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Paul"},"license":"SEE LICENSE IN ./LICENSE","homepage":"https://github.com/stjude/proteinpaint#readme","repository":{"url":"git+https://github.com/stjude/proteinpaint.git","type":"git","directory":"rust"},"description":"Rust-based utilities for proteinpaint","maintainers":[{"name":"siosonel","email":"siosonel@gmail.com"},{"name":"ppteamuser","email":"ppteamuser@STJUDE.ORG"}],"readme":"# Rust-compiled utilities\n\nThis directory holds the source code for rust-compiled utilities.\n\n\n## Rust version\n\nThe current rust version is defined in `rust/rust-toolchain.toml`. When updating the rust version inside the rust docker image the `container/rust/build.sh` script parses the rust version from `rust-toolchain.toml` into `container/rust/Dockerfile` at runtime. This ensures consistency between local PP builds and the docker container in CI and production.\n\nThe Github Actions workflow file `.github/workflows/CD-rust-build.yml` and `.github/workflows/CI-unit.yml` also parses the rust version from the `rust-toolchain.toml` to ensure the correct rust version is used for compiling the current rust code.\n\nWhen bumping the rust version and publish the new rust build env image using:\n\nhttps://github.com/stjude/proteinpaint/actions/workflows/CD-publish-rust-bookworm-env-image.yml\n\nFor publishing updated rust binaries, use this workflow.\n\nhttps://github.com/stjude/proteinpaint/actions/workflows/CD-publish-rust-binaries.yml\n\n## Code layout\n\nAll source code files should be directly under the `src/` directory. For a source\ncode file to be compiled, create a `[[bin]]` entry for it in the Cargo.toml file:\n\n```toml\n[[bin]]\nname=\"tool0\"\npath=\"src/tool0.rs\"\n\n[[bin]]\nname=\"othertool1\"\npath=\"src/othertool1.rs\"\n```\n\nNote that the default package.autobins has been disabled, so that we avoid using\nthe src/bin subdirectory to hold uncompiled source code files. The convention in\nthe Proteinpaint project is to put bundled or compiled code under a `bin/` folder,\nwhich goes against rust cargo's assumptions of having source code under `src/bin`.\n\n## Using from nodejs\n\n```js\n// Assuming a js or ts file from server/src \n\nimport { run_rust } from '@sjcrh/proteinpaint-rust'\n\n\n// 'indel' may be replaced by any binary name as specified in Cargo.toml\nconst out = await run_rust('indel', input_data)\n```\n\n## Test\n\nFor running the tests written in nodejs, from the `proteinpaint` directory run,\n\n```bash\nnpm run test:unit --workspace=\"rust\"\n```\n\nFor running the tests written in native rust, from the `proteinpaint/rust` directory run.\n```bash\ncargo test\n```\n\nFor running AI tests using cargo, they need to be run locally since CI does not have access to the LLM server. These tests are \"ignored\" in CI and need the `ignored` flag to be run. These tests must be run from the `proteinpaint/rust` directory. 3 tests wil be run using the command below. One each to see if the SJ and ollama server are accessible and the third one is unit test for the actual ai chatbot. \n\n```bash\ntime cargo test -- --ignored --nocapture\n```\n\n## Build\n\n```bash\nnpm run build # cargo build --release\n```\n\nThe compiled dependencies and target binaries will be generated under `./target/release`.\n\n## Release\n\nUse Github Actions to coordinate the release of related package updates.\nThe package versioning, build, and deployment uses the standard npm tooling under the hood\n(`version`, `pack`, and `publish`, respectively).\n","readmeFilename":"README.md"}