0.7.0 - layout invariants, fragility reduction, and new directives

A big one! 228 commits since 0.6.1, with the layout engine considerably more robust and a handful of nice new directives to play with.

Existing .mmd files render with no changes - everything new here is additive.

Highlights

Embed your maps anywhere

nf-metro render mypipeline.mmd --format html now produces a self-contained, interactive HTML file you can drop straight into a docs page or a blog post (#374).

Three new %%metro directives

• off_track: ... lifts file inputs above the line tracks so they sit clear of the metro lines instead of breaking them (#265). Great for FASTA/GTF inputs hanging off a workflow.
• center_ports: true (or --center-ports) centres inter-section ports on the shorter section, which tidies up many fan-in/fan-out cases (#320).
• legend_min_height: ... lets you reserve a minimum legend height so a tall map's legend doesn't look stranded.

Richer file icons

• New files (stacked) and dir (folder) icon types, joining the existing single file (#175).
• All three accept an optional caption: node[Label]:::files:Read 1, Read 2 to call out exactly what's flowing in (#269).

Optional / conditional paths

Lines can now be dashed or dotted to indicate optional or conditional routes through the pipeline. Add a fourth field to your %%metro line: directive:

%%metro line: qc | Quality Control | #ff8800 | dashed

Gallery additions

• differentialabundance pipeline metro map (#319)
• genomeassembly example
• New topology fixtures: upward_bypass, mismatched_tracks, fan_in_merge
• A new nf-core Pipelines gallery page on the docs site (#239)

Better-looking maps out of the box

• Sections are now numbered in visual reading order, so "1, 2, 3..." matches how you actually scan the map (#217)
• Fan-in merge junctions route cleanly onto the trunk (#207)
• Per-line path grouping gives a consistent line z-order, so the colours stack predictably where lines cross (#305)
• Animated balls no longer fly off-piste at merge junctions (#251)
• Dozens of fan-out, fan-in, bypass, and off-track routing fixes - too many to list individually, but the cumulative effect on real pipelines is significant

Under the hood

This release also represents a substantial reliability push:

• A layout invariant framework with phase-boundary guards (compute_layout(validate=True)), full-corpus parametrised tests, and the C13 row-gap runtime guard (#326, #371). When the layout engine misbehaves, you find out at the offending phase, not three phases later.
• The layout pipeline is now organised into six named stages with flat Stage X.Y naming - much easier to reason about than the old monolithic phase 13 (#375, #376).
• Major fragility-reduction series (#340 and follow-ups) tightening clearances, hoisting helpers, and documenting load-bearing phase pairs.
• Performance work: spatial-index validation guards with closed-form intersection (#368), cached station_lines() (~40 call sites, O(1) amortised), pre-computed diamond groups.
• Several large refactors splitting 300-500-line functions into focused helpers, deduplicating section iteration, unifying diagonal routing, and centralising corner-radius math.

Contributing

A new CONTRIBUTING.md covers the visual review workflow, the invariant ratchet, and git hygiene expectations (#341). If you've been meaning to file that "why does my map look like THIS?" issue, now's a good moment.

Full Changelog: 0.6.1...0.7.0