From 32ca4ccbbfcdaaa3996ca30711e73ed76b8f1acd Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:30:04 -0700 Subject: [PATCH 1/8] .github/workflows/macos-builds.yml: updating to g++-14 and doing a build on both macos-13 (x86) and macos-15 (arm64) --- .github/workflows/macos-builds.yml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index eaac3e6..1055639 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -1,4 +1,4 @@ -name: Abismal builds on macOS (x86) +name: Abismal builds on macOS on: workflow_dispatch: @@ -9,7 +9,10 @@ on: jobs: build: - runs-on: macos-14 + strategy: + matrix: + os: [macos-13, macos-15] + runs-on: ${{ matrix.os }} steps: - uses: actions/checkout@v4 with: @@ -22,7 +25,7 @@ jobs: run: brew install htslib - name: Generate configure script run: ./autogen.sh - - name: configure with g++-13 - run: ./configure CXX="g++-13" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - - name: Build with g++ + - name: configure with g++-14 + run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" + - name: Build with g++-14 run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" From 8e614924555735034cbfa0f7f0f55232dcb06cbe Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:30:20 -0700 Subject: [PATCH 2/8] renaming --- .../{abismal_linux_release.yml => abismal_release_linux.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{abismal_linux_release.yml => abismal_release_linux.yml} (100%) diff --git a/.github/workflows/abismal_linux_release.yml b/.github/workflows/abismal_release_linux.yml similarity index 100% rename from .github/workflows/abismal_linux_release.yml rename to .github/workflows/abismal_release_linux.yml From 32f970b0a31c06b7089a6bc94ee24081ca95ccd1 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:37:47 -0700 Subject: [PATCH 3/8] .github/workflows/macos-builds.yml: updating the make command --- .github/workflows/macos-builds.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 1055639..86c0f02 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -28,4 +28,4 @@ jobs: - name: configure with g++-14 run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" - name: Build with g++-14 - run: make CXXFLAGS="-O3 -DNDEBUG -Wl,-ld_classic" + run: make -j4 From 11ac2ac2ea3725223d6db6646053e32c3d51e492 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:46:09 -0700 Subject: [PATCH 4/8] .github/workflows/ubuntu-distcheck.yml: removing redundancy --- .github/workflows/ubuntu-distcheck.yml | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ubuntu-distcheck.yml b/.github/workflows/ubuntu-distcheck.yml index 36b71b1..09dd53d 100644 --- a/.github/workflows/ubuntu-distcheck.yml +++ b/.github/workflows/ubuntu-distcheck.yml @@ -1,4 +1,4 @@ -name: Abismal distribution check on Ubuntu +name: Abismal 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 @@ -22,9 +20,5 @@ jobs: run: sudo apt-get install -y libhts-dev - name: Generate configure script run: ./autogen.sh - - name: configure - run: ./configure - - name: make check with two threads - run: make -j2 check - - name: make distcheck - run: make distcheck + - name: Distcheck + run: make -j4 distcheck From e8c2392144aea9ff0aa134f0e92d1feb02e20cfa Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:48:09 -0700 Subject: [PATCH 5/8] .github/workflows/ubuntu-distcheck.yml: bugfix --- .github/workflows/ubuntu-distcheck.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ubuntu-distcheck.yml b/.github/workflows/ubuntu-distcheck.yml index 09dd53d..8b93039 100644 --- a/.github/workflows/ubuntu-distcheck.yml +++ b/.github/workflows/ubuntu-distcheck.yml @@ -20,5 +20,7 @@ jobs: run: sudo apt-get install -y libhts-dev - name: Generate configure script run: ./autogen.sh + - name: Generate the Makefile + run: ./configure - name: Distcheck run: make -j4 distcheck From 2e86851b1e1b1e3c3cee517af72c8010ee8caac3 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 18:53:26 -0700 Subject: [PATCH 6/8] .github/workflows/ubuntu-builds.yml: separating gcc and clang builds into two jobs --- .github/workflows/ubuntu-builds.yml | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/.github/workflows/ubuntu-builds.yml b/.github/workflows/ubuntu-builds.yml index a993a91..9d1eacb 100644 --- a/.github/workflows/ubuntu-builds.yml +++ b/.github/workflows/ubuntu-builds.yml @@ -1,4 +1,4 @@ -name: Abismal builds on Ubuntu +name: Abismal build (Ubuntu) on: workflow_dispatch: @@ -8,10 +8,8 @@ on: branches: [ "master" ] jobs: - build: - + build-with-gcc: runs-on: ubuntu-latest - steps: - uses: actions/checkout@v4 with: @@ -25,14 +23,20 @@ jobs: - name: configure for GCC run: ./configure CXX="g++" - name: make with g++ - run: make - - name: cleanup after GCC - run: make distclean - - name: install Clang dependencies - run: sudo apt-get install -y libomp-dev + run: make -j4 + build-with-clang: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + submodules: recursive + - name: Update apt + run: sudo apt update + - name: Install dependencies + run: sudo apt-get install -y libhts-dev libomp-dev + - name: Generate configure script + run: ./autogen.sh - name: configure for Clang run: ./configure CXX="clang++" - name: make with clang++ - run: make - - name: cleanup after clang++ - run: make clean + run: make -j4 From b7d9b92f05a2ff1bd5b24cbfc67a8984b9548730 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 19:00:28 -0700 Subject: [PATCH 7/8] .github/workflows/macos-builds.yml: separating x86 and arm64 builds into two jobs --- .github/workflows/macos-builds.yml | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/macos-builds.yml index 86c0f02..358a4fc 100644 --- a/.github/workflows/macos-builds.yml +++ b/.github/workflows/macos-builds.yml @@ -1,4 +1,4 @@ -name: Abismal builds on macOS +name: Abismal build (macOS) on: workflow_dispatch: @@ -8,11 +8,26 @@ on: branches: [ "master" ] jobs: - build: - strategy: - matrix: - os: [macos-13, macos-15] - runs-on: ${{ matrix.os }} + build-on-x86: + runs-on: macos-13 + steps: + - uses: actions/checkout@v4 + with: + submodules: recursive + - name: Update Homebrew + run: brew update + - name: Install automake + run: brew install automake + - name: Install dependencies + run: brew install htslib + - name: Generate configure script + run: ./autogen.sh + - name: configure with g++-14 + run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" + - name: Build with g++-14 + run: make -j4 + build-on-arm64: + runs-on: macos-15 steps: - uses: actions/checkout@v4 with: From 929c65da3abc954ca659d6aa96214b5ca8bac6c9 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Thu, 12 Jun 2025 19:04:51 -0700 Subject: [PATCH 8/8] renaming workflow files --- .github/workflows/{macos-builds.yml => abismal_build_macos.yml} | 0 .github/workflows/{ubuntu-builds.yml => abismal_build_ubuntu.yml} | 0 .../{ubuntu-distcheck.yml => abismal_distcheck_ubuntu.yml} | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{macos-builds.yml => abismal_build_macos.yml} (100%) rename .github/workflows/{ubuntu-builds.yml => abismal_build_ubuntu.yml} (100%) rename .github/workflows/{ubuntu-distcheck.yml => abismal_distcheck_ubuntu.yml} (100%) diff --git a/.github/workflows/macos-builds.yml b/.github/workflows/abismal_build_macos.yml similarity index 100% rename from .github/workflows/macos-builds.yml rename to .github/workflows/abismal_build_macos.yml diff --git a/.github/workflows/ubuntu-builds.yml b/.github/workflows/abismal_build_ubuntu.yml similarity index 100% rename from .github/workflows/ubuntu-builds.yml rename to .github/workflows/abismal_build_ubuntu.yml diff --git a/.github/workflows/ubuntu-distcheck.yml b/.github/workflows/abismal_distcheck_ubuntu.yml similarity index 100% rename from .github/workflows/ubuntu-distcheck.yml rename to .github/workflows/abismal_distcheck_ubuntu.yml