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 ntlink_CI
    displayName: Create Anaconda environment
  - script: |
      source activate ntlink_CI
      conda install --yes --quiet --name ntlink_CI -c conda-forge -c bioconda python=3.9 mamba
      mamba install --yes --quiet -c conda-forge -c bioconda pylint pytest pandas abyss
      mamba install --yes --quiet -c conda-forge -c bioconda --file requirements.txt
    displayName: Install Anaconda packages
  - script: |
      source activate ntlink_CI
      cd bin
      pylint ntlink_pair.py ntlink_utils.py ntlink_stitch_paths.py ntlink_overlap_sequences.py ntlink_filter_sequences.py
      cd ..
    displayName: Run pylint
  - script: |
      source activate ntlink_CI
      cd tests
      pytest -vs ntlink_pytest.py
    displayName: Run pytests

- 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 ntlink_CI
    displayName: Create Anaconda environment
  - script: |
      source activate ntlink_CI
      mamba install --yes --quiet -c conda-forge -c bioconda pylint pytest pandas abyss python=3.12
      mamba install --yes --quiet -c conda-forge -c bioconda --file requirements.txt
    displayName: Install Anaconda packages
  - script: |
      source activate ntlink_CI
      cd tests
      pytest -vs ntlink_pytest.py
    displayName: Run pytests