splitGraph 0.3.0

This release broadens the vocabulary of leakage relations splitGraph can model, hardens the split_spec interchange format into a formally specified contract, and demonstrates that contract across a language boundary. splitGraph continues to stop at the constraint / split_spec boundary: generating folds, fitting models, applying purge/embargo, and producing statistical leakage evidence remain the responsibility of downstream consumers such as bioLeak.

New features

New leakage relations

• Site node type and sample_collected_at_site edge. Multi-site / multi-center structure is now a first-class typed relation. graph_from_metadata() auto-detects a site_id column; validate_graph() flags samples assigned to multiple sites (sample_multiple_site_assignments); derive_split_constraints(mode = "site") groups samples by collection site (and rejects ambiguous multi-site assignments); and as_split_spec() carries site_group as a blocking annotation in sample_data. Site also participates in mode = "composite" derivations and the typed plot() layout.
• Region node type and sample_located_in_region edge. Categorical tissue / anatomical region structure is now a first-class typed relation, mirroring Site: region_id auto-detection, multi-region validation (sample_multiple_region_assignments), derive_split_constraints(mode = "region"), a region_group blocking annotation in split_spec, and composite / plot support.
• Platform node type and sample_run_on_platform edge, plus platform and assay constraint modes. Sequencing / measurement-platform structure is now a first-class typed relation: graph_from_metadata() auto-detects a platform_id column, validate_graph() flags samples run on multiple platforms (sample_multiple_platform_assignments), and derive_split_constraints(mode = "platform") groups samples by platform. mode = "assay" reuses the existing sample_measured_by_assay relation to group by assay / modality. Both carry a blocking annotation in split_spec (platform_group, assay_group), participate in mode = "composite" (via = c("Subject", "Platform")), and are covered by the typed plot() layout. The assay_uses_platform edge (Assay -> Platform) is also part of the schema for manually encoding which platform an assay runs on.
• Pairwise (thresholded) leakage relations: relatedness and spatial modes. Some leakage sources are pairwise and continuous rather than clean groups. Two new undirected, thresholded edge types model them — subject_related_to (genetic relatedness between subjects) and sample_adjacent_to (spatial proximity between samples) — together with the edge-building helpers relatedness_edges_from_kinship(pairs, threshold) and spatial_edges_from_coords(coords, radius). derive_split_constraints(mode = "relatedness") and mode = "spatial" form groups as connected components (transitive closure) over the thresholded edges, so a chain of individually near neighbours still lands in one group — a grouping that column-based approaches structurally cannot express. Both modes honor the samples= subset (components are recomputed within the subset, so an excluded bridge sample cannot leak structure across the split).

Interchange-format hardening

• Formal JSON Schema. The dependency_graph and split_spec on-disk formats now have formal JSON Schemas (Draft 2020-12) shipped in inst/schema/, and every written file references its schema via a $schema key.
• JSON validators. validate_graph_json() and validate_split_spec_json() check a handoff file against the contract — required fields, value types, node/edge-type enumerations, and referential integrity of edge endpoints — with no dependency beyond jsonlite.
• Schema-version policy and one-shot upgraders. schema_version is now "0.2.0", and the compatibility rule is explicit and enforced: the major version is the compatibility boundary, so files sharing the installed major (including all "0.1.0" files) load silently, while a differing major loads with a warning. migrate_dependency_graph_json() and migrate_split_spec_json() upgrade an older file in place, filling fields introduced since it was written and stamping the current version and $schema.
• Provenance. split_spec metadata now records derivation provenance (splitgraph_version, derived_at) alongside the existing source_mode / source_strategy / relations_used.

Cross-language interoperability

• Python reference consumer. A pure-Python reader (inst/python/splitspec/) parses the split_spec JSON and exposes the grouping, ordering, and stratum annotations needed to drive scikit-learn GroupKFold / StratifiedGroupKFold / TimeSeriesSplit (the reader itself needs only the standard library). A conformance script (inst/python/conformance.py) and an accompanying R test assert that the Python reader recovers exactly the grouping (grouping_vector()) and order_rank that R emitted; the test is skipped when python3 is absent and never runs on CRAN.

Bug fixes

• Composite-strict subset scoping. derive_split_constraints(mode = "composite", strategy = "strict", samples = ...) now recomputes connected components within the requested subset. Previously two in-subset samples connected only through an out-of-subset sample could inherit a shared group, silently leaking excluded structure into the split.
• Mode-aware leakage summaries. summarize_leakage_risks() now reports a severed column indicating whether the chosen constraint mode structurally eliminates each leakage path (TRUE/FALSE), or NA when no constraint is supplied. Previously the same risk report was returned regardless of the mode.
• query_paths() truncation is now visible. When the search hits the finite max_length cap, the result metadata carries a truncated = TRUE flag so suppressed longer paths are no longer silent.
• Timestamp round-trips. A missing or unparseable created_at now round-trips as NA (POSIXct) instead of falling back to the current time.
• split_spec JSON round-trip fidelity. The new site_group / region_group / platform_group / assay_group columns are written and read back correctly; earlier development builds dropped them on serialization.

Breaking changes

• Removed the unused leakage_constraint() constructor and its print / summary / as.data.frame methods. The object was exported but never produced or consumed anywhere in the package; leakage_risk_summary() (produced by summarize_leakage_risks()) is the supported leakage-reporting type and is unaffected.
• The data-model schema_version moved from "0.1.0" to "0.2.0". This is backward compatible — existing "0.1.0" files load without warning — but the stamped version in newly written files changes.

Documentation and infrastructure

• New vignette cross-language-handoff: the full R -> JSON -> Python -> scikit-learn path, showing split_spec as an interchange format rather than downstream plumbing.
• New vignette modeling-structure: modeling site, platform, assay, relatedness, and spatial structure end to end.
• The README gains a “Scope & Relationship to bioLeak” section, and the ?splitGraph package doc now states scope and non-goals explicitly.
• A contract test (Suggests: bioLeak, skipped if absent) pins the seam to the reference consumer, asserting that a splitGraph split_spec satisfies bioLeak::as_leaksplits().
• The package ships GitHub Actions workflows (multi-OS R-CMD-check, test-coverage) and a JOSS paper.md framed on the representation and interchange-format contribution.
• stats and utils are now declared in Imports (both were already used).

splitGraph 0.2.0

New features

• JSON serialization for both core handoff objects: write_dependency_graph() / read_dependency_graph() and write_split_spec() / read_split_spec(). The on-disk format is documented under ?write_dependency_graph and ?write_split_spec, carries a schema_version field, and round-trips NA values faithfully. This makes splitGraph objects portable across R sessions and across language boundaries (Python, Julia, CLI tools — anything that can read JSON). Requires jsonlite (added to Suggests); a helpful error is raised if it is not installed.
• A new vignette, adapter-cookbook, walks through three small adapter patterns: a base-R leave-one-group-out adapter (executed), a grouped-CV adapter built on rsample::group_vfold_cv() (illustrative), and an ordered-evaluation adapter built on rsample::rolling_origin() (illustrative). It also shows the JSON cross-language handoff path.
• validate_graph() and validate_depgraph() now accept a documented validation_overrides argument. Currently supported override: allow_multi_subject_samples (default FALSE); when TRUE, samples linked to multiple subjects are not flagged by the semantic validator and derive_split_constraints(mode = "subject") keeps the first listed assignment instead of erroring. The override mechanism is now first-class and merges into any graph-level override for the duration of the call only.
• derive_split_constraints(mode = "subject") honors allow_multi_subject_samples consistently with validate_graph(). When the override is active and ambiguity exists, the choice is recorded in metadata$warnings so it is not invisible.
• query_paths() now applies a finite default safety cap on max_length (8 edges) so that igraph::all_simple_paths() cannot blow up on dense graphs. Pass max_length = Inf to opt out and search exhaustively, or any non-negative integer for an explicit cap. Negative values and non-numeric inputs are rejected with a clear error.

Improvements

• build_dependency_graph() returns a more useful error when edge endpoints don’t match any node ID and the mismatch looks like a prefix problem (e.g. edges built with from_prefix = TRUE but nodes built with prefix = FALSE). The error now points at the likely cause.
• graph_from_metadata() warns when it constructs Outcome nodes from a numeric outcome_value column (which produces outcome:0 / outcome:1 nodes that are usually not what the user wants). To silence the warning, pass outcome_id (character class label) instead, or coerce outcome_value to character first.
• The data-model schema_version is now explicitly decoupled from the package version. Bumping the package will not bump the schema; only an explicit, documented schema change should.

Deprecations

These remain functional in 0.2.0 but emit .Deprecated() warnings and are scheduled for removal in a future release. Use the canonical names instead:

• validate_graph(checks = …) → use levels = … and severities = ….
• build_depgraph() → use build_dependency_graph().
• validate_depgraph() → use validate_graph().
• new_depgraph_nodes() → use graph_node_set().
• new_depgraph_edges() → use graph_edge_set().
• new_depgraph() → use dependency_graph().

Documentation

• README and the main vignette now use outcome_id (character) in their quick-start example instead of numeric outcome_value, matching the new warning behavior.
• The validation_overrides parameter and the allow_multi_subject_samples key are now documented on ?build_dependency_graph / ?validate_graph.

splitGraph 0.1.0

Initial public release. Highlights:

• Typed dependency-graph construction from canonical metadata via graph_from_metadata(), or from explicit node and edge tables via create_nodes() / create_edges() / build_dependency_graph().
• Structural, semantic, and leakage-relevant validation (validate_graph()), typed query helpers, and projected sample-dependency detection.
• Split-constraint derivation (derive_split_constraints()) for subject, batch, study, time, and composite modes, translated into a stable, tool-agnostic split_spec via as_split_spec() with preflight validation and leakage-risk summaries.
• plot() method for dependency_graph with a typed, layered layout, per-type node colors, and an auto-generated node-type legend.
• splitGraph emits split_spec objects without runtime dependencies on downstream tooling. Adapters are expected to live in consumer packages (e.g. packages built on top of rsample) so that splitGraph itself stays neutral.

See the README for a full feature overview and a runnable Quick Start.