Use single quote to quote SQL string literal (#24) #636
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: build | |
| on: [push, pull_request] | |
| env: | |
| APT_DEPS: libzstd-dev samtools tabix libhts-dev pigz python3-pip libcurl4-openssl-dev | |
| BREW_DEPS: zstd samtools pigz coreutils sqlite | |
| PIP_DEPS: pytest pytest-xdist | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: deps | |
| run: | | |
| sudo apt-get -qq update | |
| sudo apt-get install -y clang-format cppcheck python3-pip | |
| sudo pip3 install --system pre-commit $PIP_DEPS black flake8 pylint | |
| - name: pre-commit | |
| run: pre-commit run --all-files | |
| - name: mvn spotless:check | |
| run: mvn spotless:check -B -f bindings/jdbc/genomicsqlite-jdbc/pom.xml | |
| - name: rust toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| components: rustfmt, clippy | |
| toolchain: stable | |
| default: true | |
| - name: rust lint | |
| run: | | |
| cd bindings/rust | |
| ./cargo check --no-default-features | |
| ./cargo fmt -- --check | |
| test: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| BUILD_TYPE: [Debug, Release] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: deps | |
| run: | | |
| sudo apt-get -qq update | |
| sudo apt-get install -y $APT_DEPS | |
| sudo pip3 install --system $PIP_DEPS | |
| - name: rust toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| default: true | |
| - name: build | |
| run: cmake -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -B build . && cmake --build build -j $(nproc) | |
| - name: test | |
| run: env -C build SQLITE_WEB_LOG=99 ctest -V | |
| linux-x86-64-so: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: build loaders | |
| run: | | |
| sudo apt-get -qq update | |
| sudo apt-get install -y $APT_DEPS | |
| sudo pip3 install --system $PIP_DEPS | |
| cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' -B build . && cmake --build build -j $(nproc) | |
| rm build/libgenomicsqlite.so | |
| sudo apt-get remove -y libzstd-dev # should be linked into libgenomicsqlite.so | |
| - name: build portable .so in docker | |
| run: docker build -t genomicsqlite . && docker run -v $(pwd):/mnt --rm genomicsqlite cp /usr/local/lib/{libgenomicsqlite.so,libsqlite3.so.0} /mnt/build/ | |
| - name: symbols & digests | |
| run: | | |
| readelf -d build/libgenomicsqlite.so | |
| ldd -r build/libgenomicsqlite.so | |
| echo "----" | |
| echo "libgenomicsqlite.so GLIBC version requirements:" | |
| objdump -t build/libgenomicsqlite.so | grep -o 'GLIBC_.*' | sort -Vr | head -n1 | |
| objdump -t build/libgenomicsqlite.so | grep -o 'GLIBCXX_.*' | sort -Vr | head -n1 | |
| echo "libsqlite3.so.0 GLIBC version requirements:" | |
| objdump -t build/libsqlite3.so.0 | grep -o 'GLIBC_.*' | sort -Vr | head -n1 | |
| echo "----" | |
| sha256sum build/libgenomicsqlite.so build/libsqlite3.so.0 | |
| sudo cp build/libsqlite3.so.0 /usr/local/lib | |
| sudo ldconfig | |
| - name: rust toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| default: true | |
| - name: test portable .so | |
| run: env -C build SQLITE_WEB_LOG=99 ctest -V | |
| - name: test rust crate | |
| run: | | |
| set -e | |
| cp build/libgenomicsqlite.so bindings/rust | |
| SQLITE_WEB_LOG=99 bindings/rust/cargo test --release | |
| bindings/rust/cargo package --list | grep libgenomicsqlite.so | |
| - name: prepare artifacts | |
| run: cp build/{libgenomicsqlite.so,libsqlite3.so.0} . | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: libgenomicsqlite.so | |
| path: libgenomicsqlite.so | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: libsqlite3.so.0 | |
| path: libsqlite3.so.0 | |
| macOS-x86-64-dylib: | |
| runs-on: macOS-11 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: dependencies | |
| run: | | |
| rm -f /usr/local/bin/2to3 # https://github.com/pypa/pipenv/issues/3831 | |
| brew update || (sleep 2; brew update) | |
| for dep in $BREW_DEPS ; do | |
| brew install $dep || brew upgrade $dep | |
| done | |
| pip install $PIP_DEPS | |
| - name: rust toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| default: true | |
| - name: build environment | |
| run: | | |
| echo "PATH=$(brew --prefix)/bin:$(brew --prefix)/opt/sqlite/bin:${PATH}" >> $GITHUB_ENV | |
| echo "CFLAGS=-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include -march=ivybridge" >> $GITHUB_ENV | |
| echo "CXXFLAGS=-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include -march=ivybridge" >> $GITHUB_ENV | |
| echo "LDFLAGS=-L$(brew --prefix)/lib -L$(brew --prefix)/opt/sqlite/lib" >> $GITHUB_ENV | |
| # used by rusqlite: | |
| echo "SQLITE3_INCLUDE_DIR=$(brew --prefix)/opt/sqlite/include" >> $GITHUB_ENV | |
| echo "SQLITE3_LIB_DIR=$(brew --prefix)/opt/sqlite/lib" >> $GITHUB_ENV | |
| - name: build | |
| run: | | |
| cmake -DCMAKE_BUILD_TYPE=Release \ | |
| -DCMAKE_PREFIX_PATH=$(brew --prefix)/opt/sqlite \ | |
| -B build . | |
| cmake --build build -j 4 | |
| - name: symbols & digests | |
| run: | | |
| otool -L build/libgenomicsqlite.dylib | |
| sha256sum build/libgenomicsqlite.dylib | |
| - name: ctest | |
| run: | | |
| cd build | |
| otool -L test/capi_smoke_test | |
| SQLITE_WEB_LOG=99 ctest -V | |
| - name: test rust crate | |
| run: | | |
| set -e | |
| cp build/libgenomicsqlite.dylib bindings/rust | |
| SQLITE_WEB_LOG=99 bindings/rust/cargo test --release | |
| bindings/rust/cargo package --list | grep libgenomicsqlite.dylib | |
| - name: prepare artifacts | |
| run: cp build/libgenomicsqlite.dylib include/genomicsqlite.h . | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: libgenomicsqlite.dylib | |
| path: libgenomicsqlite.dylib | |
| artifacts: | |
| runs-on: ubuntu-20.04 | |
| needs: [linux-x86-64-so, macOS-x86-64-dylib] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: fetch libgenomicsqlite.so | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: libgenomicsqlite.so | |
| - name: fetch libsqlite3.so.0 | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: libsqlite3.so.0 | |
| - name: fetch libgenomicsqlite.dylib | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: libgenomicsqlite.dylib | |
| - name: detect GIT_REVISION | |
| run: | | |
| cp include/genomicsqlite.h . | |
| echo "GIT_REVISION=$(git describe --tags --always)" >> $GITHUB_ENV | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: GenomicSQLite-${{ env.GIT_REVISION }} | |
| path: | | |
| LICENSE | |
| genomicsqlite.h | |
| libgenomicsqlite.so | |
| libgenomicsqlite.dylib | |
| - name: build jar | |
| run: | | |
| cp libgenomicsqlite.so libgenomicsqlite.dylib bindings/jdbc/genomicsqlite-jdbc/src/main/resources/ | |
| mvn deploy -Drevision=${{ env.GIT_REVISION }} -B -f bindings/jdbc/genomicsqlite-jdbc/pom.xml | |
| - name: digests | |
| run: sha256sum *genomicsqlite* bindings/jdbc/genomicsqlite-jdbc/target/genomicsqlite*.jar libsqlite3.so.0 | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: genomicsqlite-jdbc-${{ env.GIT_REVISION }} | |
| path: bindings/jdbc/genomicsqlite-jdbc/target/mvn-repo |