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Use matrix in GitHub actions #61

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merged 6 commits into from
Dec 12, 2023
Merged

Use matrix in GitHub actions #61

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matrix
milkschen Dec 12, 2023
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setup-node
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runs-on
milkschen Dec 12, 2023
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fix
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uses htslib=1.18
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233 changes: 29 additions & 204 deletions .github/workflows/cmake_htslib.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name: CMake-htslib
name: Build and ctest

on:
push:
Expand Down Expand Up @@ -26,212 +26,37 @@ env:
BUILD_TYPE: Release

jobs:
htslib_1_11:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3
htslib_matrix:
strategy:
matrix:
version: [1.11, 1.12, 1.13, 1.14, 1.15, 1.16, 1.17, 1.18]
os: [ubuntu-22.04, ubuntu-20.04, ubuntu-latest]

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 && tar -vxjf htslib-1.11.tar.bz2 && cd htslib-1.11 && ./configure && make && sudo make install && cd ../ && rm htslib-1.11.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_12:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest
runs-on: ${{ matrix.os }}

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 && tar -vxjf htslib-1.12.tar.bz2 && cd htslib-1.12 && ./configure && make && sudo make install && cd ../ && rm htslib-1.12.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_13:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2 && tar -vxjf htslib-1.13.tar.bz2 && cd htslib-1.13 && ./configure && make && sudo make install && cd ../ && rm htslib-1.13.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_14:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.14/htslib-1.14.tar.bz2 && tar -vxjf htslib-1.14.tar.bz2 && cd htslib-1.14 && ./configure && make && sudo make install && cd ../ && rm htslib-1.14.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_15:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.15/htslib-1.15.tar.bz2 && tar -vxjf htslib-1.15.tar.bz2 && cd htslib-1.15 && ./configure && make && sudo make install && cd ../ && rm htslib-1.15.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_16:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && tar -vxjf htslib-1.16.tar.bz2 && cd htslib-1.16 && ./configure && make && sudo make install && cd ../ && rm htslib-1.16.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}

htslib_1_17:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ubuntu-latest

steps:
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2 && tar -vxjf htslib-1.17.tar.bz2 && cd htslib-1.17 && ./configure && make && sudo make install && cd ../ && rm htslib-1.17.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}
- uses: actions/checkout@v3

- name: Set up SDSL
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/${{ matrix.version }}/htslib-${{ matrix.version }}.tar.bz2 && tar -vxjf htslib-${{ matrix.version }}.tar.bz2 && cd htslib-${{ matrix.version }} && ./configure && make && sudo make install && cd ../ && rm htslib-${{ matrix.version }}.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
# See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}

- name: Build
# Build your program with the given configuration
run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

- name: Test
working-directory: ${{github.workspace}}/build
# Execute tests defined by the CMake configuration.
# See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
run: ctest -C ${{env.BUILD_TYPE}}
2 changes: 1 addition & 1 deletion .github/workflows/integration-test.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ jobs:
run: sudo apt-get -y install libsdsl-dev

- name: Set up htslib
run: wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 && tar -vxjf htslib-1.16.tar.bz2 && cd htslib-1.16 && ./configure && make && sudo make install && cd ../ && rm htslib-1.16.tar.bz2
run: wget https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2 && tar -vxjf htslib-1.18.tar.bz2 && cd htslib-1.18 && ./configure && make && sudo make install && cd ../ && rm htslib-1.18.tar.bz2

- name: Configure CMake
# Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
Expand Down