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[ci] Interop-CI update #1679

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merged 5 commits into from
Sep 15, 2023
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[ci] Interop-CI update #1679

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2d1896c
Interop canary [WIP]
johnkerl Sep 15, 2023
485acea
debug
johnkerl Sep 15, 2023
617b59b
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johnkerl Sep 15, 2023
ed41e98
copy from r-ci.yaml
johnkerl Sep 15, 2023
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code-review feedback
johnkerl Sep 15, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/r-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,11 @@ jobs:
- name: Install BioConductor package SingleCellExperiment
run: cd apis/r && tools/r-ci.sh install_bioc SingleCellExperiment

- name: Install rc version of tiledb-r (macOS)
- name: Install r-universe build of tiledb-r (macOS)"
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stray quote marks

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eek thx

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#1681
Thank you @thetorpedodog ! :)

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 rc version of tiledb-r (linux)
- 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'))"

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27 changes: 21 additions & 6 deletions .github/workflows/r-python-interop-testing.yml
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Expand Up @@ -2,10 +2,12 @@ name: TileDB-SOMA R-Python interop testing

on:
pull_request:
paths:
- "apis/python/**"
- "apis/r/**"
- "apis/system/**"
# TODO: leave this enabled for pre-merge signal for now. At some point we may want to go back to
# only having this signal post-merge.
#paths:
# - "apis/python/**"
# - "apis/r/**"
# - "apis/system/**"
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push:
branches:
- main
Expand Down Expand Up @@ -38,6 +40,14 @@ jobs:
- name: MkVars
run: mkdir ~/.R && echo "CXX17FLAGS=-Wno-deprecated-declarations -Wno-deprecated" > ~/.R/Makevars

- 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 (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'))"

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- name: Build and install libtiledbsoma
run: sudo scripts/bld --prefix=/usr/local && sudo ldconfig

Expand All @@ -48,6 +58,9 @@ jobs:
FILE=$(ls -1t *.tar.gz | head -n 1)
R CMD INSTALL $FILE

- name: Show R package versions
run: Rscript -e 'tiledbsoma::show_package_versions()'

- name: Install testing prereqs
run: python -m pip -v install -U pip pytest-cov 'typeguard<3.0' types-setuptools

Expand All @@ -61,8 +74,10 @@ jobs:
- name: Install tiledbsoma
run: python -m pip -v install -e apis/python

- name: Show package versions
run: python scripts/show-versions.py
- name: Show Python package versions
run: |
python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
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python scripts/show-versions.py

- name: Interop Tests
run: python -m pytest apis/system/tests/