arg-needle/.github/workflows/python_examples.yml at main · PalamaraLab/arg-needle · GitHub

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name: Python examples

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - '**'
  workflow_dispatch:

jobs:

  build-and-test:
    name: Python examples
    runs-on: ${{ matrix.os }}
    timeout-minutes: 10

    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-24.04
            py: "3.10"
            sys_install: "sudo apt -y update && sudo apt -y install libboost-iostreams-dev"
          - os: macos-15
            py: "3.13"
            sys_install: "brew install boost"

    steps:
      - name: checkout repo & submodules
        uses: actions/checkout@v5
        with:
          submodules: true
          fetch-depth: 0

      - name: install deps
        run: |
          ${{ matrix.sys_install }}

      - name: Set up Python ${{ matrix.py }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.py }}

      - name: install python bindings
        run: |
          python -m pip install --upgrade pip setuptools wheel
          python -m pip install .

      - name: prepare example
        run: |
          prepare_example

      - name: regular ARG-Needle
        run: |
          infer_args

      - name: ARG-Needle with ASMC-clust
        run: |
          infer_args --asmc_clust 1

      - name: ARG-Needle without ARG normalization
        run: |
          infer_args --normalize 0

      - name: ARG-Needle (sequence mode)
        run: |
          prepare_example --mode sequence --length 5e5
          infer_args --mode sequence

      - name: ARG-Needle advanced mode (multistep)
        run: |
          prepare_example
          infer_args_advanced --step 1 --num_snp_samples 200
          infer_args_advanced --step 2
          infer_args_advanced --step 3 --trim_num_snps 0,50