204: trial search improvements and PyPI trusted publisher#146
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- Add boolean-aware eligibility query handling for --mutation (OR/AND/NOT) - Add --criteria flag for free-text eligibility search - Push keyword into trial condition for search all relevance - Add PyPI publish via Trusted Publishers (OIDC, no token needed) - Bump version to 0.8.10 - Update README, CHANGELOG, SKILL.md for new features
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src/entities/trial.rs
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| if term.is_empty() { | ||
| return None; |
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split_boolean_expression rejects any operator token that has an empty left segment, so inputs like "dMMR AND NOT MSI-H" return None at the NOT token and are later treated as a single quoted literal instead of a boolean query. This breaks the new AND/NOT behavior for a common form (AND NOT ...) and can also poison eligibility post-filtering because the literal string gets tokenized as ordinary words.
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| - uses: dtolnay/rust-toolchain@stable | ||
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The pypi-build job builds non-host targets (for example aarch64-unknown-linux-gnu) but the dtolnay/rust-toolchain step does not request with: targets: ${{ matrix.target }}. On GitHub runners the default toolchain only has the host target installed, so cross-target maturin build --target ... fails with missing std for that target, which blocks pypi-publish because it depends on all matrix jobs.
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Cargo.lock
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| [[package]] | ||
| name = "biomcp-cli" | ||
| version = "0.8.9" | ||
| version = "0.9.0" |
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This commit sets the root package entry in Cargo.lock to 0.9.0 while Cargo.toml and pyproject.toml are 0.8.10, creating an inconsistent release state. That mismatch can cause confusing version reporting and lockfile churn when developers run packaging/release commands locally, since tooling expects the root package version to match the source manifests.
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…ockfile sync - Handle unary NOT in boolean expressions (e.g., "dMMR AND NOT MSI-H") - Add Rust target to pypi-build toolchain for cross-compilation - Regenerate Cargo.lock to match 0.8.10 version
Copy install.sh into docs/ so MkDocs serves it at biomcp.org/install.sh. Update all references from the raw.githubusercontent.com URL.
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Summary
--mutationflag (OR/AND/NOT operators)--criteriaflag for free-text eligibility text search against ClinicalTrials.govsearch allrelevance improvementContext
Project 204 fixes trial search gaps identified during the dMMR adjuvant endometrial cancer validation scenario. The three P0/P1 gaps (GAP-2 boolean mutation, GAP-1 criteria search, GAP-4 keyword pushdown) are addressed. The release workflow is updated to use PyPI Trusted Publishers instead of token-based auth.
Verification
cargo fmt --check: passcargo test: 373 passedpytest tests/: 6 passed (including MCP contract)