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change the ex-zd to encode using value 2 in slow5 header #605

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change the ex-zd to encode using value 2 in slow5 header

change the ex-zd to encode using value 2 in slow5 header #605

Workflow file for this run

.github/workflows/c-cpp.yml at b8f282d
name: CI
on:
push:
branches: [ '*' ]
pull_request:
branches: [ master, dev ]
env:
ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
jobs:
ubuntu_14:
name: ubuntu_14
runs-on: ubuntu-20.04
container: ubuntu:14.04
steps:
- name: install git
run: sudo apt-get install -y software-properties-common && sudo add-apt-repository ppa:git-core/ppa && sudo apt-get update -y && sudo apt-get install git -y
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make
- name: env
run: lsb_release -a && ldd --version && gcc --version && g++ --version
- name: build
run: autoreconf && ./configure && make -j8
- name: test
run: make test
ubuntu_16:
name: Ubuntu 16
runs-on: ubuntu-20.04
container: ubuntu:16.04
steps:
- name: install git
run: apt-get update && apt-get install -y software-properties-common && add-apt-repository ppa:git-core/ppa && apt-get update -y && apt-get install git -y
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: apt-get update && apt-get install -y zlib1g-dev libhdf5-dev libzstd1-dev gcc g++ autoconf automake make
- name: build
run: autoreconf && ./configure && make -j8
- name: test
run: make test
- name: build zstd
run: make clean && make -j8 zstd=1
- name: test zstd
run: export zstd=1 && make test
ubuntu_18:
name: Ubuntu 18 hdf5 install script
runs-on: ubuntu-20.04
container: ubuntu:18.04
steps:
- name: install git
run: apt-get update && apt-get install -y software-properties-common && add-apt-repository ppa:git-core/ppa && apt-get update -y && apt-get install git -y
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: apt-get update && apt-get install -y zlib1g-dev valgrind libzstd-dev gcc g++ autoconf automake make wget
- name: build
run: autoreconf && ./scripts/install-hdf5.sh && ./configure --enable-localhdf5 && make -j8
- name: test
run: make test
- name: test valgrind
run: ./test/test.sh mem
- name: build zstd
run: make clean && make -j8 zstd=1
- name: test zstd
run: export zstd=1 && make test
- name: test valgrind zstd
run: export zstd=1 && ./test/test.sh mem
ubuntu_20:
name: Ubuntu 20
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev libzstd-dev
- name: build-gcc
run: autoreconf && ./configure && make -j8
- name: test-gcc
run: make test
- name: build-clang zstd
run: make clean && make CC=clang CXX=clang++ -j8 zstd=1
- name: test-clang zstd
run: export zstd=1 && make test
ubuntu_22:
name: Ubuntu 22
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
- name: build
run: make -j8 disable_hdf5=1
ubuntu_24:
name: Ubuntu 24
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
- name: build
run: make -j8 disable_hdf5=1
ubuntu_20_icc:
name: Ubuntu 20 icc
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: Intel Apt repository
timeout-minutes: 1
run: |
wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
- name: install packages
run: sudo apt-get install -y zlib1g-dev libhdf5-dev libzstd-dev intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
- name: Setup Intel oneAPI environment
run: |
source /opt/intel/oneapi/setvars.sh
printenv >> $GITHUB_ENV
- name: build
run: autoreconf && ./configure && make CC=icc CXX=icpc -j8
- name: test
run: make test
- name: build zstd
run: make clean && make CC=icc CXX=icpc -j8 zstd=1
- name: test zstd
run: export zstd=1 && make test
# os_x_11:
# name: OSX 11
# runs-on: macos-11
# steps:
# - uses: actions/checkout@v2
# with:
# submodules: recursive
# - name: install packages
# run: brew install hdf5 autoconf automake
# - name: build
# run: autoreconf --install && ./configure && make -j8
# - name: test
# run: make test
os_x_12:
name: OSX 12
runs-on: macos-12
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./configure && make -j8
- name: test
run: make test
os_x_12_zstd:
name: OSX 12 zstd
runs-on: macos-12
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: brew install hdf5 autoconf automake zstd
- name: build
run: autoreconf --install && ./configure && make -j8 zstd=1
- name: test
run: export zstd=1 && make test
os_x_13:
name: OSX 13
runs-on: macos-13
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./configure && make -j8
- name: test
run: make test
os_x_14:
name: OSX 14
runs-on: macos-14
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./configure LDFLAGS=-L/opt/homebrew/lib/ CPPFLAGS=-I/opt/homebrew/include/ && make -j8
- name: test
run: make test
# arm64:
# name: ubuntu arm
# runs-on: ubuntu-latest
# steps:
# - run: docker run --rm --privileged multiarch/qemu-user-static:register --reset
# - uses: docker://multiarch/ubuntu-core:arm64-bionic
# with:
# args: 'uname -a'
# - uses: actions/checkout@v2
# with:
# submodules: recursive
# - uses: docker://multiarch/ubuntu-core:arm64-bionic
# with:
# args: >
# bash -c "apt-get update &&
# apt-get install -y zlib1g-dev gcc make zlib1g-dev libhdf5-dev g++ autoconf automake &&
# ldd --version && gcc --version &&
# autoreconf && ./configure && make && make test
# os_x2:
# name: OSX hdf5 hdf5 install script
# runs-on: macos-10.15
# steps:
# - uses: actions/checkout@v2
# with:
# submodules: recursive
# ssh-key: ${{ secrets.SUBMODULE_CONTENT_PULL_KEY }}
# - name: install packages
# run: brew install gcc autoconf automake
# - name: build
# run: autoreconf --install && CC=gcc CXX=g++ CFLAGS="-Wno-implicit-function-declaration" ./scripts/install-hdf5.sh && ./configure --enable-localhdf5 && make -j8
# - name: test
# run: make test