \
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NAUTYLIB=$(brew --prefix nauty)/lib \
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CCOPT="-O3"
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: ${{ matrix.artifact }}
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path: src/${{ matrix.binary }}
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create-release:
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needs: build-release
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Download all artifacts
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uses: actions/download-artifact@v4
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with:
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path: artifacts
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- name: Package binaries
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run: |
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cd artifacts
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for dir in */; do
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name="${dir%/}"
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cd "$name"
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chmod +x * 2>/dev/null || true
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tar czf "../${name}.tar.gz" *
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cd ..
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done
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- name: Create Release
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uses: softprops/action-gh-release@v2
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with:
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name: "Surge ${{ github.ref_name }}"
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draft: true
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generate_release_notes: false
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body: |
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## Surge 2.0
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A fast open-source chemical graph generator.
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### What's New in 2.0
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- **64-bit word size**: Supports larger molecular structures
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- **Aromaticity detection** (`-R`): Filter duplicate Kekule structures under carbon-ring aromaticity
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- **Hexagon restrictions** (`-h#`, `-h#:#`): Control 6-membered cycle counts
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- **Carbon 6-ring restrictions** (`-C#`, `-C#:#`): Limit carbon-only 6-membered rings
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- **Improved summary reporting**
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### Installation
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Download the binary for your platform below, or build from source (see README).
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### Binaries
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- `surge-linux-x86_64.tar.gz` - Linux (x86_64)
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- `surge-macos-arm64.tar.gz` - macOS (Apple Silicon)
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- `surge-windows-x86_64.tar.gz` - Windows (x86_64, built with MSYS2)
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files: |
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artifacts/*.tar.gz
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doc/surge2_0.pdf

‎.gitignore‎

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# Editor backup files
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*~
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# Surge binaries
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surge
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surge_[0-9]
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canonsdf

‎Dockerfile‎

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FROM ubuntu:21.04
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FROM alpine:3.21 AS builder
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RUN apt-get update && \
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apt-get -y install curl gcc make zlib1g-dev && \
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apt-get -y clean && \
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rm -rf \
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/var/lib/apt/lists/* \
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/usr/share/doc \
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/usr/share/doc-base \
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/usr/share/man \
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/usr/share/locale \
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/usr/share/zoneinfo
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WORKDIR /root
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RUN curl -o nauty27r3.tar.gz http://users.cecs.anu.edu.au/~bdm/nauty/nauty27r3.tar.gz \
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&& tar xzvf nauty27r3.tar.gz \
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&& cd nauty27r3 \
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&& ./configure && make
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ENV NAUTY_HOME=/root/nauty27r3
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COPY src/surge.c $NAUTY_HOME
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COPY src/Makefile /root
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WORKDIR $NAUTY_HOME
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RUN ln -s /root/nauty27r3 /root/nauty
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RUN make -f ../Makefile clean ; make -f ../Makefile surge
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RUN apk add --no-cache build-base curl zlib-dev
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FROM ubuntu:21.04
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WORKDIR /build
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RUN apt-get update && \
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apt-get -y install curl time gnupg zlib1g && \
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apt-get -y clean && \
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rm -rf \
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/var/lib/apt/lists/* \
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/usr/share/doc \
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/usr/share/doc-base \
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/usr/share/man \
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/usr/share/locale \
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/usr/share/zoneinfo
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RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && apt-get update -y && apt-get install google-cloud-sdk -y
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# Download and build nauty
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RUN curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz \
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&& tar xzf nauty2_9_3.tar.gz \
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&& cd nauty2_9_3 \
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&& ./configure && make -j4
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COPY --from=0 /root/nauty27r3/surge /usr/bin
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# Copy source and build surge (static linking for minimal runtime image)
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COPY src/ /build/src/
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WORKDIR /build/src
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RUN make surge \
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NAUTY=/build/nauty2_9_3 \
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NAUTYLIB=/build/nauty2_9_3 \
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CCOPT="-O3 -static"
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# Minimal runtime image (~9MB)
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FROM alpine:3.21
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COPY --from=builder /build/src/surge /usr/local/bin/surge
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ENTRYPOINT ["surge"]

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