Adding workflows to make binaries for releases

.github/workflows/dnmtools_release_linux.yml

@@ -0,0 +1,58 @@
+name: dnmtools Release (Linux)
+
+on:
+  workflow_dispatch:
+
+env:
+  CONTAINER: andrewdavidsmith/transferase-build
+
+jobs:
+  linux-releases:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Start docker container
+        # Pull the container, run it in detached mode, mount the workspace
+        run: |
+          docker pull $CONTAINER
+          docker run --name build-container \
+          -d -v ${{ github.workspace }}:/workspace $CONTAINER tail -f /dev/null
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Configure and build
+        env:
+          SCRIPT: |
+            export DEBIAN_FRONTEND=noninteractive && \
+            apt-get update && apt-get install --no-install-recommends -y automake && \
+            find /usr -name libz.so -exec rm {} \; && \
+            git clone --recursive https://github.com/samtools/htslib.git && \
+            cd htslib && \
+            autoreconf -i && \
+            mkdir build && cd build && \
+            ../configure \
+                --disable-bz2 \
+                --disable-libcurl \
+                --disable-lzma \
+                --disable-ref-cache \
+                LDADD="-L/usr/local/lib" && \
+            make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \
+            cp libhts.a /usr/local/lib/ && \
+            cp -r ../htslib /usr/local/include/ && \
+            cd /workspace && \
+            autoreconf -i && \
+            mkdir build && cd build && \
+            ../configure && \
+            make -j4 LDFLAGS="-static-libgcc -static-libstdc++ -s"
+        run: |
+          docker exec build-container bash -c "$SCRIPT"
+      - name: Get version number
+        id: get-vn
+        run: |
+          awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed -e "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
+        env:
+          GH_TOKEN: ${{ github.token }}
+      - name: Upload the binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: dnmtools-${{ steps.get-vn.outputs.vn }}-Linux
+          path: build/dnmtools

.github/workflows/dnmtools_release_macos.yml

@@ -0,0 +1,89 @@
+name: dnmtools Release (macOS)
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-macos-binaries:
+    strategy:
+      matrix:
+        os: [macos-13, macos-14]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Make dnmtools dependency directories
+        run: sudo mkdir -p /opt/dnmtools/lib /opt/dnmtools/include
+      - name: Install dependency headers and static libs
+        run: |
+          brew install zlib gsl automake
+          sudo cp $(brew --prefix zlib)/lib/*.a /opt/dnmtools/lib
+          sudo cp $(brew --prefix gsl)/lib/*.a /opt/dnmtools/lib
+          sudo cp -r $(brew --prefix zlib)/include/* /opt/dnmtools/include
+          sudo cp -r $(brew --prefix gsl)/include/* /opt/dnmtools/include
+      - name: Build and install HTSlib
+        run: |
+          git clone --recursive https://github.com/samtools/htslib.git
+          cd htslib
+          sudo cp -r htslib /opt/dnmtools/include
+          autoreconf -i
+          mkdir build && cd build
+          ../configure \
+            --disable-bz2 \
+            --disable-libcurl \
+            --disable-lzma \
+            --disable-ref-cache \
+            --without-libdeflate \
+            LDADD="-L/usr/local/lib"
+          make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a
+          sudo cp libhts.a /opt/dnmtools/lib
+      - name: Build dnmtools
+        run: |
+          ./autogen.sh
+          mkdir build && cd build
+          ../configure CXX=g++-14 LDFLAGS="-L/opt/dnmtools/lib -static-libgcc -static-libstdc++ -Wl,-dead_strip" CPPFLAGS="-I/opt/dnmtools/include"
+          make -j4
+      - name: Rename the binary
+        run: mv build/dnmtools dnmtools_$(uname -m)
+      - name: Get version number
+        id: vars
+        run: |
+          awk '/AC_INIT/ {print "vn="$2}' configure.ac | \
+            sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
+          uname -m | awk '{print "arch="$0}' >> "$GITHUB_OUTPUT"
+        env:
+          GH_TOKEN: ${{ github.token }}
+      - name: Upload the binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: dnmtools-${{ steps.vars.outputs.arch }}
+          path: |
+            dnmtools_${{ steps.vars.outputs.arch }}
+  make-lipo:
+    needs: build-macos-binaries
+    runs-on: macos-15
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: binaries
+          pattern: dnmtools-*
+          merge-multiple: false
+      - name: Create universal binary
+        run: |
+          lipo -create \
+          binaries/dnmtools-*/dnmtools_* \
+          -output dnmtools
+          chmod +x dnmtools
+      - name: Get version number
+        id: vn
+        run: awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT"
+        env:
+          GH_TOKEN: ${{ github.token }}
+      - name: Upload the lipo binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: dnmtools-${{ steps.vn.outputs.vn }}-macOS
+          path: dnmtools

.github/workflows/macos-builds.yml

@@ -1,26 +1,46 @@
-name: DNMTools builds on macOS
+name: DNMTools build (macOS)
 
 on:
   workflow_dispatch:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
 
 jobs:
-  build:
-
+  build-on-x86:
     runs-on: macos-13
-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Update Homebrew
+      run: brew update
+    - name: Install autotools
+      run: brew install automake
+    - name: Install dependencies
+      run: brew install htslib gsl
+    - name: Generate configure script
+      run: ./autogen.sh
+    - name: configure with g++-14
+      run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
+    - name: make
+      run: make -j4
+  build-on-arm64:
+    runs-on: macos-15
+    steps:
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Update Homebrew
       run: brew update
     - name: Install autotools
-      run: brew install autoconf automake libtool
+      run: brew install automake
     - name: Install dependencies
       run: brew install htslib gsl
     - name: Generate configure script
       run: ./autogen.sh
-    - name: configure with g++-12
-      run: ./configure CXX="g++-12" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
+    - name: configure with g++-14
+      run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
     - name: make
-      run: make
+      run: make -j4

.github/workflows/ubuntu-builds.yml

@@ -1,10 +1,14 @@
-name: DNMTools builds on Ubuntu
+name: DNMTools build (Ubuntu)
 
 on:
   workflow_dispatch:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
 
 jobs:
-  build:
+  build-with-gcc:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -14,21 +18,25 @@ jobs:
       run: sudo apt-get install -y libhts-dev libgsl-dev
     - name: Generate configure script
       run: ./autogen.sh
-    - name: Configure for g++
+    - name: Configure for GCC
       run: ./configure CXX="g++"
     - name: Build with g++
-      run: make
+      run: make -j4
     - name: Test the g++ build
-      run: make check-TESTS
-    - name: Cleanup after the g++ build
-      run: make distclean
-    - name: Install Clang/LLVM dependencies
-      run: sudo apt-get install -y libomp-dev
-    - name: Configure for clang++
+      run: make -j4 check-TESTS
+  build-with-clang:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: Install dependencies
+      run: sudo apt-get install -y libhts-dev libgsl-dev
+    - name: Generate configure script
+      run: ./autogen.sh
+    - name: Configure for Clang
       run: ./configure CXX="clang++"
     - name: Build with clang++
-      run: make
+      run: make -j4
     - name: Test the clang++ build
-      run: make
-    - name: Cleanup after the clang++ build
-      run: make distclean
+      run: make -j4 check-TESTS

.github/workflows/ubuntu-distcheck.yml

@@ -1,4 +1,4 @@
-name: DNMTools distribution check on Ubuntu
+name: DNMTools distcheck (Ubuntu)
 
 on:
   workflow_dispatch:
@@ -9,11 +9,9 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Update packages
@@ -25,4 +23,4 @@ jobs:
     - name: configure
       run: ./configure
     - name: make distcheck
-      run: make distcheck
+      run: make -j4 distcheck