azure-pipelines.yml

# 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 tigmint_CI
    displayName: Create Anaconda environment
  - script: |
      source activate tigmint_CI
      conda install --yes --quiet --name tigmint_CI -c conda-forge -c bioconda mamba python=3.8
      mamba install --yes --quiet -c conda-forge -c bioconda pytest bedtools bwa samtools=1.9 minimap2 pylint btllib compilers ntlink
      mamba install --yes --quiet -c conda-forge -c bioconda --file requirements.txt
    displayName: Install Anaconda packages
  - script: |
      source activate tigmint_CI
      make -C src all
    displayName: Compile C++ executables
  - script: |
      source activate tigmint_CI
      mamba install --yes -c bioconda -c conda-forge clang clang-tools
      make -C src lint
    displayName: Run clang-format and clang-tidy
  - script: |
      source activate tigmint_CI
      cd bin
      pylint tigmint-cut tigmint_molecule.py tigmint_molecule_paf.py tigmint_estimate_dist.py tigmint-ntlink-map tigmint-filter-paf
      cd ../
    displayName: Run pylint
  - script: |
      source activate tigmint_CI
      export PATH=$(pwd)/bin:$PATH
      cd tests
      pytest -vs tigmint_test.py
    displayName: Run pytests