basic.yml

#
# basic.yml
#
# The MIT License
#
# Copyright (c) 2023 Omics Data Automation, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#

#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.

name: Build and Test

on:
  push:
    paths-ignore:
      - '**/*.md'
  pull_request:
    paths-ignore:
      - '**/*.md'

env:
  GENOMICSDB_BUILD_DIR: ${{ github.workspace }}
  GENOMICSDB_HOME: ${{ github.workspace }}/install
  GENOMICSDB_BRANCH: develop 

jobs:
  native-build:
    name: GenomicsDB Build
    runs-on: ubuntu-22.04
    steps:
      - name: Cache Native GenomicsDB
        uses: actions/cache@v3
        env:
          GENOMICSDB_TARBALL: ${{ env.GENOMICSDB_HOME }}_${{ env.GENOMICSDB_BRANCH }}.tar
        with:
          path: ${{ env.GENOMICSDB_TARBALL }}
          key: ${{ env.GENOMICSDB_TARBALL }}.v1
            
      - name: Native Build
        env:
          GENOMICSDB_TARBALL: ${{ env.GENOMICSDB_HOME }}_${{ env.GENOMICSDB_BRANCH }}.tar
        run: |
          echo "GENOMICSDB_TARBALL=$GENOMICSDB_TARBALL" >> $GITHUB_ENV
          if [[ ! -f ${GENOMICSDB_TARBALL} ]]; then
            sudo apt-get update -q && sudo apt install -y libcurl4-openssl-dev curl mpich
            git clone https://github.com/GenomicsDB/GenomicsDB.git -b $GENOMICSDB_BRANCH $GENOMICSDB_BUILD_DIR
            cd $GENOMICSDB_BUILD_DIR
            cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_HOME 
            cd build && make -j4 && make install
            cd $(dirname $GENOMICSDB_HOME)
            tar -cvf ${GENOMICSDB_TARBALL} $(basename $GENOMICSDB_HOME)
          fi

      - name: Upload GenomicsDB Tarball
        uses: actions/upload-artifact@v3
        with:
          name: GenomicsDB-Tarball-${{ runner.os }}
          path: ${{ env.GENOMICSDB_TARBALL }}
          retention-days: 5
          
  r-build:
    name: R Build
    needs: native-build
    runs-on: ubuntu-22.04
    env:
      R_LIBS: ${{ github.workspace }}/R-libs
    strategy:
      matrix:
        r-version: ['4.2']

    steps:
      - uses: actions/checkout@v3

      - name: Download GenomicsDB Tarball
        uses: actions/download-artifact@v3
        with:
          name: GenomicsDB-Tarball-${{runner.os}}

      - name: Extract GenomicsDB from Tarball
        env:
          GENOMICSDB_TARBALL: ${{ env.GENOMICSDB_HOME }}_${{ env.GENOMICSDB_BRANCH }}.tar
        run: tar -xvf ${GENOMICSDB_TARBALL} -C $(dirname $GENOMICSDB_HOME)
        
      - name: Setup R ${{ matrix.r-version }}
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r-version }}

      - name: Setup R_LIBS
        run: |
          mkdir -p $R_LIBS
          echo "R_LIBS=$R_LIBS" > .Renviron

      - name: Cache installed Packages
        uses: actions/cache@v3
        with:
          path: ${{ env.R_LIBS }}
          key: R-libs-${{ runner.os }}-${{ matrix.r-version }}-${{ hashFiles('DESCRIPTION') }}
          
      - name: Install Dependencies
        run: |
          system("sudo apt-get install libcurl4-openssl-dev")
          r_libs=Sys.getenv("R_LIBS")
          install.packages(c("remotes", "rcmdcheck"), lib=r_libs)
          remotes::install_deps(dependencies = TRUE, lib=r_libs)
        shell: Rscript {0}
        
      - name: Build and Check
        run: rcmdcheck::rcmdcheck(args=c("--no-manual", "--ignore-vignettes"), build_args="--no-build-vignettes", error_on = "error")
        shell: Rscript {0}