React to changed GenomicsDB api and create GitHub Actions workflows for basic build/test #44
Workflow file for this run
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| # | |
| # 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} | |