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Add CI, fix the test build, commit Cargo.lock - #10

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Add CI, fix the test build, commit Cargo.lock#10
bmesuere wants to merge 4 commits into
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phase1/ci-and-test-fix

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@bmesuere

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Groundwork so that a release can be verified before it goes out. Four small commits, reviewable one at a time.

cargo test did not compile. fixtures is declared #[cfg(test)] pub mod, so its public items fall under the crate-level #![deny(missing_docs)], giving five hard errors under --test. cargo build skips the module entirely, which is why nothing ever surfaced it. With doc comments added, the 38 tests that were already there run and pass.

cargo fmt --check failed on a missing space in the impl added in 1f8e460 (Feb 2024).

There was no Cargo.lock and no .gitignore. Every build resolved fresh, which is how the README came to claim Rust 1.35 support while the real floor moved to 1.88, and git status was dirty after every build.

rust-version = "1.88" is the highest MSRV declared by anything in the locked tree. It comes from the icu crates via attohttpc -> url -> idna, so it is the HTTP client setting the floor, not our code. The msrv CI job builds against exactly that version, so if the number is wrong CI says so rather than a user finding out.

CI

Three jobs on PRs and pushes to master: build + test on stable, cargo fmt --check on nightly (.rustfmt.toml sets wrap_comments and comment_width, both still nightly-only, same as .hooks/pre-commit), and a build pinned to 1.88.

Clippy is deliberately left out. It currently reports 96 warnings, so switching it on means either a permanently red build or a large cleanup unrelated to this PR. It fits better alongside the dependency upgrades.

It uses dtolnay/rust-toolchain and Swatinem/rust-cache, both third-party but effectively standard for Rust CI. Happy to drop the cache action if you would rather keep the action surface minimal.

Not in here

  • Clippy, and the clap 2 / structopt / fst 0.3 upgrades that would clear the six RustSec advisories currently in the tree.
  • README corrections (it documents source install only, never cargo install umgap, points at the archived FragGeneScanPlusPlus, and links a case study path that no longer exists).

bmesuere and others added 4 commits August 18, 2026 14:27
`fixtures` is declared as `#[cfg(test)] pub mod`, so its public items fall
under the crate-level `#![deny(missing_docs)]`. Under `--test` that made five
hard errors and `cargo test` could not compile at all. `cargo build` skips the
module, which is why the release build never showed it.

With the doc comments added, the existing 38 tests run and pass.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
`cargo fmt --check` failed on a missing space in the impl added in 1f8e460.

There was also no .gitignore, so `git status` was dirty after every build.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Without a lock file every build resolves fresh, which is how the README came
to claim support for Rust 1.35 while the tree had quietly moved on.

1.88 is the highest MSRV declared by anything in the locked tree. It comes
from the icu crates, pulled in through attohttpc -> url -> idna. The CI job
added in the next commit builds against exactly this version, so the number
is checked rather than asserted.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Builds and tests on stable, checks formatting, and builds against the declared
minimum Rust version. Runs on pull requests and on pushes to master.

Formatting runs on nightly because .rustfmt.toml sets wrap_comments and
comment_width, which are still nightly-only. This matches .hooks/pre-commit.

Clippy is deliberately not included yet: it currently reports 96 warnings, so
turning it on would mean either a red build or a large unrelated cleanup. It
belongs with the dependency upgrades.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Copilot AI lite review requested due to automatic review settings August 18, 2026 12:27

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@bmesuere

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@ninewise Could you cargo add me, or ideally the github:unipept:core team, so we can release as well? The fix for #8 has been on master since last year, but was never tagged or published.

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