azure-pipelines.yml

# 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_viz_ci
    displayName: Create Anaconda environment

  - script: |
      source activate ntsynt_viz_ci
      conda install --yes -c bioconda -c conda-forge python=3.12 mamba
      mamba install --yes -c conda-forge -c bioconda quicktree r-base bioconductor-treeio r-ggpubr bioconductor-ggtree r-phytools r-dplyr r-argparse r-scales r-stringr pylint intervaltree snakemake
      # NOTE: Once treeio is updated in bioconda, you may be able to use r-gggenomes instead. I am getting conflicting package errors currently
      R -e 'install.packages(c("gggenomes"), repos = "https://cran.r-project.org")'
    displayName: Install dependencies

  - script: |
      source activate ntsynt_viz_ci
      cd bin
      pylint *py
    displayName: Run pylint

  - script: |
      source activate ntsynt_viz_ci
      ./bin/ntsynt_viz.py --help
    displayName: Print ntSynt-viz help message

  - script: |
      source activate ntsynt_viz_ci
      export PATH=$(pwd)/bin:$PATH
      cd tests
      ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv --tree great-apes.mt-tree.nwk --name_conversion great-apes.name-conversions.tsv --normalize --prefix great-apes_ribbon-plots --ribbon_adjust 0.14 --scale 1e9
    displayName: Run Example 1 test

  - script: |
      source activate ntsynt_viz_ci
      export PATH=$(pwd)/bin:$PATH
      cd tests
      ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv  --name_conversion great-apes.name-conversions.tsv  --prefix great-apes_ribbon-plots_no-tree --ribbon_adjust 0.15 --scale 1e9 --target-genome Homo_sapiens --force
      diff -q great-apes_ribbon-plots_no-tree_est-distances.order.tsv expected/great-apes_ribbon-plots_no-tree_est-distances.order.tsv
    displayName: Run Example 2 test


- 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_viz_ci
    displayName: Create Anaconda environment

  - script: |
      source activate ntsynt_viz_ci
      mamba install --yes -c conda-forge -c bioconda quicktree r-base bioconductor-treeio r-ggpubr bioconductor-ggtree r-phytools r-dplyr r-argparse r-scales r-stringr pylint intervaltree snakemake
      # NOTE: Once treeio is updated in bioconda, you may be able to use r-gggenomes instead. I am getting conflicting package errors currently
      R -e 'install.packages(c("gggenomes"), repos = "https://cran.r-project.org")'
    displayName: Install dependencies

  - script: |
      source activate ntsynt_viz_ci
      cd bin
      pylint *py
    displayName: Run pylint

  - script: |
      source activate ntsynt_viz_ci
      ./bin/ntsynt_viz.py --help
    displayName: Print ntSynt-viz help message

  - script: |
      source activate ntsynt_viz_ci
      export PATH=$(pwd)/bin:$PATH
      cd tests
      ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv --tree great-apes.mt-tree.nwk --name_conversion great-apes.name-conversions.tsv --normalize --prefix great-apes_ribbon-plots --ribbon_adjust 0.14 --scale 1e9
    displayName: Run Example 1 test

  - script: |
      source activate ntsynt_viz_ci
      export PATH=$(pwd)/bin:$PATH
      cd tests
      ntsynt_viz.py --blocks great-apes.ntSynt.synteny_blocks.tsv --fais fais.tsv  --name_conversion great-apes.name-conversions.tsv  --prefix great-apes_ribbon-plots_no-tree --ribbon_adjust 0.15 --scale 1e9 --target-genome Homo_sapiens --force
      diff -q great-apes_ribbon-plots_no-tree_est-distances.order.tsv expected/great-apes_ribbon-plots_no-tree_est-distances.order.tsv
    displayName: Run Example 2 test