Release Surge 2.0

.github/workflows/build.yml

@@ -0,0 +1,141 @@
+name: Build and Test
+
+on:
+  push:
+    branches: [ main, 'release/**' ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc make zlib1g-dev
+
+      - name: Build nauty
+        run: |
+          curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
+          tar xzf nauty2_9_3.tar.gz
+          cd nauty2_9_3
+          ./configure && make
+
+      - name: Build surge
+        working-directory: src
+        run: |
+          make surge \
+            NAUTY=${{ github.workspace }}/nauty2_9_3 \
+            NAUTYLIB=${{ github.workspace }}/nauty2_9_3 \
+            CCOPT="-O3"
+
+      - name: Test surge
+        working-directory: src
+        run: |
+          ./surge -help 2>&1 | head -3
+          ./surge -u C6H6
+          ./surge -u C4H10
+
+      - name: Build canonsdf
+        working-directory: src
+        run: |
+          make canonsdf \
+            NAUTY=${{ github.workspace }}/nauty2_9_3 \
+            NAUTYLIB=${{ github.workspace }}/nauty2_9_3 \
+            CCOPT="-O3"
+
+      - name: Upload Linux binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: surge-linux-x86_64
+          path: src/surge
+
+  build-macos:
+    strategy:
+      matrix:
+        include:
+          - os: macos-14
+            arch: arm64
+          - os: macos-15
+            arch: arm64-m15
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install nauty
+        run: brew install nauty
+
+      - name: Create nauty library symlink
+        run: |
+          NAUTY_LIB=$(brew --prefix nauty)/lib
+          ln -sf "$NAUTY_LIB/libnautyL1.a" "$NAUTY_LIB/nautyL1.a"
+
+      - name: Build surge
+        working-directory: src
+        run: |
+          make surge \
+            NAUTY=$(brew --prefix nauty)/include/nauty \
+            NAUTYLIB=$(brew --prefix nauty)/lib \
+            CCOPT="-O3"
+
+      - name: Test surge
+        working-directory: src
+        run: |
+          ./surge -help 2>&1 | head -3
+          ./surge -u C6H6
+          ./surge -u C4H10
+
+      - name: Upload macOS binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: surge-macos-${{ matrix.arch }}
+          path: src/surge
+
+  build-windows:
+    runs-on: windows-latest
+    defaults:
+      run:
+        shell: msys2 {0}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: msys2/setup-msys2@v2
+        with:
+          msystem: UCRT64
+          install: >-
+            mingw-w64-ucrt-x86_64-gcc
+            make
+            mingw-w64-ucrt-x86_64-zlib
+            curl
+            tar
+
+      - name: Build nauty
+        run: |
+          curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
+          tar xzf nauty2_9_3.tar.gz
+          cd nauty2_9_3
+          ./configure && make
+
+      - name: Build surge
+        working-directory: src
+        run: |
+          make surge \
+            NAUTY=$(cygpath -u "$GITHUB_WORKSPACE")/nauty2_9_3 \
+            NAUTYLIB=$(cygpath -u "$GITHUB_WORKSPACE")/nauty2_9_3 \
+            CCOPT="-O3"
+
+      - name: Test surge
+        working-directory: src
+        run: |
+          ./surge.exe -help 2>&1 | head -3
+          ./surge.exe -u C6H6
+          ./surge.exe -u C4H10
+
+      - name: Upload Windows binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: surge-windows-x86_64
+          path: src/surge.exe

.github/workflows/release.yml

@@ -0,0 +1,137 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build-release:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            artifact: surge-linux-x86_64
+            binary: surge
+          - os: macos-14
+            artifact: surge-macos-arm64
+            binary: surge
+          - os: windows-latest
+            artifact: surge-windows-x86_64
+            binary: surge.exe
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: ${{ matrix.os == 'windows-latest' && 'msys2 {0}' || 'bash' }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup MSYS2 (Windows only)
+        if: matrix.os == 'windows-latest'
+        uses: msys2/setup-msys2@v2
+        with:
+          msystem: UCRT64
+          install: >-
+            mingw-w64-ucrt-x86_64-gcc
+            make
+            mingw-w64-ucrt-x86_64-zlib
+            curl
+            tar
+
+      - name: Install dependencies (Linux)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y gcc make zlib1g-dev
+
+      - name: Install nauty (macOS)
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          brew install nauty
+          NAUTY_LIB=$(brew --prefix nauty)/lib
+          ln -sf "$NAUTY_LIB/libnautyL1.a" "$NAUTY_LIB/nautyL1.a"
+
+      - name: Build nauty from source (Linux/Windows)
+        if: matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
+        run: |
+          curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz
+          tar xzf nauty2_9_3.tar.gz
+          cd nauty2_9_3
+          ./configure && make
+
+      - name: Build surge (Linux/Windows)
+        if: matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
+        working-directory: src
+        run: |
+          make surge \
+            NAUTY=$(cygpath -u "$GITHUB_WORKSPACE" 2>/dev/null || echo "$GITHUB_WORKSPACE")/nauty2_9_3 \
+            NAUTYLIB=$(cygpath -u "$GITHUB_WORKSPACE" 2>/dev/null || echo "$GITHUB_WORKSPACE")/nauty2_9_3 \
+            CCOPT="-O3"
+
+      - name: Build surge (macOS)
+        if: startsWith(matrix.os, 'macos')
+        working-directory: src
+        run: |
+          make surge \
+            NAUTY=$(brew --prefix nauty)/include/nauty \
+            NAUTYLIB=$(brew --prefix nauty)/lib \
+            CCOPT="-O3"
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.artifact }}
+          path: src/${{ matrix.binary }}
+
+  create-release:
+    needs: build-release
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+
+      - name: Package binaries
+        run: |
+          cd artifacts
+          for dir in */; do
+            name="${dir%/}"
+            cd "$name"
+            chmod +x * 2>/dev/null || true
+            tar czf "../${name}.tar.gz" *
+            cd ..
+          done
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: "Surge ${{ github.ref_name }}"
+          draft: true
+          generate_release_notes: false
+          body: |
+            ## Surge 2.0
+
+            A fast open-source chemical graph generator.
+
+            ### What's New in 2.0
+            - **64-bit word size**: Supports larger molecular structures
+            - **Aromaticity detection** (`-R`): Filter duplicate Kekule structures under carbon-ring aromaticity
+            - **Hexagon restrictions** (`-h#`, `-h#:#`): Control 6-membered cycle counts
+            - **Carbon 6-ring restrictions** (`-C#`, `-C#:#`): Limit carbon-only 6-membered rings
+            - **Improved summary reporting**
+
+            ### Installation
+            Download the binary for your platform below, or build from source (see README).
+
+            ### Binaries
+            - `surge-linux-x86_64.tar.gz` - Linux (x86_64)
+            - `surge-macos-arm64.tar.gz` - macOS (Apple Silicon)
+            - `surge-windows-x86_64.tar.gz` - Windows (x86_64, built with MSYS2)
+          files: |
+            artifacts/*.tar.gz
+            doc/surge2_0.pdf

.gitignore

@@ -53,3 +53,8 @@ dkms.conf
 
 # Editor backup files
 *~
+
+# Surge binaries
+surge
+surge_[0-9]
+canonsdf

Dockerfile

@@ -1,39 +1,26 @@
-FROM ubuntu:21.04
+FROM alpine:3.21 AS builder
 
-RUN apt-get update && \
-    apt-get -y install curl gcc make zlib1g-dev && \
-    apt-get -y clean && \
-    rm -rf \
-      /var/lib/apt/lists/* \
-      /usr/share/doc \
-      /usr/share/doc-base \
-      /usr/share/man \
-      /usr/share/locale \
-      /usr/share/zoneinfo
-WORKDIR /root
-RUN curl -o nauty27r3.tar.gz http://users.cecs.anu.edu.au/~bdm/nauty/nauty27r3.tar.gz \
-  && tar xzvf nauty27r3.tar.gz \
-  && cd nauty27r3 \
-  && ./configure && make
-ENV NAUTY_HOME=/root/nauty27r3
-COPY src/surge.c $NAUTY_HOME
-COPY src/Makefile /root
-WORKDIR $NAUTY_HOME
-RUN ln -s /root/nauty27r3 /root/nauty
-RUN make -f ../Makefile clean ; make -f ../Makefile surge
+RUN apk add --no-cache build-base curl zlib-dev
 
-FROM ubuntu:21.04
+WORKDIR /build
 
-RUN apt-get update && \
-    apt-get -y install  curl time gnupg zlib1g && \
-    apt-get -y clean && \
-    rm -rf \
-      /var/lib/apt/lists/* \
-      /usr/share/doc \
-      /usr/share/doc-base \
-      /usr/share/man \
-      /usr/share/locale \
-      /usr/share/zoneinfo
-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
+# Download and build nauty
+RUN curl -L -o nauty2_9_3.tar.gz https://users.cecs.anu.edu.au/~bdm/nauty/nauty2_9_3.tar.gz \
+    && tar xzf nauty2_9_3.tar.gz \
+    && cd nauty2_9_3 \
+    && ./configure && make -j4
 
-COPY --from=0 /root/nauty27r3/surge /usr/bin
+# Copy source and build surge (static linking for minimal runtime image)
+COPY src/ /build/src/
+WORKDIR /build/src
+RUN make surge \
+    NAUTY=/build/nauty2_9_3 \
+    NAUTYLIB=/build/nauty2_9_3 \
+    CCOPT="-O3 -static"
+
+# Minimal runtime image (~9MB)
+FROM alpine:3.21
+
+COPY --from=builder /build/src/surge /usr/local/bin/surge
+
+ENTRYPOINT ["surge"]