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Remove duplicate alphabets and replace seqan2::String #632

Remove duplicate alphabets and replace seqan2::String

Remove duplicate alphabets and replace seqan2::String #632

Workflow file for this run

name: CI misc
on:
push:
branches:
# Push events to branches matching refs/heads/main
- 'main'
pull_request:
workflow_dispatch:
concurrency:
group: misc-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
env:
CMAKE_VERSION: 3.16.9
SEQAN3_NO_VERSION_CHECK: 1
TZ: Europe/Berlin
defaults:
run:
shell: bash -ex {0}
jobs:
build:
name: ${{ matrix.name }}
runs-on: ubuntu-22.04
timeout-minutes: 120
strategy:
fail-fast: false
matrix:
include:
- name: "Documentation"
build: documentation
build_threads: 2
test_threads: 2
cmake: 3.16.9
doxygen: 1.9.4
requires_toolchain: false
requires_ccache: false
skip_build_tests: true
skip_run_tests: false
- name: "Header gcc12"
cxx: "g++-12"
cc: "gcc-12"
build_type: Release
build: header
build_threads: 2
test_threads: 2
cmake: 3.16.9
requires_toolchain: true
requires_ccache: true
skip_build_tests: false
skip_run_tests: true
- name: "Header gcc10"
cxx: "g++-10"
cc: "gcc-10"
build_type: Release
build: header
build_threads: 2
test_threads: 2
cmake: 3.16.9
requires_toolchain: true
requires_ccache: true
skip_build_tests: false
skip_run_tests: true
steps:
- name: Set repository name
run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
- name: Checkout
uses: actions/checkout@v3
with:
path: ${{ env.REPOSITORY_NAME }}
fetch-depth: 2
submodules: recursive
- name: Add package source
run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/configure_apt.sh
- name: Install CMake
env:
BUILD: ${{ matrix.build }}
CMAKE_VERSION: ${{ matrix.cmake }}
run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_cmake.sh
- name: Install Doxygen
if: matrix.build == 'documentation'
env:
DOXYGEN_VERSION: ${{ matrix.doxygen }}
run: bash ./${{ env.REPOSITORY_NAME }}/lib/seqan3/.github/workflows/scripts/install_doxygen.sh
- name: Install ccache
if: matrix.requires_ccache
run: |
conda install --yes --override-channels --channel conda-forge ccache
sudo ln -s $CONDA/bin/ccache /usr/bin/ccache
- name: Install compiler ${{ matrix.cxx }}
if: matrix.requires_toolchain
run: sudo apt-get install --yes ${{ matrix.cxx }}
- name: Load ccache
if: matrix.requires_ccache
uses: actions/cache@v3
with:
path: .ccache
key: ${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }}
# Restoring: From current branch, otherwise from base branch, otherwise from any branch.
restore-keys: |
${{ matrix.name }}-ccache-${{ github.ref }}
${{ matrix.name }}-ccache-${{ github.base_ref }}
${{ matrix.name }}-ccache-
- name: Tool versions
run: |
env cmake --version
env doxygen --version || true
env ${{ matrix.cxx }} --version || true
- name: Configure tests
env:
CXX: ${{ matrix.cxx }}
CC: ${{ matrix.cc }}
run: |
mkdir build
cd build
header_test_flag=$(echo "${{ env.REPOSITORY_NAME }}_HEADER_TEST_ONLY" | tr '[:lower:]' '[:upper:]')
cmake ../${{ env.REPOSITORY_NAME }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" \
-D${header_test_flag}=${{ matrix.build == 'header' && 'ON' || 'OFF'}}
if [[ "${{ matrix.build }}" =~ ^(header)$ ]]; then
make -j${{ matrix.build_threads }} gtest_build
fi
- name: Build tests
if: ${{!matrix.skip_build_tests}}
env:
CCACHE_BASEDIR: ${{ github.workspace }}
CCACHE_DIR: ${{ github.workspace }}/.ccache
CCACHE_COMPRESS: true
CCACHE_COMPRESSLEVEL: 12
CCACHE_MAXSIZE: 75M
CMAKE_BUILD_PARALLEL_LEVEL: ${{ matrix.build_threads }}
run: |
ccache -p || true
cd build
make -k test
ccache -s || true
- name: Run tests
if: ${{!matrix.skip_run_tests}}
run: |
cd build
if [[ "${{ matrix.build }}" =~ ^(documentation)$ ]]; then
make -k -j${{ matrix.test_threads }} doc 2>doxygen_warnings.txt
cat doxygen_warnings.txt
# test ! -s doxygen_warnings.txt
else
ctest . -j${{ matrix.test_threads }} --output-on-failure
fi
- name: Package documentation
if: matrix.build == 'documentation'
continue-on-error: true
run: tar -zcf documentation.tar.gz build
- name: Upload documentation
if: matrix.build == 'documentation'
continue-on-error: true
uses: actions/upload-artifact@v3
with:
name: documentation
path: documentation.tar.gz