FORMAT.md

# Data contract, archive schema version 1

Toolkit 1.3.0 retains the legacy archive/record version for compatibility and adds
version-1 registered benchmark artifacts. See [ARTIFACTS.md](ARTIFACTS.md) and
[BENCHMARK_WORKFLOW.md](BENCHMARK_WORKFLOW.md) for the strict benchmark contract.
Runs without `benchmark_contract` remain legacy/general-purpose runs.


Raw files are immutable through the application and authoritative. The normalized
records are an analysis representation. They do not replace the source data or
define the scientific meaning of the producer's metrics.

## One normalized record

One record represents a model result for one question, variant, filter, and repeat
within a run. A paired input line produces two records.

| Field | Meaning |
|---|---|
| `schema_version` | Integer `1`. |
| `run_id` | Run folder identifier. |
| `question_id` | Persistent identity of the underlying question; shared by its variants. |
| `variant_id` | E.g. `original`, `rephrased`, or a distinct rephrasing identifier. |
| `benchmark` | Benchmark/task name, supplied by the record or run metadata. |
| `script` (optional in legacy records) | Script identifier; separate scripts never share an item identity. Required for strict benchmark records. |
| `language` | Language identifier or null. No language is guessed from a path. |
| `model` | Evaluated model; must match run metadata. |
| `rephrasing_model` | Model that generated the variant, when known. |
| `filter` | Harness processing/filter pipeline; defaults to `none`. |
| `repeat_id` | Distinguishes deliberate repeated measurements; defaults to `0`. |
| `identity_scope` | `stable` or `run-local`. Run-local identities are not paired. |
| `input` | Available question, prompt, choices, document, and/or model request arguments. |
| `target` | Supplied answer/reference. Paired choice keys use `{"index": 0}`. |
| `prediction` | Supplied prediction. Paired choice results use index/index_norm/index_pmi. |
| `correct` | Boolean true/false, or null when correctness is unavailable/ambiguous. |
| `scores` | Existing likelihoods and score arrays; no measurements are invented. |
| `metrics` | Other producer metrics retained without redefining their meaning. |
| `response` | Generated text or original harness raw/filtered responses. |
| `source` | Archived raw file path and one-based source line number. |
| `warnings` | Interpretation/provenance caveats associated with this record. |

Within a run, the unique key is `(benchmark, language, question_id, variant_id,
filter, repeat_id)`. Names and ordered answer choices are significant. A
comparison joins the same key without variant_id, explicitly selecting the two
variants/runs. A rephrasing can reorder choices; correctness must use its own key.

## Stable IDs

Automatic lookup checks `original_question_id`, `doc.original_question_id`,
`question_id`, `doc.question_id`, `id`, and `doc.id`, in that order. The producer
must ensure those IDs identify the same underlying question across versions.
`--id-field some.dotted.path` overrides the lookup. Selecting `doc_id` still marks
an identity as run-local because harness enumeration is not a persistent identity.

Without a stable ID, a source/line-derived identity prevents accidental record
collisions, but the record is excluded from pair analysis. It still contributes
to independent summaries when correctness is available.

## Paired adapter

Required shape: top-level identity/benchmark/model context and `original` plus
`rephrased` objects. Each variant may contain question, choices, correct_index,
pred_acc, pred_acc_norm, pred_acc_pmi, logprobs, logprobs_norm, logprobs_pmi,
generated_text, and additional metrics. Indices are zero-based nonnegative
integers, and arrays must agree with supplied choice counts.

`pred_acc` names a choice index. Correctness is obtained by comparing it with a
known correct_index for that version, never by converting the index to Boolean.
Normalized and PMI prediction indices are retained but do not silently replace
the raw correctness criterion used by the default summary.

An explicit variant answer key takes precedence. A shared top-level key can be
used for the original, and for a rephrase with identical explicit choices. Where
choice order is unavailable, run metadata `shared_answer_key: true` explicitly
asserts that sharing the key is valid; the assertion is recorded as a warning.
Explicitly different choice ordering still requires a per-variant key.

## Harness adapter

Accepts `doc`, `resps` and/or `filtered_resps`, `target`, and optional `arguments`,
filter, metric names/values, and hashes. The saved logger format can have
`arguments` as a `gen_args_N` object and likelihood pair values as strings;
those supported numeric likelihood values are converted to numbers in `scores`,
while original responses remain preserved.

The harness's `metrics` may be a list of names whose values are at the top level
or a dictionary. By default, a binary `acc` or `exact_match` populates `correct`.
Set run metadata `correctness_metric` to choose another explicit binary metric,
for example `acc_norm`. A nonbinary value is not coerced into correctness.

Likelihoods remain in request order. Task-specific PMI requests and filtering can
change request meaning, so the adapter does not infer a multiple-choice winner
from the largest observed likelihood. Original request arguments and responses
remain available for task-aware analysis.

## Canonical adapter

Use `--format canonical` for producers that write this contract directly.
`question_id` and `variant_id` are required (unless explicitly selected through
CLI options), and benchmark/model/run context must be present or supplied by
the destination run. Run/model conflicts are rejected. The importer supplies its
own archived source location; records imported into another run must first have
their old run_id removed or intentionally updated by the producer.

## Validation and missing values

Inputs must be UTF-8 JSON Lines with one object per nonblank line. A UTF-8 BOM
on the first line and CRLF line endings are accepted and preserved in raw files.
Duplicate JSON keys, non-finite numbers, invalid field types, duplicate record
identities, and inconsistent supplied choice counts are rejected. Failed batch
imports publish no partial data.

Null means unknown, not zero. Metrics with different scientific definitions must
not be compared solely because their names match. Store producer version and
metric definitions in run metadata or attachments.

Manifests contain file paths, original and normalized SHA-256 hashes, record
counts, source basenames, timestamps, metadata, attachment hashes/sizes, and
open/sealed status. Validation checks registered bytes, record schema, source
line references, duplicate identities, counts, and untracked files in managed
run directories. Each import also records format, variant override, ID selection,
and normalizer version. Validation does not reconstruct all derived records by
rerunning the adapter or verify the scientific correctness of a model score.

## Item-level comparison reports

`compare RUN --items REPORT.html` adds an item-level report to the ordinary
comparison summary. `.html`, `.csv`, and `.jsonl` select the format; an explicit
`--format html|csv|jsonl` with `--items` overrides suffix inference. `--baseline`,
`--variant`, and `--other-run` select the same records for the summary and report.
Known conflicting dataset revisions in a cross-run comparison are rejected.

One report item represents the union of stable identities on the two selected
sides. Its identity is `(benchmark, language, script, question_id, filter, repeat_id)`.
Matched items contain both records; unmatched items retain the available side.
Run-local identities are excluded, with counts for each side in the summary.
Duplicate stable identities are an error, not an arbitrary choice of one record.

Outcome categories distinguish both correct, both wrong, correct to wrong,
wrong to correct, unscored pairs, and items present on only one side. Unknown
correctness does not become an incorrect answer. Aggregate accuracy and its delta
use only matched pairs with known correctness on both sides.

- HTML contains the comparison summary and each side's input, prediction,
  response, target, correctness, scores, warnings, and source location. Its search
  and outcome/language filters work offline; it requires no server.
- CSV contains one row per report item, with side-by-side fields. Nested values
  are JSON-encoded, null is blank, and formula-like strings are escaped for
  spreadsheet use. Use JSONL when distinctions between null and blank matter.
- JSONL retains the full normalized record for each available side, including
  additional producer fields. These nested records retain their archived
  `source` references; the raw JSONL remains the authoritative source.

Scores are displayed with their existing names and structure. The report does
not derive arbitrary log-probability differences or infer semantic answer
agreement from equal prediction indices. Correctness is read from each record,
which must have been scored against its own version's target. Comparable IDs do
not prove that a rephrasing preserved meaning or that metric definitions match.

Reports are derived local files. Writing is atomic and refuses to overwrite an
existing destination. Report generation does not change or reseal runs, and the
Hub uploader does not automatically upload derived reports.

## Recovery and restoration

The application holds a local writer lock. A manifest replacement commits an
import. If a process stops partway through, its transaction journal lets the next
write keep committed files and remove files that were never committed. An
operating-system lock is released automatically when the writer exits.

After downloading a Hub repository, run `python3 -m babel_fs --root DOWNLOADED_FOLDER
init` to recreate empty local operational directories that remote repositories
cannot preserve. Then run `validate`. Missing registered data remains an error;
initialization does not fabricate or recover lost results.

## Registered benchmark extensions

The five artifact registries are `item-banks/`, `protocols/`, `model-panels/`,
`calibrations/`, and `releases/`. Each immutable ID stores `manifest.json` and
`artifact.json`; references pin the payload SHA-256. `validate` checks all
registered artifacts and their dependencies as well as runs. `hub-plan` includes
all registered artifacts and adds calibration input runs even when a narrower
run selection was requested. `hub-pull` restores and validates that dependency
set from one pinned commit.

For strict runs, identity also includes the explicit script; comparisons require
the same bank and protocol references. Different checkpoints are intentionally
comparable. A response matrix preserves shared global IDs across languages while
keeping their separate observations and all family/split/grouping identifiers.
It does not pool correctness across languages or estimate any IRT parameters.