From 4d750272d9e98956e5b894abd0c187e498b02ec9 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Tue, 16 Apr 2024 10:49:01 -0400 Subject: [PATCH] experimental commit to look for green CI with new technique --- .github/workflows/r-ci.yml | 56 +++++++++---------- .../workflows/r-python-interop-testing.yml | 54 +++++++++--------- 2 files changed, 53 insertions(+), 57 deletions(-) diff --git a/.github/workflows/r-ci.yml b/.github/workflows/r-ci.yml index 188cc06468..bbd1a7085d 100644 --- a/.github/workflows/r-ci.yml +++ b/.github/workflows/r-ci.yml @@ -61,37 +61,26 @@ jobs: run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment - - name: Install 0.25 build of tiledb-r with core 2.21 - run: | - cd apis/r - wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz - Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' - R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9 - - # Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for - # which source is available but CRAN releases (and hence update r2u binaries) are not yet: - # - # IMPORTANT: these two stanzas should remain uncommented _only_ during the propagation time - # between (a) publication of source for a new TileDB-R _upon which_ TileDB-SOMA depends in its - # apis/R/DESCRIPTION file and (b) appearance of binaries. - # # Please see https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases which # is crucial for anyone doing releases of TileDB-SOMA. # - # Please edit both files in the same way: - # * r-ci.yml - # * r-python-interop-testing.yml + # As documented there, we have a cadence for updating tiledb-inc.r-universe.dev. + # + # Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2447 regarding R CI YAML. + # + # Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2406 regarding + # our upcoming elimination of TileDB-SOMA's dependency on TileDB-R entirely. # # Do not remove these comments until such time as we have eliminated our dependency on # the TileDB-R package. - #- name: Install r-universe build of tiledb-r (macOS) - # if: ${{ matrix.os == 'macOS-latest' }} - # run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))" + - name: Install r-universe build of tiledb-r (macOS) + if: ${{ matrix.os == 'macOS-latest' }} + run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))" - #- name: Install r-universe build of tiledb-r (linux) - # if: ${{ matrix.os != 'macOS-latest' }} - # run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" + - name: Install r-universe build of tiledb-r (linux) + if: ${{ matrix.os != 'macOS-latest' }} + run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://tiledb-inc.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" - name: Dependencies run: cd apis/r && tools/r-ci.sh install_all @@ -116,12 +105,21 @@ jobs: - name: Update Packages run: Rscript -e 'update.packages(ask=FALSE)' - - name: Re-install 0.25 build of tiledb-r with core 2.21 - run: | - cd apis/r - wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz - Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' - R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9 + # WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI + #- name: Install 0.25 build of tiledb-r with core 2.21 + # run: | + # cd apis/r + # wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz + # Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' + # R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9 + + # WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI + #- name: Re-install 0.25 build of tiledb-r with core 2.21 + # run: | + # cd apis/r + # wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz + # Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' + # R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9 # - name: Build Package # run: cd apis/r && R CMD build --no-build-vignettes --no-manual . diff --git a/.github/workflows/r-python-interop-testing.yml b/.github/workflows/r-python-interop-testing.yml index f589edba7e..cf1ff666da 100644 --- a/.github/workflows/r-python-interop-testing.yml +++ b/.github/workflows/r-python-interop-testing.yml @@ -41,37 +41,34 @@ jobs: - name: MkVars run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars - - name: Install 0.25 build of tiledb-r with core 2.21 - run: | - cd apis/r - wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz - Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' - R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9 + # WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI + #- name: Install 0.25 build of tiledb-r with core 2.21 + # run: | + # cd apis/r + # wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz + # Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' + # R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by TileDB-SOMA 1.9 - # Uncomment these next two stanzas as needed whenever we've just released a new tiledb-r for - # which source is available but CRAN releases (and hence update r2u binaries) are not yet: - # - # IMPORTANT: these two stanzas should remain uncommented _only_ during the propagation time - # between (a) publication of source for a new TileDB-R _upon which_ TileDB-SOMA depends in its - # apis/R/DESCRIPTION file and (b) appearance of binaries. - # # Please see https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases which # is crucial for anyone doing releases of TileDB-SOMA. # - # Please edit both files in the same way: - # * r-ci.yml - # * r-python-interop-testing.yml + # As documented there, we have a cadence for updating tiledb-inc.r-universe.dev. + # + # Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2447 regarding R CI YAML. + # + # Please also see https://github.com/single-cell-data/TileDB-SOMA/issues/2406 regarding + # our upcoming elimination of TileDB-SOMA's dependency on TileDB-R entirely. # # Do not remove these comments until such time as we have eliminated our dependency on # the TileDB-R package. - #- name: Install r-universe build of tiledb-r (macOS) - # if: ${{ matrix.os == 'macOS-latest' }} - # run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev', 'https://cloud.r-project.org'))" + - name: Install r-universe build of tiledb-r (macOS) + if: ${{ matrix.os == 'macOS-latest' }} + run: cd apis/r && Rscript -e "install.packages('tiledb', repos = c('https://tiledb-inc.r-universe.dev', 'https://cloud.r-project.org'))" - #- name: Install r-universe build of tiledb-r (linux) - # if: ${{ matrix.os != 'macOS-latest' }} - # run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://eddelbuettel.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" + - name: Install r-universe build of tiledb-r (linux) + if: ${{ matrix.os != 'macOS-latest' }} + run: cd apis/r && Rscript -e "options(bspm.version.check=TRUE); install.packages('tiledb', repos = c('https://tiledb-inc.r-universe.dev/bin/linux/jammy/4.3/', 'https://cloud.r-project.org'))" - name: Build and install libtiledbsoma run: sudo scripts/bld --prefix=/usr/local && sudo ldconfig @@ -107,12 +104,13 @@ jobs: - name: Update Packages run: Rscript -e 'update.packages(ask=FALSE)' - - name: Re-install 0.25 build of tiledb-r with core 2.21 - run: | - cd apis/r - wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz - Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' - R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9 + # WIP (NOT READY FOR REVIEW) -- LOOKING FOR GREEN CI + #- name: Re-install 0.25 build of tiledb-r with core 2.21 + # run: | + # cd apis/r + # wget https://github.com/TileDB-Inc/TileDB-R/archive/refs/tags/0.25.0.tar.gz + # Rscript -e 'remotes::install_deps("0.25.0.tar.gz")' + # R CMD INSTALL 0.25.0.tar.gz # as 0.25.0 is needed by SOMA 1.9 - name: Show package versions run: |