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azure-pipelines.yml
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# ntSynt CI
jobs:
- job:
displayName: ubuntu-latest
pool:
vmImage: 'ubuntu-latest'
steps:
- checkout: self
persistCredentials: true
submodules: true
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name ntsynt_ci
displayName: Create Anaconda environment
- script: |
source activate ntsynt_ci
conda install --yes -c bioconda -c conda-forge python=3.12 mamba
mamba install --yes -c bioconda -c conda-forge intervaltree pybedtools ncls python-igraph compilers btllib meson ninja snakemake samtools pytest seqtk pylint
displayName: Install dependencies
- script: |
source activate ntsynt_ci
meson setup build --prefix=$(pwd)/ntSynt_build
cd build
ninja install
displayName: Install ntSynt
- script: |
source activate ntsynt_ci
cd ntSynt_build/bin/
pylint --rcfile ../../bin/.pylintrc --extension-pkg-allow-list=btllib *py
displayName: Run pylint
- script: |
source activate ntsynt_ci
./ntSynt_build/bin/ntSynt --help
displayName: Print ntSynt help message
- script: |
source activate ntsynt_ci
export PATH=$(pwd)/ntSynt_build/bin:$PATH
cd tests
pytest -vs ntsynt_tests.py
displayName: Run pytests
- job:
displayName: macOS-latest
pool:
vmImage: 'macOS-latest'
steps:
- checkout: self
persistCredentials: true
submodules: true
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name ntsynt_ci
displayName: Create Anaconda environment
- script: |
source activate ntsynt_ci
mamba install --yes -c bioconda -c conda-forge intervaltree pybedtools ncls python-igraph compilers btllib meson ninja snakemake samtools pytest seqtk
displayName: Install dependencies
- script: |
source activate ntsynt_ci
meson setup build --prefix=$(pwd)/ntSynt_build
cd build
ninja install
displayName: Install ntSynt
- script: |
source activate ntsynt_ci
./ntSynt_build/bin/ntSynt --help
displayName: Print ntSynt help message
- script: |
source activate ntsynt_ci
export PATH=$(pwd)/ntSynt_build/bin:$PATH
cd tests
pytest -vs ntsynt_tests.py
displayName: Run pytests