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azure-pipelines.yml
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azure-pipelines.yml
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# See https://docs.microsoft.com/azure/devops/pipelines/languages/python
jobs:
- job:
displayName: ubuntu-latest
pool:
vmImage: 'ubuntu-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name ntjoin_CI
displayName: Create Anaconda environment
- script: |
curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-11 main"
sudo apt-get update
sudo apt-get install -y --no-install-recommends clang-format clang-tidy
displayName: Install clang-format and clang-tidy
- script: |
source activate ntjoin_CI
conda install --yes --quiet --name ntjoin_CI -c conda-forge -c bioconda python=3.9 mamba
mamba install --yes --quiet -c conda-forge -c bioconda pylint samtools
mamba install --yes --quiet -c conda-forge -c bioconda --file requirements.txt
displayName: Install Anaconda packages
- script: |
source activate ntjoin_CI
cd bin
pylint ntjoin_assemble.py read_fasta.py ntjoin_utils.py
cd ..
displayName: Run pylint
- script: |
source activate ntjoin_CI
mamba install --yes --quiet -c conda-forge -c bioconda pytest
cd tests
pytest -vs ntjoin_test.py
displayName: Run pytests
- script: |
source activate ntjoin_CI
python3 -c 'import pybedtools; print(pybedtools.__version__)'
mamba install --yes --quiet -c conda-forge -c bioconda pybedtools=0.9.0
python3 -c 'import pybedtools; print(pybedtools.__version__)'
cd tests
pytest -vs ntjoin_test.py
displayName: Run pytests with lower pybedtools version
- job: macOS_default_clang
pool:
vmImage: macOS-latest
steps:
- script: |
mkdir -p ~/miniforge3
curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o ~/miniforge3/miniforge.sh
bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
rm -rf ~/miniforge3/miniforge.sh
~/miniforge3/bin/conda init bash
~/miniforge3/bin/conda init zsh
export CONDA=$(realpath ~/miniforge3/bin)
echo "##vso[task.prependpath]$CONDA"
displayName: Install conda
- script: conda create --yes --quiet --name ntjoin_CI
displayName: Create Anaconda environment
- script: |
source activate ntjoin_CI
mamba install --yes --quiet -c conda-forge -c bioconda pylint samtools python-igraph pybedtools pymannkendall btllib
displayName: Install Anaconda packages
- script: |
source activate ntjoin_CI
mamba install --yes --quiet -c conda-forge -c bioconda pytest
cd tests
pytest -vs ntjoin_test.py
displayName: Run pytests