[FIX] Missing SQ header in BAM output #280
Workflow file for this run
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name: Windows | |
on: | |
push: | |
branches: | |
- 'main' | |
pull_request: | |
workflow_dispatch: | |
concurrency: | |
group: windows-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: ${{ github.event_name != 'push' }} | |
env: | |
TZ: Europe/Berlin | |
jobs: | |
build: | |
name: ${{ matrix.name }} | |
runs-on: windows-2022 | |
timeout-minutes: 180 | |
if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' | |
strategy: | |
fail-fast: false | |
matrix: | |
include: | |
- name: "Visual Studio 17 2022" | |
vsversion : 2022 | |
build_type: Release | |
cxx_flags: "/std:c++latest" | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: Setup MSVC | |
uses: ilammy/msvc-dev-cmd@v1 | |
with: | |
vsversion: ${{ matrix.vsversion }} | |
- name: Setup Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: 3.x | |
- name: Install Python dependencies | |
run: | | |
pip install setuptools wheel | |
pip install -r manual/requirements.txt | |
- name: Setup conda | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
activate-environment: "" | |
auto-activate-base: true | |
auto-update-conda: false | |
- name: Install conda dependencies | |
run: | | |
conda install -c conda-forge boost-cpp bzip2 libxml2 zlib | |
$CONDA_BASE = conda info --base | |
"$CONDA_BASE\Library\include" | Out-File -FilePath $env:GITHUB_PATH -Append | |
"$CONDA_BASE\Library\lib" | Out-File -FilePath $env:GITHUB_PATH -Append | |
- name: Configure tests | |
run: | | |
New-Item -Name "build" -ItemType "directory" -Force | |
cd build | |
cmake .. -G "${{ matrix.name }}" ` | |
-DCMAKE_BUILD_TYPE=${{ matrix.build_type }} ` | |
-DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} /EHsc /W2 /wd4244 /wd4146" ` | |
-DSEQAN_DISABLE_VERSION_CHECK=ON ` | |
-DSEQAN_GH_ACTIONS_BUILD:BOOL=ON ` | |
-DPython3_ROOT_DIR=$env:pythonLocation ` | |
-DPython3_EXECUTABLE=$env:pythonLocation/bin/python3 | |
- name: Build tests | |
run: | | |
cd build | |
cmake --build . --config "${{ matrix.build_type }}" --parallel 2 -- /p:ContinueOnError=ErrorAndContinue | |
- name: Run tests | |
continue-on-error: true | |
id: test | |
run: | | |
cd build | |
ctest . -j2 -C "${{ matrix.build_type }}" --output-on-failure --timeout 240 -E "app_test_yara" | |
- name: Rerun failed tests | |
if: steps.test.outcome == 'failure' | |
run: | | |
cd build | |
ctest . -j2 -C "${{ matrix.build_type }}" --output-on-failure --timeout 240 --rerun-failed |