Nightly builds on linux #430
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name: Nightly builds on linux | |
on: | |
push: | |
paths: | |
- '.github/workflows/linux.yml' | |
- 'scripts/**' | |
pull_request: | |
paths: | |
- '.github/workflows/linux.yml' | |
- 'scripts/**' | |
schedule: | |
- cron: "0 2 * * *" # Every night at 2 AM UTC (9 PM EST; 10 PM EDT) | |
workflow_dispatch: | |
inputs: | |
LIBTILEDB_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB | |
default: dev | |
TILEDB_PY_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Py | |
default: dev | |
TILEDB_R_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-R | |
default: master | |
TILEDB_VCF_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout | |
TileDB-Inc/TileDB-VCF | |
default: main | |
TILEDB_SOMA_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout | |
single-cell-data/TileDB-SOMA | |
default: main | |
TILEDB_MARIADB_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-MariaDB | |
default: master | |
TILEDB_GO_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Go | |
default: master | |
TILEDB_CLOUD_PY_REF: | |
description: >- | |
The Git reference (tag, branch, commit) to checkout TileDB-Inc/TileDB-Cloud-Py | |
default: main | |
jobs: | |
libtiledb: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Clone TileDB | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB | |
ref: ${{ github.event.inputs.LIBTILEDB_REF || 'dev' }} | |
- name: Download release tarball | |
if: github.ref_name != 'main' | |
run: wget https://github.com/TileDB-Inc/TileDB/releases/download/2.24.0/tiledb-linux-x86_64-2.24.0-ff3879b.tar.gz | |
- name: Unpack release tarball | |
if: github.ref_name != 'main' | |
run: | | |
mkdir install-libtiledb | |
tar xzf tiledb-linux-x86_64-*.tar.gz -C install-libtiledb | |
ls -R install-libtiledb/ | |
- name: Patch tiledb.pc from release tarball | |
if: github.ref_name != 'main' | |
run: | | |
new_prefix=prefix=\"$(pwd)/install-libtiledb\" | |
echo $new_prefix | |
sed -i "1 s+.*+$new_prefix+" install-libtiledb/lib/pkgconfig/tiledb.pc | |
cat install-libtiledb/lib/pkgconfig/tiledb.pc | |
- name: Configure TileDB | |
if: github.ref_name == 'main' | |
run: | | |
cmake -B build-libtiledb \ | |
-D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledb/ \ | |
-D TILEDB_WERROR=ON \ | |
-D TILEDB_SERIALIZATION=ON \ | |
-D CMAKE_BUILD_TYPE=Release \ | |
-D TILEDB_S3=ON \ | |
-D VCPKG_TARGET_TRIPLET=x64-linux-release | |
- name: Build TileDB | |
if: github.ref_name == 'main' | |
run: cmake --build build-libtiledb -j $(nproc) --config Release | |
- name: Install TileDB | |
if: github.ref_name == 'main' | |
run: cmake --build build-libtiledb --config Release --target install-tiledb | |
- name: Upload libtiledb as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: | | |
install-libtiledb/* | |
retention-days: 14 | |
if-no-files-found: error | |
# Unable to run the test suite with `TILEDB_S3=ON` (required for | |
# tiledbvcf-py tests) without configuring S3 credentials | |
# - name: Test TileDB | |
# if: github.ref_name == 'main' | |
# run: | | |
# make -C build-libtiledb/tiledb tests -j $(nproc) | |
# ./build-libtiledb/tiledb/test/tiledb_unit --vfs native | |
tiledb-py: | |
runs-on: ubuntu-latest | |
needs: libtiledb | |
env: | |
LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib | |
PKG_CONFIG_PATH: ${{ github.workspace }}/install-libtiledb/lib/pkgconfig | |
steps: | |
- name: Clone TileDB-Py | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-Py | |
ref: ${{ github.event.inputs.TILEDB_PY_REF || 'dev' }} | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Install dependencies | |
run: python -m pip install --upgrade -r misc/requirements_ci.txt | |
- name: Build TileDB-Py | |
run: | | |
echo $LD_LIBRARY_PATH | |
python setup.py develop --tiledb=$(pwd)/install-libtiledb/ | |
- name: Import TileDB-Py | |
run: | | |
python -c "import tiledb; print('successful import')" | |
python -c "import tiledb; print(tiledb.libtiledb.version())" | |
python -c "import tiledb; print(tiledb.version())" | |
- name: Test TileDB-Py | |
run: pytest -vv | |
- name: Create a wheel | |
run: python setup.py bdist_wheel --tiledb=$(pwd)/install-libtiledb/ | |
- name: Upload Python wheel as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledb-py-linux | |
path: dist/tiledb-*-linux_x86_64.whl | |
retention-days: 14 | |
if-no-files-found: error | |
tiledb-r: | |
runs-on: ubuntu-latest | |
needs: libtiledb | |
env: | |
_R_CHECK_FORCE_SUGGESTS_: "FALSE" | |
steps: | |
- name: Clone TileDB-R | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-R | |
ref: ${{ github.event.inputs.TILEDB_R_REF || 'master' }} | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Bootstrap | |
run: ./.github/r-ci.sh bootstrap | |
- name: Dependencies | |
run: ./.github/r-ci.sh install_all | |
- name: Build | |
run: R CMD build --no-manual --no-build-vignettes . | |
- name: Install | |
run: | | |
R CMD INSTALL --configure-args=--with-tiledb=$(pwd)/install-libtiledb --build tiledb_*.tar.gz | |
- name: Upload R binary tarball as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledb-r-linux | |
path: tiledb_*_R_x86_64-pc-linux-gnu.tar.gz | |
retention-days: 14 | |
if-no-files-found: error | |
- name: Test | |
run: R -e 'tinytest::test_package("tiledb")' | |
libtiledbvcf: | |
runs-on: ubuntu-latest | |
needs: libtiledb | |
env: | |
LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib | |
steps: | |
- name: Clone TileDB-VCF | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-VCF | |
ref: ${{ github.event.inputs.TILEDB_VCF_REF || 'main' }} | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Setup | |
run: | | |
sudo apt-get update | |
sudo apt-get install --yes cmake | |
- name: Configure libtiledbvcf | |
run: | | |
cmake -S libtiledbvcf -B build-libtiledbvcf \ | |
-D CMAKE_BUILD_TYPE=Release \ | |
-D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \ | |
-D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledbvcf/ \ | |
-D OVERRIDE_INSTALL_PREFIX=OFF \ | |
-D TILEDB_WERROR=OFF | |
- name: Build libtiledbvcf | |
run: cmake --build build-libtiledbvcf -j $(nproc) --config Release | |
- name: Install libtiledbvcf | |
run: | | |
cmake --build build-libtiledbvcf --config Release --target install-libtiledbvcf | |
ls -R install-libtiledbvcf/ | |
- name: Upload libtiledbvcf as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-libtiledbvcf-linux | |
path: | | |
install-libtiledbvcf/* | |
retention-days: 14 | |
if-no-files-found: error | |
- name: libtiledbvcf version | |
run: ./install-libtiledbvcf/bin/tiledbvcf version | |
- name: Confirm linking | |
run: ldd install-libtiledbvcf/lib/libtiledbvcf.so | |
- name: Install bcftools (for tests) | |
run: sudo apt-get install --yes bcftools | |
- name: Test libtiledbvcf | |
run: | | |
make -j $(nproc) -C build-libtiledbvcf/libtiledbvcf tiledb_vcf_unit | |
./build-libtiledbvcf/libtiledbvcf/test/tiledb_vcf_unit | |
# cli tests (require bcftools) | |
# USAGE: run-cli-tests.sh <build-dir> <inputs-dir> | |
libtiledbvcf/test/run-cli-tests.sh build-libtiledbvcf libtiledbvcf/test/inputs | |
tiledbvcf-py: | |
runs-on: ubuntu-latest | |
needs: [libtiledb, libtiledbvcf, tiledb-py] | |
env: | |
LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbvcf/lib" | |
steps: | |
- name: Clone TileDB-VCF | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-VCF | |
ref: ${{ github.event.inputs.TILEDB_VCF_REF || 'main' }} | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Download nightly-libtiledbvcf | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledbvcf-linux | |
path: install-libtiledbvcf | |
- name: Download nightly-tiledb-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-py-linux | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Install dependencies | |
run: python -m pip install --prefer-binary \ | |
pyarrow==11 | |
- name: Install nightly tiledb-py | |
run: | | |
pip install --prefer-binary tiledb-*-linux_x86_64.whl | |
pip list | |
- name: Build tiledbvcf-py | |
run: | | |
export LIBTILEDBVCF_PATH=$(pwd)/install-libtiledbvcf/lib/ | |
export TileDB_DIR=$(pwd)/install-libtiledb/lib/cmake/TileDB | |
python -m pip install -v apis/python[test] | |
- name: Confirm linking | |
run: | | |
echo "Shared objects in build directory" | |
find apis/python -name '*.so*' | |
echo "Installed shared objects" | |
find $pythonLocation/lib/python*/site-packages/tiledbvcf -name '*.so*' | |
echo "Run ldd on installed shared objects" | |
find $pythonLocation/lib/python*/site-packages/tiledbvcf -name '*.so*' | xargs ldd | |
echo "Check RPATH of installed shared object" | |
readelf -d $pythonLocation/lib/python*/site-packages/tiledbvcf/libtiledbvcf.cpython-*-x86_64-linux-gnu.so | grep R*PATH | |
echo "Check RPATH of shared object in build directory" | |
readelf -d apis/python/build/cp311-cp311-linux_x86_64/libtiledbvcf.cpython-311-x86_64-linux-gnu.so | grep R*PATH | |
- name: Install bcftools (for tests) | |
run: | | |
sudo apt-get update | |
sudo apt-get install --yes bcftools | |
- name: Test tiledbvcf-py | |
run: | | |
python -c "import tiledbvcf; print(tiledbvcf.version)" | |
cd apis/python | |
pytest | |
- name: Create a wheel | |
run: | | |
export LIBTILEDBVCF_PATH=$(pwd)/install-libtiledbvcf/lib/ | |
python -m pip wheel -v --wheel-dir=apis/python/dist apis/python | |
- name: Upload Python wheel as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledbvcf-py-linux | |
path: apis/python/dist/tiledbvcf-*-linux_x86_64.whl | |
retention-days: 14 | |
if-no-files-found: error | |
libtiledbsoma: | |
runs-on: ubuntu-latest | |
needs: [libtiledb] | |
env: | |
TileDB_DIR: ${{ github.workspace }}/install-libtiledb | |
LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib | |
steps: | |
- name: Clone TileDB-SOMA | |
uses: actions/checkout@v4 | |
with: | |
repository: single-cell-data/TileDB-SOMA | |
ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }} | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Setup | |
run: | | |
sudo apt-get update | |
sudo apt-get install --yes cmake | |
- name: Configure libtiledbsoma | |
run: | | |
cmake -S libtiledbsoma -B build-libtiledbsoma \ | |
-D CMAKE_BUILD_TYPE=Release \ | |
-D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \ | |
-D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/install-libtiledbsoma/ \ | |
-D OVERRIDE_INSTALL_PREFIX=OFF \ | |
-D DOWNLOAD_TILEDB_PREBUILT=OFF \ | |
-D FORCE_BUILD_TILEDB=OFF | |
- name: Build libtiledbsoma | |
run: cmake --build build-libtiledbsoma -j $(nproc) | |
- name: Install libtiledbsoma | |
run: | | |
cmake --build build-libtiledbsoma --target install-libtiledbsoma | |
ls -R $(pwd)/install-libtiledb/ | |
- name: Upload libtiledbsoma as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-libtiledbsoma-linux | |
path: | | |
install-libtiledbsoma/* | |
- name: Confirm linking | |
run: ldd install-libtiledbsoma/lib/libtiledbsoma.so | |
- name: Test libtiledbsoma | |
run: | | |
cmake --build build-libtiledbsoma/libtiledbsoma --target build_tests -j $(nproc) | |
ctest --test-dir build-libtiledbsoma/libtiledbsoma -C Release --verbose --rerun-failed --output-on-failure | |
tiledbsoma-py: | |
runs-on: ubuntu-latest | |
needs: [libtiledb, libtiledbsoma, tiledb-py] | |
env: | |
LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbsoma/lib" | |
TILEDB_PATH: ${{ github.workspace }}/install-libtiledb | |
TILEDBSOMA_PATH: ${{ github.workspace }}/install-libtiledbsoma | |
PKG_CONFIG_PATH: "${{ github.workspace }}/install-libtiledb/lib/pkgconfig:${{ github.workspace }}/install-libtiledbsoma/lib/pkgconfig" | |
steps: | |
- name: Clone TileDB-SOMA | |
uses: actions/checkout@v4 | |
with: | |
repository: single-cell-data/TileDB-SOMA | |
ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }} | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Download nightly-libtiledbsoma | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledbsoma-linux | |
path: install-libtiledbsoma | |
- name: Download nightly-tiledb-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-py-linux | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
# https://github.com/single-cell-data/TileDB-SOMA/blob/main/apis/python/pyproject.toml | |
- name: Install dependencies | |
run: | | |
python -m pip install \ | |
-r apis/python/requirements_dev.txt \ | |
"pybind11[global]>=2.10.0" \ | |
"setuptools>=65.5.1" \ | |
"wheel>=0.37.1" \ | |
"cmake>=3.21" | |
- name: Install nightly tiledb-py | |
run: | | |
pip install tiledb-*-linux_x86_64.whl | |
pip list | |
- name: Install tiledbsoma-py | |
run: | | |
python -m pip -v install --no-build-isolation -e apis/python | |
pip list | |
- name: Confirm linking | |
run: | | |
find apis/python -name '*.so*' | |
find apis/python -name '*.so*' | xargs ldd | |
readelf -d apis/python/src/tiledbsoma/pytiledbsoma.*.so | grep R*PATH | |
- name: Fail if unnecessary libtiledbsoma.so is created | |
# https://github.com/single-cell-data/TileDB-SOMA/pull/1937 | |
run: | | |
if [[ -f apis/python/src/tiledbsoma/libtiledbsoma.so ]] | |
then | |
echo "An unnecessary libtiledbsoma.so was created during the package build" | |
exit 1 | |
fi | |
- name: Test tiledbsoma-py | |
run: | | |
python -c "import tiledbsoma; print('successful import')" | |
python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())" | |
python -c "import tiledbsoma; print(f'tiledbsoma-py={tiledbsoma.__version__}')" | |
# Obtain test data | |
cd test | |
tar zxf soco.tgz | |
cd .. | |
# Run test suite | |
PYTHONPATH=$(pwd)/apis/python/src python -m pytest apis/python/tests | |
- name: Create a wheel | |
run: | | |
cd apis/python | |
python setup.py bdist_wheel | |
- name: Upload Python wheel as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledbsoma-py-linux | |
path: apis/python/dist/tiledbsoma-*-linux_x86_64.whl | |
retention-days: 14 | |
if-no-files-found: error | |
tiledbsoma-r: | |
runs-on: ubuntu-latest | |
needs: [libtiledb, libtiledbsoma, tiledb-r] | |
env: | |
LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib:${{ github.workspace }}/install-libtiledbsoma/lib" | |
PKG_CONFIG_PATH: "${{ github.workspace }}/install-libtiledb/lib/pkgconfig:${{ github.workspace }}/install-libtiledbsoma/lib/pkgconfig" | |
steps: | |
- name: Clone TileDB-SOMA | |
uses: actions/checkout@v4 | |
with: | |
repository: single-cell-data/TileDB-SOMA | |
ref: ${{ github.event.inputs.TILEDB_SOMA_REF || 'main' }} | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Download nightly-libtiledbsoma | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledbsoma-linux | |
path: install-libtiledbsoma | |
- name: Download nightly-tiledb-r | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-r-linux | |
- name: Bootstrap | |
run: cd apis/r && tools/r-ci.sh bootstrap | |
- name: Install nightly tiledb-r (and its dependencies) | |
shell: Rscript {0} | |
run: | | |
install.packages("remotes") | |
library("remotes") | |
binary_tarball <- Sys.glob("tiledb_*_R_x86_64-pc-linux-gnu.tar.gz") | |
message(binary_tarball) | |
install_deps(binary_tarball, dependencies = TRUE, upgrade = "never") | |
install.packages(binary_tarball, repos = NULL) | |
- name: Dependencies | |
run: cd apis/r && tools/r-ci.sh install_all | |
- name: Build | |
run: | | |
export CXX17FLAGS="-Wno-deprecated-declarations -Wno-deprecated" | |
cd apis/r && R CMD build --no-manual --no-build-vignettes . | |
- name: Install | |
run: | |
cd apis/r && R CMD INSTALL --install-tests --build tiledbsoma_*.tar.gz | |
- name: Upload R binary tarball as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledbsoma-r-linux | |
path: apis/r/tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz | |
retention-days: 14 | |
if-no-files-found: error | |
- name: Test | |
run: | |
Rscript -e 'testthat::test_package("tiledbsoma")' | |
tiledb-mariadb: | |
runs-on: ubuntu-latest | |
needs: [libtiledb] | |
env: | |
CFLAGS: -Wno-error=deprecated-declarations -Wno-error=missing-braces | |
CXXFLAGS: -Wno-error=deprecated-declarations -Wno-error=missing-braces | |
LD_LIBRARY_PATH: ${{ github.workspace }}/install-libtiledb/lib | |
steps: | |
- name: Clone MariaDB | |
uses: actions/checkout@v4 | |
with: | |
repository: MariaDB/server.git | |
ref: mariadb-11.0.2 | |
- name: Clone TileDB-MariaDB into MariaDB | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-MariaDB | |
ref: ${{ github.event.inputs.TILEDB_MARIADB_REF || 'master' }} | |
path: storage/mytile | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Configure TileDB-MariaDB | |
run: | | |
cmake \ | |
-S . -B builddir \ | |
-D CMAKE_PREFIX_PATH=$(pwd)/install-libtiledb/ \ | |
-D PLUGIN_OQGRAPH=NO \ | |
-D WITH_MARIABACKUP=OFF \ | |
-D PLUGIN_TOKUDB=NO \ | |
-D PLUGIN_ROCKSDB=NO \ | |
-D PLUGIN_MROONGA=NO \ | |
-D PLUGIN_SPIDER=NO \ | |
-D PLUGIN_SPHINX=NO \ | |
-D PLUGIN_FEDERATED=NO \ | |
-D PLUGIN_FEDERATEDX=NO \ | |
-D PLUGIN_CONNECT=NO \ | |
-D CMAKE_BUILD_TYPE=Debug \ | |
-D WITH_DEBUG=1 \ | |
-D CMAKE_INCLUDE_PATH="/usr/local/include" \ | |
-D TILEDB_FORCE_ALL_DEPS=${TILEDB_FORCE_ALL_DEPS-OFF} | |
- name: Build TileDB-MariaDB | |
run: | | |
cd builddir | |
make -j $(nproc) | |
- name: Confirm linking | |
run: | | |
du -sh builddir | |
du -sh builddir/storage/mytile | |
ldd builddir/storage/mytile/ha_mytile.so | \ | |
grep -q $(pwd)/install-libtiledb/lib/libtiledb.so | |
- name: Test TileDB-MariaDB | |
run: | | |
cd builddir | |
./mysql-test/mysql-test-run.pl --suite=mytile --debug | |
tiledb-go: | |
runs-on: ubuntu-latest | |
needs: [libtiledb] | |
steps: | |
- name: Clone TileDB-Go | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-Go | |
ref: ${{ github.event.inputs.TILEDB_GO_REF || 'master' }} | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Install dependencies | |
run: go get -t . | |
- name: Test TileDB-Go | |
run: | | |
export CPATH=$(pwd)/install-libtiledb/include | |
export LIBRARY_PATH=$(pwd)/install-libtiledb/lib | |
export LD_LIBRARY_PATH=$(pwd)/install-libtiledb/lib | |
go test -v ./... | |
tiledb-cloud-py: | |
runs-on: ubuntu-latest | |
needs: [libtiledb, tiledb-py] | |
env: | |
LD_LIBRARY_PATH: "${{ github.workspace }}/install-libtiledb/lib" | |
steps: | |
- name: Clone TileDB-Cloud-Py | |
uses: actions/checkout@v4 | |
with: | |
repository: TileDB-Inc/TileDB-Cloud-Py | |
ref: ${{ github.event.inputs.TILEDB_CLOUD_PY_REF || 'main' }} | |
fetch-depth: 0 # fetch everything for python setuptools_scm | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Download nightly-tiledb-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-py-linux | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Install dependencies | |
run: python -m pip install \ | |
"attrs>=21.4.0" \ | |
"certifi" \ | |
"cloudpickle>=1.4.1,<3" \ | |
"importlib-metadata" \ | |
"packaging" \ | |
"pandas>=1.2.4" \ | |
"pyarrow>=3.0.0" \ | |
"python-dateutil" \ | |
"six>=1.10" \ | |
"tblib~=1.7" \ | |
"tiledb>=0.15.2" \ | |
"typing-extensions" \ | |
"urllib3>=1.26" \ | |
"wheel" | |
- name: Install nightly tiledb-py | |
run: | | |
pip install tiledb-*-linux_x86_64.whl | |
pip list | |
- name: Build tiledb-cloud | |
run: | | |
echo $LD_LIBRARY_PATH | |
pip install --no-build-isolation . | |
- name: Create a wheel | |
run: python setup.py bdist_wheel | |
- name: Upload Python wheel as artifact | |
uses: actions/upload-artifact@v4 | |
with: | |
name: nightly-tiledb-cloud-py-linux | |
path: dist/tiledb_cloud-*-none-any.whl | |
retention-days: 14 | |
if-no-files-found: error | |
build-all: | |
# this is simply a target to build everything locally with `act` without | |
# creating a new release | |
name: Build everything | |
runs-on: ubuntu-latest | |
needs: [libtiledb, tiledb-py, tiledb-r, libtiledbvcf, tiledbvcf-py, libtiledbsoma, | |
tiledbsoma-py, tiledbsoma-r, tiledb-mariadb, tiledb-go, tiledb-cloud-py] | |
steps: | |
- run: echo "Success! Everything was built" | |
create-release: | |
name: Create a new release | |
if: github.ref_name == 'main' && github.repository_owner == 'jdblischak' && github.event_name != 'pull_request' | |
runs-on: ubuntu-latest | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Create release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
if ! gh release list | cut -f3 | grep -q $the_date | |
then | |
echo "Creating new release: $the_date" | |
gh release create $the_date --notes "Nightly binaries created on $the_date" | |
else | |
echo "Release already exists: $the_date" | |
fi | |
upload-libtiledb: | |
runs-on: ubuntu-latest | |
needs: [create-release, libtiledb] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-libtiledb | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledb-linux | |
path: install-libtiledb | |
- name: Upload libtiledb to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
tar -C install-libtiledb -cvzf libtiledb-${the_date}.tar.gz ./ | |
gh release upload ${the_date} libtiledb-${the_date}.tar.gz --clobber | |
upload-tiledb-py: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledb-py] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledb-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-py-linux | |
- name: Upload tiledb-py to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
unzip -l tiledb-*-linux_x86_64.whl | |
gh release upload ${the_date} tiledb-*-linux_x86_64.whl --clobber | |
upload-tiledb-r: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledb-r] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledb-r | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-r-linux | |
- name: Upload tiledb-r to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
tar --list -f tiledb_*_R_x86_64-pc-linux-gnu.tar.gz | |
gh release upload ${the_date} tiledb_*_R_x86_64-pc-linux-gnu.tar.gz --clobber | |
upload-libtiledbvcf: | |
runs-on: ubuntu-latest | |
needs: [create-release, libtiledbvcf] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-libtiledbvcf | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledbvcf-linux | |
path: install-libtiledbvcf | |
- name: Upload libtiledbvcf to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
tar -C install-libtiledbvcf -cvzf libtiledbvcf-${the_date}.tar.gz ./ | |
gh release upload ${the_date} libtiledbvcf-${the_date}.tar.gz --clobber | |
upload-tiledbvcf-py: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledbvcf-py] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledbvcf-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledbvcf-py-linux | |
- name: Upload tiledbvcf-py to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
unzip -l tiledbvcf-*-linux_x86_64.whl | |
gh release upload ${the_date} tiledbvcf-*-linux_x86_64.whl --clobber | |
upload-libtiledbsoma: | |
runs-on: ubuntu-latest | |
needs: [create-release, libtiledbsoma] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-libtiledbsoma | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-libtiledbsoma-linux | |
path: install-libtiledbsoma | |
- name: Upload libtiledbsoma to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
tar -C install-libtiledbsoma -cvzf libtiledbsoma-${the_date}.tar.gz ./ | |
gh release upload ${the_date} libtiledbsoma-${the_date}.tar.gz --clobber | |
upload-tiledbsoma-py: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledbsoma-py] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledbsoma-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledbsoma-py-linux | |
- name: Upload tiledbsoma-py to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
unzip -l tiledbsoma-*-linux_x86_64.whl | |
gh release upload ${the_date} tiledbsoma-*-linux_x86_64.whl --clobber | |
upload-tiledbsoma-r: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledbsoma-r] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledbsoma-r | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledbsoma-r-linux | |
- name: Upload tiledbsoma-r to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
tar --list -f tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz | |
gh release upload ${the_date} tiledbsoma_*_R_x86_64-pc-linux-gnu.tar.gz --clobber | |
upload-tiledb-cloud-py: | |
runs-on: ubuntu-latest | |
needs: [create-release, tiledb-cloud-py] | |
permissions: | |
contents: write | |
env: | |
GH_TOKEN: ${{ github.token }} | |
TZ: "America/New_York" | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Download nightly-tiledb-cloud-py | |
uses: actions/download-artifact@v4 | |
with: | |
name: nightly-tiledb-cloud-py-linux | |
- name: Upload tiledb-cloud-py to release | |
run: | | |
the_date=$(date +%Y-%m-%d) | |
unzip -l tiledb_cloud-*-none-any.whl | |
gh release upload ${the_date} tiledb_cloud-*-none-any.whl --clobber | |
issue: | |
permissions: | |
issues: write | |
runs-on: ubuntu-latest | |
needs: [build-all] | |
if: ( failure() || cancelled() ) && github.repository_owner == 'jdblischak' && github.event_name == 'schedule' | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Open Issue | |
uses: TileDB-Inc/github-actions/open-issue@main | |
with: | |
name: centralized nightlies | |
label: nightly-failure | |
assignee: jdblischak | |
env: | |
TZ: "America/New_York" |