experimental commit to look for green CI with new technique

single-cell-data · Apr 16, 2024 · 4d75027 · 4d75027
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diff --git 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
@@ -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: |