Set up cargo-release, add CHANGELOG, and fix repo URLs#15
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Add a release.toml so releases are cut locally from main with a single `cargo release` command: it runs the full CI gate, bumps the version, rolls the CHANGELOG's [Unreleased] section into a dated version section, commits, tags, pushes, and publishes to crates.io. Guarded to main-only via allow-branch. Add CHANGELOG.md (Keep a Changelog format) back-filled from the existing v0.1.0/v0.2.0/v0.2.1 GitHub releases, with the unreleased methylation work staged under [Unreleased]. Document the release flow in CONTRIBUTING.md.
Cargo.toml repository/homepage, the README and CONTRIBUTING clone commands, and the startup log banner all pointed at github.com/fulcrumgenomics/holodeck, but the actual repository (remote, releases, badges, CI) lives at fg-labs. Align them so the crates.io metadata and docs match where the code lives. The author email is left unchanged.
Consistency with the 0.2.0/0.2.1 entries, which group items under typed ### subsections.
📝 WalkthroughWalkthroughThis PR migrates the Holodeck repository ownership from fulcrumgenomics to fg-labs, documents newly implemented methylation simulation features in the changelog, and configures cargo-release automation for versioned publishing with pre-release CI gates and automatic changelog updates. ChangesRepository Transfer and Release Automation
Estimated code review effort🎯 2 (Simple) | ⏱️ ~12 minutes Possibly related PRs
Suggested reviewers
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🚥 Pre-merge checks | ✅ 4 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (4 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches📝 Generate docstrings
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@src/main.rs`:
- Line 83: Update the startup banner string in the log::info! call in main (the
log::info!("Holodeck by Fulcrum Genomics -
https://github.com/fg-labs/holodeck"); statement) to reflect the new ownership
and URL—replace "Fulcrum Genomics" with the new owner name and ensure the URL
matches the intended repository; keep the same log::info! invocation but change
only the literal message text.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
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Configuration used: Organization UI
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📒 Files selected for processing (6)
CHANGELOG.mdCONTRIBUTING.mdCargo.tomlREADME.mdrelease.tomlsrc/main.rs
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| let cmdline = std::env::args().collect::<Vec<_>>().join(" "); | ||
| log::info!("Holodeck by Fulcrum Genomics - https://www.github.com/fulcrumgenomics/holodeck"); | ||
| log::info!("Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck"); |
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Update the startup banner text to match the new ownership.
The URL is updated, but the log message still advertises Fulcrum Genomics. If this migration is meant to be complete, this string should be renamed too.
💡 Suggested fix
- log::info!("Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck");
+ log::info!("Holodeck - https://github.com/fg-labs/holodeck");📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| log::info!("Holodeck by Fulcrum Genomics - https://github.com/fg-labs/holodeck"); | |
| log::info!("Holodeck - https://github.com/fg-labs/holodeck"); |
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@src/main.rs` at line 83, Update the startup banner string in the log::info!
call in main (the log::info!("Holodeck by Fulcrum Genomics -
https://github.com/fg-labs/holodeck"); statement) to reflect the new ownership
and URL—replace "Fulcrum Genomics" with the new owner name and ensure the URL
matches the intended repository; keep the same log::info! invocation but change
only the literal message text.
1 participant
Summary
Sets up local-from-
mainreleases withcargo release, adds aCHANGELOG.md, documents the release flow, and fixes repo-URL inconsistencies.release.tomlA single
cargo release patch|minor|major --execute(dry-run by default) now: runs the full CI gate (ci-fmt && ci-lint && ci-test) as a pre-release hook, bumps the version inCargo.toml/Cargo.lock, rolls the CHANGELOG's[Unreleased]section into a dated version section, commits, creates an annotatedvX.Y.Ztag, pushes, and publishes to crates.io. Guarded tomain-only viaallow-branch.CHANGELOG.mdNew, in Keep a Changelog format, back-filled from the existing v0.1.0/v0.2.0/v0.2.1 GitHub releases. The unreleased methylation/bisulfite stack is staged under
[Unreleased].cargo releaserolls this forward automatically viapre-release-replacements.Repo URL fix
Cargo.tomlrepository/homepage, the README and CONTRIBUTING clone commands, and the startup log banner pointed atgithub.com/fulcrumgenomics/holodeck, but the repo actually lives atfg-labs/holodeck(remote, releases, badges, CI). Aligned them so the crates.io metadata and docs match reality. The author email is intentionally unchanged.Docs
CONTRIBUTING.mdgains a "Releasing" section and the previously-undocumentedsecurity/cargo auditCI job.Notes
gh release create vX.Y.Z --generate-notesis still a manual step, documented in CONTRIBUTING.holodeckis already published and owned on crates.io, sopublish = trueis safe.cargo releasedry-run: regexes match exactly once, the tag (v0.2.2) matches existing convention, and the CHANGELOG diff is well-formed.Test plan
cargo ci-fmt,cargo ci-lint,cargo ci-test(418 tests pass)cargo release patchdry-run validates config + CHANGELOG replacementSummary by CodeRabbit
Documentation
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