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mlinmlin
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rust bindings (#10)
1 parent 63d2060 commit 5746c66

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Lines changed: 721 additions & 9 deletions

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‎.github/workflows/build.yml‎

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@@ -12,6 +12,8 @@ jobs:
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: deps
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run: |
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sudo apt-get install -y clang-format cppcheck python3-pip
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run: pre-commit run --all-files
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- name: mvn spotless:check
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run: mvn spotless:check -B -f bindings/jdbc/genomicsqlite-jdbc/pom.xml
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- name: rust toolchain
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uses: actions-rs/toolchain@v1
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with:
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components: rustfmt, clippy
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toolchain: stable
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default: true
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- name: rust lint
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run: |
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cd bindings/rust
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./cargo check --no-default-features
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./cargo fmt -- --check
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test:
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runs-on: ubuntu-20.04
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BUILD_TYPE: [Debug, Release]
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: deps
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run: |
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sudo apt-get install -y $APT_DEPS
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sudo pip3 install --system $PIP_DEPS
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- name: rust toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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default: true
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- name: build
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run: cmake -DCMAKE_BUILD_TYPE=${{ matrix.BUILD_TYPE }} -B build . && cmake --build build -j $(nproc)
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- name: test
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runs-on: ubuntu-20.04
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: build loaders
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run: |
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sudo apt-get install -y $APT_DEPS
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docker run genomicsqlite ldd -v -r build/libgenomicsqlite.so
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echo "----"
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ldd -v -r build/libgenomicsqlite.so
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- name: rust toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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default: true
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- name: test portable .so
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run: env -C build ctest -V
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- name: test rust crate
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run: |
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set -e
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cp build/libgenomicsqlite.so bindings/rust
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bindings/rust/cargo test --release
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bindings/rust/cargo package --list | grep libgenomicsqlite.so
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- name: prepare artifacts
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run: cp build/libgenomicsqlite.so include/genomicsqlite.h .
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- uses: actions/upload-artifact@v2
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runs-on: macOS-10.15
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: dependencies
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run: |
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brew update
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brew upgrade
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brew install $BREW_DEPS
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/usr/local/bin/pip3 install $PIP_DEPS
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- name: rust toolchain
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uses: actions-rs/toolchain@v1
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with:
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toolchain: stable
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default: true
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- name: build environment
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run: |
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echo "PREFIX=$(brew --prefix)" >> $GITHUB_ENV
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echo "PATH=${PREFIX}/opt/python/libexec/bin:${PREFIX}/opt/sqlite/bin:${PATH}" >> $GITHUB_ENV
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echo "CFLAGS=-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include -march=sandybridge" >> $GITHUB_ENV
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echo "CXXFLAGS=-I$(brew --prefix)/include -march=sandybridge" >> $GITHUB_ENV
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echo "LDFLAGS=-L$(brew --prefix)/lib -L$(brew --prefix)/opt/sqlite/lib" >> $GITHUB_ENV
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# used by rusqlite:
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echo "SQLITE3_INCLUDE_DIR=$(brew --prefix)/opt/sqlite/include" >> $GITHUB_ENV
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echo "SQLITE3_LIB_DIR=$(brew --prefix)/opt/sqlite/lib" >> $GITHUB_ENV
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- name: build
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run: |
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CFLAGS="-I$(brew --prefix)/include -I$(brew --prefix)/opt/sqlite/include -march=sandybridge" \
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CXXFLAGS="-I$(brew --prefix)/include -march=sandybridge" \
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LDFLAGS="-L$(brew --prefix)/lib -L$(brew --prefix)/opt/sqlite/lib" \
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cmake -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_PREFIX_PATH=$(brew --prefix)/opt/sqlite \
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-B build .
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cmake -DCMAKE_BUILD_TYPE=Release \
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-DCMAKE_PREFIX_PATH=$(brew --prefix)/opt/sqlite \
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-B build .
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cmake --build build -j 4
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- name: otool
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run: otool -L build/libgenomicsqlite.dylib
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- name: ctest
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run: |
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export PREFIX=$(brew --prefix)
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export PATH=${PREFIX}/opt/python/libexec/bin:${PREFIX}/opt/sqlite/bin:$PATH
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cd build
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otool -L test/capi_smoke_test
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ctest -V
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- name: test rust crate
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run: |
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set -e
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cp build/libgenomicsqlite.dylib bindings/rust
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bindings/rust/cargo test --release
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bindings/rust/cargo package --list | grep libgenomicsqlite.dylib
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- name: prepare artifacts
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run: cp build/libgenomicsqlite.dylib include/genomicsqlite.h .
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- uses: actions/upload-artifact@v2
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- name: detect GIT_REVISION
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run: |
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cp include/genomicsqlite.h .
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git fetch origin --tags
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echo "GIT_REVISION=$(git describe --tags --always)" >> $GITHUB_ENV
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- uses: actions/upload-artifact@v2
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with:

‎CMakeLists.txt‎

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@@ -58,5 +58,6 @@ if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
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add_test(NAME smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} python3 ${CMAKE_CURRENT_SOURCE_DIR}/test/genomicsqlite_smoke_test.py)
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add_test(NAME capi_smoke_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_BINARY_DIR}/test/capi_smoke_test)
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add_test(NAME JdbcTests COMMAND ${GENOMICSQLITE_TEST_ENV} mvn test -B -f ${CMAKE_CURRENT_SOURCE_DIR}/bindings/jdbc/genomicsqlite-jdbc/pom.xml)
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add_test(NAME cargo_test COMMAND ${GENOMICSQLITE_TEST_ENV} ${CMAKE_CURRENT_SOURCE_DIR}/bindings/rust/cargo test --no-default-features)
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add_test(NAME pytest COMMAND ${GENOMICSQLITE_TEST_ENV} python3 -m pytest -xv -n 4 --tb=short ${CMAKE_CURRENT_SOURCE_DIR}/test)
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endif()

‎bindings/rust/.gitignore‎

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# Generated by Cargo
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# will have compiled files and executables
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debug/
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target/
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# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
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# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
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Cargo.lock
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# These are backup files generated by rustfmt
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**/*.rs.bk
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# Cargo.toml is generated from Cargo.toml.in by ./cargo
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Cargo.toml
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libgenomicsqlite.*

‎bindings/rust/Cargo.toml.in‎

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[package]
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name = "genomicsqlite"
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version = "{{GENOMICSQLITE_VERSION}}"
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authors = ["Mike Lin <dna@mlin.net>"]
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edition = "2018"
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license = "Apache"
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repository = "https://github.com/mlin/GenomicSQLite"
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documentation = "https://mlin.github.io/GenomicSQLite"
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include = ["src/**/*", "Cargo.toml", "libgenomicsqlite.*"]
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[features]
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# Use default-features=false to prevent bundling a platform-specific libgenomicsqlite into your
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# compilation unit. Then at runtime, you must either set env LIBGENOMICSQLITE to the library path,
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# or place it somewhere it'll be found by dlopen("libgenomicsqlite").
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default = ["bundle_libgenomicsqlite"]
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bundle_libgenomicsqlite = []
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[dependencies]
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json = "^0"
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tempfile = "^3"
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[dependencies.rusqlite]
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version = "^0"
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features = ["load_extension", "vtab"]
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[dev-dependencies.uuid]
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version = "^0"
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features = ["v4"]
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# TODO:
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# update Programming Guide

‎bindings/rust/cargo‎

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#!/bin/bash
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# wrapper for cargo that generates Cargo.toml from Cargo.toml.in, filling in git revision as
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# crate version
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set -e
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cd `dirname $0`
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revision="$(git describe --tags --dirty)"
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revision="${revision#v}" # strip 'v' prefix
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>&2 echo "$revision"
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sed "s/{{GENOMICSQLITE_VERSION}}/${revision}/" Cargo.toml.in > Cargo.toml
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cargo "$@"

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