Patch htslib-rs/noodles git deps to rv-managed local paths#76
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bcftools-rs and samtools-rs (and htslib-rs itself) now declare htslib-rs and noodles as git deps. Cargo identifies them by URL, so this workspace can [patch] both URLs to the single rv-managed local checkout under vendor/rust/, collapsing what cargo would otherwise see as three independent path sources into one lockfile entry. Also set net.git-fetch-with-cli so cargo uses the system git for the upstream verification fetch (respects ssh config and credentials).
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Keeping these as local edits on madhava/libs for now — will land via the branch's existing flow once verified end-to-end. |
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Summary
[patch."https://github.com/madhavajay/htslib-rs.git"]and[patch."https://github.com/madhavajay/noodles.git"]torust/Cargo.toml, redirecting to the rv-managed checkouts undervendor/rust/..cargo/config.tomlsettingnet.git-fetch-with-cli = trueso cargo's upstream verification fetch uses the user's git (respects SSH/credentials).Why
bcftools-rsandsamtools-rs(andhtslib-rsitself) now consumehtslib-rs/noodlesas git deps (see madhavajay/bcftools-rs#274, samtools-rs#59, htslib-rs#14). Cargo identifies them by URL, so this workspace's[patch]collapses three would-be path sources into one rv-managed local crate per dep — eliminating cargo'spackage collision in the lockfileerror.Test plan
cargo check --workspaceresolves withoutpackage collision in the lockfile