Use single quote to quote SQL string literal #635
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| 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 |