smoke-test-r.yml

name: Smoke Test

on:
  workflow_dispatch:

jobs:
  test-package:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Install system dependencies and R for macOS
        if: matrix.os == 'macos-latest'
        run: brew install xz
        shell: bash

      - name: Install system dependencies for Ubuntu
        if: matrix.os == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -y liblzma-dev libcurl4-openssl-dev
        shell: bash

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'

      - name: Install R packages
        run: |
          install.packages(c("arrow", "nanoarrow"))
          install.packages("exonr", repos = c("https://wheretrue.r-universe.dev", "https://cloud.r-project.org"))
        shell: Rscript {0}

      - name: Test exonr
        shell: Rscript {0}
        run: |
          library(exonr)

          # Read in an example file
          batch_reader <- exonr::read_fasta_file("exon/exon-core/test-data/datasources/fasta/test.fasta")

          # Convert to a data.frame
          batch_df <- as.data.frame(batch_reader)

          # Print the head of the dataframe
          print(head(batch_df))