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feat: minted keys, VRF seeds, RFC 9162 proofs, history roots, tag URIs and a transparency log

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Keys (spec/02 §2.4), the rule paperstack settled on:
- A work key is a Scholar-style citation key, a hyphen and the first four
  Crockford base32 characters of SHA-256("scienting-key/1:" + identity),
  where the identity is the first of doi, arxiv, isbn, pmid, pmcid and
  openalex in same_as, else the folded title, year and family name. A
  collision lengthens the later key by two characters; a key is minted
  once and never recomputed. A document key adds .si, .v<seq> or .<type>
  for versions other than the version of record.
- Every fixture key is now minted (hale2026harmonic-damb,
  okafor2025solvent-acth, writer2027fixed-ynr7.v3, tiny2026tiny-j4qm), so
  every node and record ID was re-minted and the docs rewritten to match.
  The validator checks the document key against the work key and version
  (doc.key.work) and the hash part against the identifier (doc.key.suffix).
  vectors/keys.jsonl pins the cases paperstack's tests pin.

Review:
- Spot-check seeds are ECVRF-EDWARDS25519-SHA512-TAI proofs (RFC 9381),
  implemented in tools/oracle/vrf.py in plain Python and reproduced
  against the RFC's Example 16; the sample ranks by the VRF output. The
  earlier Ed25519 seed could be ground by a dishonest checker.
- RFC 9162 inclusion and consistency proofs (crypto.inclusion_path,
  verify_inclusion, consistency_proof, verify_consistency) with
  scienting-proof/1, vectors/proofs.jsonl and two fixture records.
- document.json carries `history`, the root over the corrections, with
  the empty-tree hash for none (spec/11 §11.5, rule doc.history).
- A provisional transparency log (spec/23): log entries, signed-note
  checkpoints with key hashes as transparency logs share them, the rule
  that a logged revocation beats a self-asserted time, and vectors.
- Reserved signature schemes cose and ml-dsa-65 (spec/08 §8.4).

Identifiers and text:
- urn:scienting: becomes tag:scient.ing,2026: (RFC 4151), since the URN
  namespace was never registered.
- Unicode 16.0 is pinned for normalization and categories (spec/01 §1.4);
  the checker refuses another version.

Checking:
- check.py: keys, proofs, VRF and checkpoint vectors; the proof and
  checkpoint records; a check that every ID and hash the prose quotes
  exists in the fixtures or vectors; three more broken packages
  (history-wrong, key-suffix, key-work).
- stress.py: key, VRF, proof and checkpoint properties.
- Docs: a keys section in the concepts and FAQ, rationale entries for
  keys, VRF, proofs, tag URIs and the Unicode pin, a "Looking ahead"
  section, media-type registration and OCI distribution notes.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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CHANGELOG.md
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@@ -6,13 +6,16 @@ A change to any computed value is a breaking change and needs a new major versio
The first release. The first release.
- The specification, in chapters 0 to 22, covering every format: 29 formats, of which 18 are `candidate` and 11 `provisional`. - The specification, in chapters 0 to 23, covering every format: 32 formats, of which 19 are `candidate` and 13 `provisional`.
- 39 JSON Schemas, using a keyword subset that independent validators read alike. - 42 JSON Schemas, using a keyword subset that independent validators read alike.
- Tables for SQLite, Dolt and PostgreSQL, a team's store, and the SQLite bundle with full-text search. - Tables for SQLite, Dolt and PostgreSQL, a team's store, and the SQLite bundle with full-text search.
- The JSON-LD context for layers, and registries of formats, rules, download-stamp rules and default stage requirements. - The JSON-LD context for layers, and registries of formats, rules, download-stamp rules and default stage requirements.
- Test vectors for every computed value, from canonical JSON to anchor resolution, grading and the target set of targeted F3. - Test vectors for every computed value, from canonical JSON to anchor resolution, grading and the target set of targeted F3.
- Example packages (a converted chemistry paper with corrections and receipts, its checks-only export, an open-access paper, a Typst draft and a tiny document, also as a zip), a record of every other format, and 28 broken packages, each breaking one named rule. - Example packages (a converted chemistry paper with corrections and receipts, its checks-only export, an open-access paper, a Typst draft and a tiny document, also as a zip), a record of every other format, and 31 broken packages, each breaking one named rule.
- Work keys minted from a Scholar-style citation key and a hash of the work's identity, with document keys for versions; `tag:` URIs for layers, annotations and documents.
- Spot-check seeds as VRF proofs (RFC 9381), RFC 9162 inclusion and consistency proofs, a history root over every document's corrections, and a provisional transparency log with signed checkpoints.
- Signed QA reports, a conformance checklist covered by a receipt, and a `description` annotation for the figure descriptions an accessible export needs. - Signed QA reports, a conformance checklist covered by a receipt, and a `description` annotation for the figure descriptions an accessible export needs.
- Reserved signature schemes for COSE and ML-DSA-65, and the character data pinned to Unicode 16.0.
- Guides for newcomers: an overview, the concepts, a walkthrough of the example paper, runnable examples, the rationale, a FAQ and a glossary. - Guides for newcomers: an overview, the concepts, a walkthrough of the example paper, runnable examples, the rationale, a FAQ and a glossary.
- Tools that build and check everything, validate packages and zipped packages and run proposed corrections through the gate, load packages into SQLite or a bundle, and stress the reference implementation with random inputs. - Tools that build and check everything, validate packages and zipped packages and run proposed corrections through the gate, load packages into SQLite or a bundle, and stress the reference implementation with random inputs.
- A pixi workspace pinned to Python 3.14, with tasks for checking, building, linting, validating and loading. - A pixi workspace pinned to Python 3.14, with tasks for checking, building, linting, validating and loading.
README.md
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@@ -21,14 +21,15 @@ Every file is JSON (a plain-text format for structured data) or JSON Lines (one
A package is the unit these formats store a paper in: a folder or a zip file of such files holding the text as nodes (sections, sentences, cells, equations), page geometry, references, corrections, review receipts and the list of suspects ([spec/12](spec/12-package.md)). A package is the unit these formats store a paper in: a folder or a zip file of such files holding the text as nodes (sections, sentences, cells, equations), page geometry, references, corrections, review receipts and the list of suspects ([spec/12](spec/12-package.md)).
```text ```text
cornell1995second#k3m9q2a@4f1a0c[12:57] cornell1995second-saqk#k3m9q2a@4f1a0c[12:57]
└──── document ──┘└ node ┘└ pin ┘└span┘ └────── document ────┘└ node ┘└ pin ┘└span┘
``` ```
A hash is a short fingerprint computed from text: the same text always gives the same fingerprint, and changing one character changes the hash. A hash is a short fingerprint computed from text: the same text always gives the same fingerprint, and changing one character changes the hash.
The string above names code points 12 to 57 of one sentence, as it read when its hash began `4f1a0c`. The string above names code points 12 to 57 of one sentence, as it read when its hash began `4f1a0c`.
The node ID `k3m9q2a` encodes no page, position or kind. The node ID `k3m9q2a` encodes no page, position or kind.
It is minted once from the document key, the node's kind, its text hash and its occurrence, and then frozen. It is minted once from the document key, the node's kind, its text hash and its occurrence, and then frozen.
The document key's last four characters, `saqk`, are the start of a hash of the paper's DOI, so two papers that a citation key alone would name alike never share a key ([spec/02 §2.4](spec/02-model.md#24-work-and-document-keys)).
Fixing a typo elsewhere in the paper leaves the ID alone, and converting the same input again mints the same IDs. Fixing a typo elsewhere in the paper leaves the ID alone, and converting the same input again mints the same IDs.
A teammate's download of the same PDF, stamped differently by the publisher, has the same page fingerprints. A teammate's download of the same PDF, stamped differently by the publisher, has the same page fingerprints.
@@ -53,7 +54,7 @@ The address grammar is in [spec/06 §6.1](spec/06-anchors.md#61-addresses), and
| Folder | Holds | | Folder | Holds |
| --- | --- | | --- | --- |
| [spec/](spec/README.md) | The specification, in 23 chapters. Normative. | | [spec/](spec/README.md) | The specification, in 24 chapters. Normative. |
| [schemas/](schemas/README.md) | JSON Schemas, which state what a valid file or record looks like, for every file and record. | | [schemas/](schemas/README.md) | JSON Schemas, which state what a valid file or record looks like, for every file and record. |
| [sql/](sql/README.md) | Tables for SQLite (a database kept in one file), Dolt and PostgreSQL, and the SQLite bundle with full-text search. | | [sql/](sql/README.md) | Tables for SQLite (a database kept in one file), Dolt and PostgreSQL, and the SQLite bundle with full-text search. |
| [context/](context/README.md) | The JSON-LD context (a file that gives JSON terms shared meanings) that makes annotation layers W3C Web Annotations. | | [context/](context/README.md) | The JSON-LD context (a file that gives JSON terms shared meanings) that makes annotation layers W3C Web Annotations. |
@@ -87,7 +88,7 @@ Without pixi, install those two with pip and run `python3 tools/check.py`.
To explore a worked package, load the example paper (a synthetic chemistry paper with 12 corrections) into SQLite and query it; [docs/examples.md](docs/examples.md) has queries to start from. To explore a worked package, load the example paper (a synthetic chemistry paper with 12 corrections) into SQLite and query it; [docs/examples.md](docs/examples.md) has queries to start from.
```sh ```sh
pixi run load --sqlite lab.db fixtures/packages/hale2026harmonic pixi run load --sqlite lab.db fixtures/packages/hale2026harmonic-damb
``` ```
## Format names ## Format names
@@ -101,8 +102,8 @@ Schemas use the identifier base `https://paperspec.scient.ing/schemas/`.
## Status and limits ## Status and limits
This is version 0.1.0. This is version 0.1.0.
Of the 29 formats, 18 are `candidate` and 11 are `provisional`. Of the 32 formats, 19 are `candidate` and 13 are `provisional`.
The `provisional` formats are project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade and checklist; where those are described, they are marked as such. The `provisional` formats are project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade, checklist, log-entry and checkpoint; where those are described, they are marked as such.
The repository includes a reference checker, test vectors and fixtures. The repository includes a reference checker, test vectors and fixtures.
The formats are built for a team-scale corpus of hundreds of documents, not hundreds of millions of papers. The formats are built for a team-scale corpus of hundreds of documents, not hundreds of millions of papers.
context/README.md
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@@ -33,7 +33,7 @@ The repository's name, paperspec, is a separate matter.
## An example from the fixtures ## An example from the fixtures
[`fixtures/records/layer/annotations.jsonl`](../fixtures/records/layer/annotations.jsonl) holds nine annotations on the example paper `hale2026harmonic`. [`fixtures/records/layer/annotations.jsonl`](../fixtures/records/layer/annotations.jsonl) holds nine annotations on the example paper `hale2026harmonic-damb`.
The first is a `gloss`, an explanation for a novice, of the phrase "bond force constant". The first is a `gloss`, an explanation for a novice, of the phrase "bond force constant".
Shortened, it reads: Shortened, it reads:
@@ -43,10 +43,10 @@ Shortened, it reads:
"body": {"type": "TextualBody", "kind": "gloss", "audience": "novice", "body": {"type": "TextualBody", "kind": "gloss", "audience": "novice",
"value": "A *harmonic* term treats a bond like a spring: ..."}, "value": "A *harmonic* term treats a bond like a spring: ..."},
"target": {"type": "SpecificResource", "target": {"type": "SpecificResource",
"source": "urn:scienting:doc:smithlab/hale2026harmonic", "source": "tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb",
"selector": [ "selector": [
{"type": "AnchorSelector", {"type": "AnchorSelector",
"anchor": {"format": "scienting-anchor/1", "node": "sxgcc9h", "anchor": {"format": "scienting-anchor/1", "node": "rr20tev",
"span": [111, 130], "quote": {"exact": "bond force constant", "...": "..."}, "...": "..."}}, "span": [111, 130], "quote": {"exact": "bond force constant", "...": "..."}, "...": "..."}},
{"type": "TextQuoteSelector", "exact": "bond force constant", {"type": "TextQuoteSelector", "exact": "bond force constant",
"prefix": "rm{eq}})^2$$ where $K_r$ is the ", "suffix": " and $r_\\mathrm{eq}$ the equilib"}]}} "prefix": "rm{eq}})^2$$ where $K_r$ is the ", "suffix": " and $r_\\mathrm{eq}$ the equilib"}]}}
@@ -94,7 +94,7 @@ Three of the nine fixture annotations have only an `AnchorSelector` (the section
- Writer: Put both URLs (web addresses), in the order shown, in `@context` of `layer.json` and of every line of `annotations.jsonl`. [Chapter 18](../spec/18-layers.md) defines layers (§18.2), annotations (§18.3) and bodies (§18.4). - Writer: Put both URLs (web addresses), in the order shown, in `@context` of `layer.json` and of every line of `annotations.jsonl`. [Chapter 18](../spec/18-layers.md) defines layers (§18.2), annotations (§18.3) and bodies (§18.4).
- Reader: Follow [chapter 6](../spec/06-anchors.md) to resolve an anchor. - Reader: Follow [chapter 6](../spec/06-anchors.md) to resolve an anchor.
The file `vectors/resolve.jsonl` resolves seventeen anchors against `fixtures/packages/hale2026harmonic` and gives every outcome. The file `vectors/resolve.jsonl` resolves seventeen anchors against `fixtures/packages/hale2026harmonic-damb` and gives every outcome.
- JSON-LD processor: Use a JSON-LD 1.1 processor; the context relies on `@json` and `@version` 1.1. - JSON-LD processor: Use a JSON-LD 1.1 processor; the context relies on `@json` and `@version` 1.1.
- Checker: `schemas/annotation.schema.json` and `schemas/layer.schema.json` validate the files. `tools/check.py` also checks that each annotation's ID derives from its content and that the receipt at `fixtures/records/layer/receipt.json` covers each `confirmed` annotation. - Checker: `schemas/annotation.schema.json` and `schemas/layer.schema.json` validate the files. `tools/check.py` also checks that each annotation's ID derives from its content and that the receipt at `fixtures/records/layer/receipt.json` covers each `confirmed` annotation.
deploy/README.md
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@@ -51,3 +51,9 @@ The workflow `.gitea/workflows/site.yml` builds the site on every push to `main`
| `SITE_SSH_KEY` | A private SSH key whose public half is in that account's `authorized_keys`, and that can do nothing else. | | `SITE_SSH_KEY` | A private SSH key whose public half is in that account's `authorized_keys`, and that can do nothing else. |
Without `SITE_HOST` the workflow still builds and checks the site, and says that it did not publish. Without `SITE_HOST` the workflow still builds and checks the site, and says that it did not publish.
## Distributing packages
A zipped package is an ordinary file, and the site serves the fixtures as such.
For a team's own packages, the Gitea instance speaks the OCI distribution protocol, so packages can be pushed to and pulled from its package registry as OCI artifacts with ORAS, and signed there with cosign; the media type of the artifact is the package's, `application/vnd.scienting.doc+zip`.
Nothing in the formats depends on how packages travel.
docs/comparison.md
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@@ -19,11 +19,11 @@ The identifiers appear inside hashed data and test vectors, so they are not rena
Suppose a research team keeps fifty papers it needs to understand completely. Suppose a research team keeps fifty papers it needs to understand completely.
A page number names a region of a PDF and cannot name a statement, and it changes between a preprint and the published version. A page number names a region of a PDF and cannot name a statement, and it changes between a preprint and the published version.
The team wants to point at one sentence or one table cell, such as `hale2026harmonic#sxgcc9h@76e06b[111:130]` in the fixtures, and have that pointer keep working after someone fixes a misread digit elsewhere in the paper. The team wants to point at one sentence or one table cell, such as `hale2026harmonic-damb#rr20tev@76e06b[111:130]` in the fixtures, and have that pointer keep working after someone fixes a misread digit elsewhere in the paper.
The pointer has four parts: The pointer has four parts:
- The document key, `hale2026harmonic`. - The document key, `hale2026harmonic-damb`.
- After `#`, the node ID, `sxgcc9h`. - After `#`, the node ID, `rr20tev`.
- After `@`, the first six digits of the node's hash, `76e06b`, so the pointer names the sentence as it then read. - After `@`, the first six digits of the node's hash, `76e06b`, so the pointer names the sentence as it then read.
- In brackets, the code-point range of the words inside the sentence, `[111:130]`. - In brackets, the code-point range of the words inside the sentence, `[111:130]`.
It also wants to know who compared a passage with the page image, and how far. It also wants to know who compared a passage with the page image, and how far.
@@ -67,7 +67,7 @@ The design choices that matter for comparison:
Resolving it gives one of five results: `current`, `changed-below`, `moved`, `reattached` or `stale`, with a drift measure for `changed-below` ([spec/06](../spec/06-anchors.md)). Resolving it gives one of five results: `current`, `changed-below`, `moved`, `reattached` or `stale`, with a drift measure for `changed-below` ([spec/06](../spec/06-anchors.md)).
- **Corrections:** Corrections are appended, never edited. - **Corrections:** Corrections are appended, never edited.
Each carries evidence, an author and a reason, and a gate refuses a digit change without image evidence ([spec/11](../spec/11-corrections.md)). Each carries evidence, an author and a reason, and a gate refuses a digit change without image evidence ([spec/11](../spec/11-corrections.md)).
In `fixtures/packages/hale2026harmonic`, correction 1 replaces `3l0.0` with `310.0` because "OCR (optical character recognition) read the digit 1 as the letter l", with a crop of the page as evidence. In `fixtures/packages/hale2026harmonic-damb`, correction 1 replaces `3l0.0` with `310.0` because "OCR (optical character recognition) read the digit 1 as the letter l", with a crop of the page as evidence.
- **Fidelity and receipts:** Levels F0 (converted) to F3 (proofread). - **Fidelity and receipts:** Levels F0 (converted) to F3 (proofread).
F3 comes only from a signed receipt that lists the node at its current `node_hash`; a correction drops the node back ([spec/08](../spec/08-fidelity.md)). F3 comes only from a signed receipt that lists the node at its current `node_hash`; a correction drops the node back ([spec/08](../spec/08-fidelity.md)).
- **Scale:** The formats are built for a team of roughly five to 20 people with a few dozen to a few hundred papers. - **Scale:** The formats are built for a team of roughly five to 20 people with a few dozen to a few hundred papers.
@@ -135,7 +135,7 @@ paperspec is not a publisher interchange format and does not replace JATS ([spec
*Interoperation.* *Interoperation.*
JATS is an input. JATS is an input.
`jats` is a witness kind, and the fixture `okafor2025open` was established from a JATS file and a PDF that agree ([fixtures/README.md](../fixtures/README.md)). `jats` is a witness kind, and the fixture `okafor2025solvent-acth` was established from a JATS file and a PDF that agree ([fixtures/README.md](../fixtures/README.md)).
The document's `meta` is one CSL-JSON item, not JATS front matter ([spec/02 §2.2](../spec/02-model.md#22-documentjson)). The document's `meta` is one CSL-JSON item, not JATS front matter ([spec/02 §2.2](../spec/02-model.md#22-documentjson)).
The specification defines no JATS exporter. The specification defines no JATS exporter.
@@ -427,8 +427,8 @@ Keep using it as a reading and distribution format.
*Status.* *Status.*
The specification is version 0.1.0. The specification is version 0.1.0.
`registry/formats.json` lists 29 formats: 18 are `candidate` (complete, with vectors and fixtures, ready to implement) and 11 are `provisional` (complete; expected to change as implementations gain experience): project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade and checklist ([spec/00 §0.4](../spec/00-introduction.md#04-status)). `registry/formats.json` lists 32 formats: 19 are `candidate` (complete, with vectors and fixtures, ready to implement) and 13 are `provisional` (complete; expected to change as implementations gain experience): project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade, checklist, log-entry and checkpoint ([spec/00 §0.4](../spec/00-introduction.md#04-status)).
The repository holds 23 chapters, 39 JSON Schemas, 21 vector files, five valid fixture packages, one of them also zipped, and 28 invalid ones, each naming the rule it breaks, and a reference checker, `tools/check.py`. The repository holds 24 chapters, 42 JSON Schemas, 25 vector files, five valid fixture packages, one of them also zipped, and 31 invalid ones, each naming the rule it breaks, and a reference checker, `tools/check.py`.
Licenses: prose CC BY 4.0; schemas, SQL, the JSON-LD context, registries, vectors and fixtures CC0 1.0; tools Apache-2.0 ([README.md](../README.md#licenses)). Licenses: prose CC BY 4.0; schemas, SQL, the JSON-LD context, registries, vectors and fixtures CC0 1.0; tools Apache-2.0 ([README.md](../README.md#licenses)).
*No adoption claim.* *No adoption claim.*
@@ -466,12 +466,12 @@ These are the places where the guides and the specification differ, and this pag
4. **Five hashes everywhere:** `docs/overview.md` lists the things that get "a permanent ID and five content hashes" without naming them. 4. **Five hashes everywhere:** `docs/overview.md` lists the things that get "a permanent ID and five content hashes" without naming them.
Table columns and figure-text items have IDs, are not nodes, and carry no five hashes ([spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids), [spec/09 §9.1](../spec/09-figures-tables-equations.md#91-figures-and-panels)). Table columns and figure-text items have IDs, are not nodes, and carry no five hashes ([spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids), [spec/09 §9.1](../spec/09-figures-tables-equations.md#91-figures-and-panels)).
5. **Dataset digits:** spec/15 says values keep their printed digits, and in JSON they are strings. 5. **Dataset digits:** spec/15 says values keep their printed digits, and in JSON they are strings.
The fixture descriptor `fixtures/packages/hale2026harmonic/datasets/ds-hale-bond-params/datapackage.json` types the field `k_r` as `number`. The fixture descriptor `fixtures/packages/hale2026harmonic-damb/datasets/ds-hale-bond-params/datapackage.json` types the field `k_r` as `number`.
How Frictionless tools treat that was not verified, so take care when comparing with Frictionless Table Schema. How Frictionless tools treat that was not verified, so take care when comparing with Frictionless Table Schema.
6. **Package tree:** `docs/concepts.md` omits `suspects.jsonl` from its package tree, and [spec/12 §12.1](../spec/12-package.md#121-files) lists it. 6. **Package tree:** `docs/concepts.md` omits `suspects.jsonl` from its package tree, and [spec/12 §12.1](../spec/12-package.md#121-files) lists it.
7. **RFC 6962 is obsolete:** spec/08 §8.5 cites it; RFC 9162 obsoletes it (see above). 7. **RFC 6962 is obsolete:** spec/08 §8.5 cites it; RFC 9162 obsoletes it (see above).
8. **Status:** The guides describe the formats as one set. 8. **Status:** The guides describe the formats as one set.
Of the 29 formats, 11 are `provisional`, including `scienting-dataset/1`, which the datasets paragraphs in `docs/concepts.md` present without that qualifier. Of the 32 formats, 13 are `provisional`, including `scienting-dataset/1`, which the datasets paragraphs in `docs/concepts.md` present without that qualifier.
*The distinguishing combination, and what it costs.* *The distinguishing combination, and what it costs.*
paperspec puts in one package permanent sentence- and cell-level IDs, five hashes per node, anchors with explicit resolution outcomes and drift, append-only evidence-gated corrections, signed fidelity receipts with spot-check bounds, per-witness rights with AI-use axes, and value-to-cell anchors. paperspec puts in one package permanent sentence- and cell-level IDs, five hashes per node, anchors with explicit resolution outcomes and drift, append-only evidence-gated corrections, signed fidelity receipts with spot-check bounds, per-witness rights with AI-use axes, and value-to-cell anchors.
docs/concepts.md
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@@ -1,6 +1,6 @@
# Concepts # Concepts
Each section introduces one idea, shows it in the example paper `hale2026harmonic` (a synthetic chemistry paper in [fixtures/packages/](../fixtures/packages/)), and links to the chapter that defines it exactly. Each section introduces one idea, shows it in the example paper `hale2026harmonic-damb` (a synthetic chemistry paper in [fixtures/packages/](../fixtures/packages/)), and links to the chapter that defines it exactly.
This page is written for three readers. This page is written for three readers.
A newcomer, such as a student who knows what a paper and a citation are and is new to hashes, JSON and annotation standards, gets each term defined where it first appears, with the reason before the rule. A newcomer, such as a student who knows what a paper and a citation are and is new to hashes, JSON and annotation standards, gets each term defined where it first appears, with the reason before the rule.
@@ -12,8 +12,8 @@ For a gentler start, read the [overview](overview.md) first; for the exact rules
Two facts apply to everything below. Two facts apply to everything below.
The specification is at version 0.1.0. The specification is at version 0.1.0.
It defines 29 formats, 18 of them `candidate` and 11 `provisional`, as [registry/formats.json](../registry/formats.json) lists. It defines 32 formats, 19 of them `candidate` and 13 `provisional`, as [registry/formats.json](../registry/formats.json) lists.
The provisional ones are the project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade and checklist formats; the sections below say so where they describe them. The provisional ones are the project, bundle, dataset, digitization, view, snapshot, draft-ids, exercise, submission, grade, checklist, log-entry and checkpoint formats; the sections below say so where they describe them.
Format identifiers such as `scienting-anchor/1` and `scienting-correction/1` begin with `scienting-`, which is the formats' namespace. Format identifiers such as `scienting-anchor/1` and `scienting-correction/1` begin with `scienting-`, which is the formats' namespace.
The repository's name, paperspec, is a separate matter, and the formats are named after what they hold. The repository's name, paperspec, is a separate matter, and the formats are named after what they hold.
@@ -53,12 +53,26 @@ Work, version, witness and document are easy to confuse, so the formats keep the
| A work is the paper across all its versions. | Hale and Osei's paper on harmonic bond parameters, `doi:10.5555/example.hale.2026`. | | A work is the paper across all its versions. | Hale and Osei's paper on harmonic bond parameters, `doi:10.5555/example.hale.2026`. |
| A version is one expression of it: a preprint, the version of record, an erratum, the Supporting Information. | The version of record. | | A version is one expression of it: a preprint, the version of record, an erratum, the Supporting Information. | The version of record. |
| A witness is one file of a version, identified by its SHA-256. | The publisher's PDF, witness `qptsanv`. | | A witness is one file of a version, identified by its SHA-256. | The publisher's PDF, witness `qptsanv`. |
| A document is the text established for one version, from one or more witnesses. | `hale2026harmonic`. | | A document is the text established for one version, from one or more witnesses. | `hale2026harmonic-damb`. |
A document's key is its work's key, with a suffix for anything other than the version of record: `hale2026harmonic.si` would be its Supporting Information. A document's key is its work's key, with a suffix for anything other than the version of record: `hale2026harmonic-damb.si` would be its Supporting Information.
A witness can be a PDF, a JATS file, a LaTeX archive, an HTML page, an EPUB, a Typst project, other XML, an image, or another file; these are the values of its `kind`. A witness can be a PDF, a JATS file, a LaTeX archive, an HTML page, an EPUB, a Typst project, other XML, an image, or another file; these are the values of its `kind`.
See [chapter 2](../spec/02-model.md). See [chapter 2](../spec/02-model.md).
## Keys
A work key is a work's permanent name, built so that a reader can say it and so that it never collides.
It is a Scholar-style citation key (first author, year, first title word), a hyphen, and four characters of a hash of the work's identity, which is its DOI when it has one:
```text
hale2026harmonic-damb
```
Two works that a citation key alone would name alike, a preprint and its published version, say, get different hashes.
A key is minted once, when the work enters a store, and never recomputed, so a corrected title changes nothing anyone has cited; if two works share four characters, the later one gets six.
A document key adds a suffix for a version other than the version of record: `hale2026harmonic-damb.si` would be the paper's Supporting Information.
See [spec/02 §2.4](../spec/02-model.md#24-work-and-document-keys); `keys.jsonl` pins the cases.
## A document is a tree of nodes ## A document is a tree of nodes
Every part of the text is a node: the document, its sections, headings, paragraphs and sentences, figures and their panels and captions, tables with their rows and cells, equations, footnotes and references. Every part of the text is a node: the document, its sections, headings, paragraphs and sentences, figures and their panels and captions, tables with their rows and cells, equations, footnotes and references.
@@ -66,11 +80,11 @@ The example has 75 nodes, 45 of them leaves (nodes that hold text themselves).
This outline shows its two sections and the equation, figure and table in them: This outline shows its two sections and the equation, figure and table in them:
```text ```text
bzqvbhd 1 Introduction p36k8t6 1 Introduction
qn08tj9 equation (1) tkxsmts equation (1)
f0tj6ca 2 Methods d400rz3 2 Methods
ajfvq4s figure Figure 1 v7cx6qs figure Figure 1
gm5z4rx table Table 1 hj4s7pb table Table 1
``` ```
`nodes.jsonl` holds one node per line, in document order: the root first, then each node before its children. `nodes.jsonl` holds one node per line, in document order: the root first, then each node before its children.
@@ -79,7 +93,7 @@ A sentence's content is a list of *runs*: plain text, styled text, inline math,
This is one table cell, shortened: This is one table cell, shortened:
```json ```json
{"id":"nkm3xn5","kind":"cell","parent":"zhe4g0k","ord":1, {"id":"c20cna6","kind":"cell","parent":"g8d2pjb","ord":1,
"attrs":{"column":"…","role":"data","rowspan":1,"colspan":1}, "attrs":{"column":"…","role":"data","rowspan":1,"colspan":1},
"content":[{"kind":"text","text":"310.0"}], "content":[{"kind":"text","text":"310.0"}],
"fidelity":"F1","text_hash":"…","match_hash":"…","align_key":"…","own_hash":"…","node_hash":"21f13b…"} "fidelity":"F1","text_hash":"…","match_hash":"…","align_key":"…","own_hash":"…","node_hash":"21f13b…"}
@@ -96,7 +110,7 @@ See [the comparison page](comparison.md).
## IDs are names, not positions ## IDs are names, not positions
`nkm3xn5` says nothing about where the cell is. `c20cna6` says nothing about where the cell is.
That is deliberate. That is deliberate.
An ID that encoded a page or an ordinal would change when a better converter ordered blocks differently, and one that encoded a kind would change when a paragraph turned out to be a caption. An ID that encoded a page or an ordinal would change when a better converter ordered blocks differently, and one that encoded a kind would change when a paragraph turned out to be a caption.
So an ID encodes no page, ordinal or kind. So an ID encodes no page, ordinal or kind.
@@ -111,12 +125,12 @@ A second reading is aligned with the document sentence by sentence.
Sentences the alignment pairs keep the document's IDs, and every difference becomes a suspect, a recorded doubtful reading that a person resolves ([chapter 5.6](../spec/05-hashes.md#56-alignment) and [5.7](../spec/05-hashes.md#57-suspects)). Sentences the alignment pairs keep the document's IDs, and every difference becomes a suspect, a recorded doubtful reading that a person resolves ([chapter 5.6](../spec/05-hashes.md#56-alignment) and [5.7](../spec/05-hashes.md#57-suspects)).
One ID is retired and points at its successor when two nodes merge; an artifact's ID is retired with no successor when the artifact is deleted. One ID is retired and points at its successor when two nodes merge; an artifact's ID is retired with no successor when the artifact is deleted.
Legacy IDs, such as a block ID from an earlier numbering scheme, live on as aliases: in the example, `b-p01-text-003` still leads to sentence `f929eq9`. Legacy IDs, such as a block ID from an earlier numbering scheme, live on as aliases: in the example, `b-p01-text-003` still leads to sentence `hca6dc5`.
Both the retirements and the aliases are recorded in `ids.jsonl`. Both the retirements and the aliases are recorded in `ids.jsonl`.
Not every addressable thing is a node. Not every addressable thing is a node.
The columns of a table and the text items found inside a figure panel get IDs by the same rule and carry no node hashes, so they do not have the five hashes described below. The columns of a table and the text items found inside a figure panel get IDs by the same rule and carry no node hashes, so they do not have the five hashes described below.
In the example, Table 1's second column has the ID `kp6grmd`, and the axis label "r (Å)" in Figure 1's first panel has the ID `nhk15ag`. In the example, Table 1's second column has the ID `wdtrcqt`, and the axis label "r (Å)" in Figure 1's first panel has the ID `rtxzjj9`.
Pinned by [vectors/ids.jsonl](../vectors/ids.jsonl). Pinned by [vectors/ids.jsonl](../vectors/ids.jsonl).
See [chapter 4](../spec/04-identity.md). See [chapter 4](../spec/04-identity.md).
@@ -132,15 +146,15 @@ An address names a node, and optionally pins it to a state and narrows it to a s
| Address | Names | | Address | Names |
| --- | --- | | --- | --- |
| `hale2026harmonic#f929eq9` | The sentence about water, whatever it says now. | | `hale2026harmonic-damb#hca6dc5` | The sentence about water, whatever it says now. |
| `hale2026harmonic#f929eq9@cd6cdb` | That sentence as it read when its `node_hash` began `cd6cdb`. | | `hale2026harmonic-damb#hca6dc5@cd6cdb` | That sentence as it read when its `node_hash` began `cd6cdb`. |
| `hale2026harmonic#f929eq9@cd6cdb[29:44]` | Code points 29 to 44 of it in that state: "first test case". | | `hale2026harmonic-damb#hca6dc5@cd6cdb[29:44]` | Code points 29 to 44 of it in that state: "first test case". |
| `smithlab/hale2026harmonic#f929eq9` | The same sentence in the `smithlab` store. | | `smithlab/hale2026harmonic-damb#hca6dc5` | The same sentence in the `smithlab` store. |
The offsets count Unicode code points in the node's plain projection, which is its text as stored with math written between dollar signs. The offsets count Unicode code points in the node's plain projection, which is its text as stored with math written between dollar signs.
The dollar signs count, which is why the span starts at 29: the sentence reads `Water, H$_2$O, served as the first test case, …`. The dollar signs count, which is why the span starts at 29: the sentence reads `Water, H$_2$O, served as the first test case, …`.
On the web the ID is the fragment, so a link to `…/smithlab/hale2026harmonic#f929eq9` lands on the sentence. On the web the ID is the fragment, so a link to `…/smithlab/hale2026harmonic-damb#hca6dc5` lands on the sentence.
Pinned by [vectors/addresses.jsonl](../vectors/addresses.jsonl). Pinned by [vectors/addresses.jsonl](../vectors/addresses.jsonl).
See [chapter 6](../spec/06-anchors.md#61-addresses). See [chapter 6](../spec/06-anchors.md#61-addresses).
@@ -190,11 +204,11 @@ A document is never edited in place.
Every fix is a correction: an operation with its evidence, its author and a reason, appended to `corrections.jsonl`. Every fix is a correction: an operation with its evidence, its author and a reason, appended to `corrections.jsonl`.
```json ```json
{"format":"scienting-correction/1","index":1,"op":"replace","target":"nkm3xn5", {"format":"scienting-correction/1","index":1,"op":"replace","target":"c20cna6",
"find":"3l0.0","replace":"310.0", "find":"3l0.0","replace":"310.0",
"evidence":[{"kind":"crop","sha256":"9b6fe6…"}],"author":{"key":"ana"}, "evidence":[{"kind":"crop","sha256":"9b6fe6…"}],"author":{"key":"ana"},
"reason":"OCR read the digit 1 as the letter l.","at":"2026-10-02T10:00:00Z", "reason":"OCR read the digit 1 as the letter l.","at":"2026-10-02T10:00:00Z",
"before":"2fd1e9…","after":"21f13b…","touched":["nkm3xn5"]} "before":"2fd1e9…","after":"21f13b…","touched":["c20cna6"]}
``` ```
A document's history is its first reading plus its corrections, and its revision is the index of the last one. A document's history is its first reading plus its corrections, and its revision is the index of the last one.
@@ -215,7 +229,7 @@ An anchor is how anything points into a document: a quotation that must match th
It is a pinned address with enough context to find its text again after the document changes: It is a pinned address with enough context to find its text again after the document changes:
```json ```json
{"format":"scienting-anchor/1","store":"smithlab","doc":"hale2026harmonic","node":"f929eq9","kind":"sentence", {"format":"scienting-anchor/1","store":"smithlab","doc":"hale2026harmonic-damb","node":"hca6dc5","kind":"sentence",
"own_hash":"d5b2eb…","node_hash":"cd6cdb…","span":[29,44], "own_hash":"d5b2eb…","node_hash":"cd6cdb…","span":[29,44],
"quote":{"exact":"first test case","prefix":"Water, H$_2$O, served as the ","suffix":", with a bending band near 1595 "}, "quote":{"exact":"first test case","prefix":"Water, H$_2$O, served as the ","suffix":", with a bending band near 1595 "},
"rev":12} "rev":12}
@@ -309,7 +323,7 @@ Values are plain SHA-256 inside the team.
Exported to another of the team's machines, they are HMACs under the team's key. Exported to another of the team's machines, they are HMACs under the team's key.
In a public layer, or in an export outside the team, the key is derived from the paper's page fingerprints (see the previous section), so only someone holding the paper can check them. In a public layer, or in an export outside the team, the key is derived from the paper's page fingerprints (see the previous section), so only someone holding the paper can check them.
Where the values go chooses the key, not whether the text is withheld. Where the values go chooses the key, not whether the text is withheld.
[fixtures/packages/hale2026harmonic.checks-only](../fixtures/packages/hale2026harmonic.checks-only) is the example paper exported to another of the team's machines, so it uses the team key. [fixtures/packages/hale2026harmonic-damb.checks-only](../fixtures/packages/hale2026harmonic-damb.checks-only) is the example paper exported to another of the team's machines, so it uses the team key.
A checks-only package also has no corrections, suspects or datasets. A checks-only package also has no corrections, suspects or datasets.
Pinned by [vectors/keyed.jsonl](../vectors/keyed.jsonl). Pinned by [vectors/keyed.jsonl](../vectors/keyed.jsonl).
@@ -347,8 +361,8 @@ This gloss, shortened, explains a phrase for a first-year student:
{"type":"Annotation","motivation":"describing","status":"confirmed", {"type":"Annotation","motivation":"describing","status":"confirmed",
"body":{"type":"TextualBody","kind":"gloss","audience":"novice", "body":{"type":"TextualBody","kind":"gloss","audience":"novice",
"value":"A *harmonic* term treats a bond like a spring: the energy grows with the square of the stretch."}, "value":"A *harmonic* term treats a bond like a spring: the energy grows with the square of the stretch."},
"target":{"type":"SpecificResource","source":"urn:scienting:doc:smithlab/hale2026harmonic", "target":{"type":"SpecificResource","source":"tag:scient.ing,2026:doc:smithlab/hale2026harmonic-damb",
"selector":[{"type":"AnchorSelector","anchor":{"node":"sxgcc9h","span":[111,130],"…":"…"}}, "selector":[{"type":"AnchorSelector","anchor":{"node":"rr20tev","span":[111,130],"…":"…"}},
{"type":"TextQuoteSelector","exact":"bond force constant"}]}} {"type":"TextQuoteSelector","exact":"bond force constant"}]}}
``` ```
@@ -366,7 +380,7 @@ See [chapter 18](../spec/18-layers.md).
## Exercises ## Exercises
Every sentence and cell has an address, so the answer to "find the evidence" is an address, and an address can be graded. Every sentence and cell has an address, so the answer to "find the evidence" is an address, and an address can be graded.
An exercise asks a student to find the cell giving the Set A bond constant for CT–CT. A student who points at `nkm3xn5` scores 1 of 1 with "That is the cell."; one who points at the Set B cell scores 0 with "Look in Table 1, row CT–CT." An exercise asks a student to find the cell giving the Set A bond constant for CT–CT. A student who points at `c20cna6` scores 1 of 1 with "That is the cell."; one who points at the Set B cell scores 0 with "Look in Table 1, row CT–CT."
Students submit under pseudonyms, and a key whose anchors have gone stale is never used to grade. Students submit under pseudonyms, and a key whose anchors have gone stale is never used to grade.
Pinned by [vectors/grading.jsonl](../vectors/grading.jsonl). Pinned by [vectors/grading.jsonl](../vectors/grading.jsonl).
@@ -401,7 +415,7 @@ See [the comparison page](comparison.md).
A document travels as a package: a folder of canonical JSON files, or the same folder zipped. A document travels as a package: a folder of canonical JSON files, or the same folder zipped.
```text ```text
hale2026harmonic/ hale2026harmonic-damb/
MANIFEST.json every other file, with its SHA-256; its own hash pins the package MANIFEST.json every other file, with its SHA-256; its own hash pins the package
document.json the work, version, metadata, policy, root hash and fidelity document.json the work, version, metadata, policy, root hash and fidelity
nodes.jsonl one node per line, in reading order nodes.jsonl one node per line, in reading order
docs/examples.md
+31 -31
View File
@@ -41,10 +41,10 @@ printf '%s' 'The two parameter sets agree to within 2% for every bond.' | sha256
175bfc8867816a9761fd5bb9ffc956df6d9e7f203870961a5485fc1912cb663a - 175bfc8867816a9761fd5bb9ffc956df6d9e7f203870961a5485fc1912cb663a -
``` ```
The same value is in the package, in the `nodes.jsonl` of `hale2026harmonic`: The same value is in the package, in the `nodes.jsonl` of `hale2026harmonic-damb`:
```sh ```sh
grep -o '"id":"j06tfhn".*' fixtures/packages/hale2026harmonic/nodes.jsonl | grep -o '"text_hash":"[0-9a-f]*"' grep -o '"id":"v3063qv".*' fixtures/packages/hale2026harmonic-damb/nodes.jsonl | grep -o '"text_hash":"[0-9a-f]*"'
``` ```
```text ```text
@@ -58,14 +58,14 @@ A package is a folder of JSON (JavaScript Object Notation, a plain-text format f
`MANIFEST.json` lists every other file of a package with its SHA-256 and size, and the SHA-256 of the manifest itself pins the whole package ([chapter 12](../spec/12-package.md#123-the-manifest)). `MANIFEST.json` lists every other file of a package with its SHA-256 and size, and the SHA-256 of the manifest itself pins the whole package ([chapter 12](../spec/12-package.md#123-the-manifest)).
```sh ```sh
cd fixtures/packages/okafor2025open cd fixtures/packages/okafor2025solvent-acth
sha256sum nodes.jsonl sha256sum nodes.jsonl
grep -o '"path":"nodes.jsonl","sha256":"[0-9a-f]*"' MANIFEST.json grep -o '"path":"nodes.jsonl","sha256":"[0-9a-f]*"' MANIFEST.json
``` ```
```text ```text
0fccd6492121fb91ebd1d32487e23ca5b30ad92627e7d3a0801d77549e1a2f94 nodes.jsonl 09c9b99eed97987e51dd0f85461ad9ad8768a0769ba7facfb7e0879d742660a3 nodes.jsonl
"path":"nodes.jsonl","sha256":"0fccd6492121fb91ebd1d32487e23ca5b30ad92627e7d3a0801d77549e1a2f94" "path":"nodes.jsonl","sha256":"09c9b99eed97987e51dd0f85461ad9ad8768a0769ba7facfb7e0879d742660a3"
``` ```
## Read a package with nothing but a JSON parser ## Read a package with nothing but a JSON parser
@@ -108,26 +108,26 @@ for n in nodes:
``` ```
```sh ```sh
python3 outline.py fixtures/packages/hale2026harmonic python3 outline.py fixtures/packages/hale2026harmonic-damb
``` ```
```text ```text
bzqvbhd 1 Introduction p36k8t6 1 Introduction
qn08tj9 equation (1) tkxsmts equation (1)
f0tj6ca 2 Methods d400rz3 2 Methods
ajfvq4s figure Figure 1 v7cx6qs figure Figure 1
gm5z4rx table Table 1 hj4s7pb table Table 1
``` ```
## Follow an address ## Follow an address
This shows how a citation points inside a sentence. This shows how a citation points inside a sentence.
An address names a node, and optionally a span of its text ([chapter 6](../spec/06-anchors.md#61-addresses)). An address names a node, and optionally a span of its text ([chapter 6](../spec/06-anchors.md#61-addresses)).
`hale2026harmonic#f929eq9[29:44]` names code points 29 to 44 of sentence `f929eq9`. `hale2026harmonic-damb#hca6dc5[29:44]` names code points 29 to 44 of sentence `hca6dc5`.
With `text()` from the script above: With `text()` from the script above:
```python ```python
print(text(by_id["f929eq9"])[29:44]) print(text(by_id["hca6dc5"])[29:44])
``` ```
```text ```text
@@ -143,15 +143,15 @@ For text with characters outside the Basic Multilingual Plane the two counts dif
This shows that the same packages can live in a database and be queried with SQL. This shows that the same packages can live in a database and be queried with SQL.
```sh ```sh
pixi run load --sqlite lab.db fixtures/packages/hale2026harmonic fixtures/packages/okafor2025open fixtures/packages/smithlab2027charges pixi run load --sqlite lab.db fixtures/packages/hale2026harmonic-damb fixtures/packages/okafor2025solvent-acth fixtures/packages/writer2027fixed-ynr7.v3
``` ```
Without pixi, run `python3 tools/load.py` with the same arguments. Without pixi, run `python3 tools/load.py` with the same arguments.
```text ```text
hale2026harmonic: 75 nodes hale2026harmonic-damb: 75 nodes
okafor2025open: 15 nodes okafor2025solvent-acth: 15 nodes
smithlab2027charges: 15 nodes writer2027fixed-ynr7.v3: 15 nodes
``` ```
The tables are those of [sql/doc.sql](../sql/doc.sql) and [sql/store.sql](../sql/store.sql), which run unchanged on Dolt and PostgreSQL as well ([chapter 13](../spec/13-database.md)); `tools/check.py` exercises them on SQLite only, and this repository has not yet run them on Dolt or PostgreSQL. The tables are those of [sql/doc.sql](../sql/doc.sql) and [sql/store.sql](../sql/store.sql), which run unchanged on Dolt and PostgreSQL as well ([chapter 13](../spec/13-database.md)); `tools/check.py` exercises them on SQLite only, and this repository has not yet run them on Dolt or PostgreSQL.
@@ -163,14 +163,14 @@ import json, sqlite3
db = sqlite3.connect("lab.db") db = sqlite3.connect("lab.db")
# Sentences the converter left below F2. Receipts can raise them; see below. # Sentences the converter left below F2. Receipts can raise them; see below.
for row in db.execute("SELECT id, fidelity FROM nodes WHERE doc_key = 'hale2026harmonic' " for row in db.execute("SELECT id, fidelity FROM nodes WHERE doc_key = 'hale2026harmonic-damb' "
"AND kind = 'sentence' AND fidelity IN ('F0', 'F1') ORDER BY seq"): "AND kind = 'sentence' AND fidelity IN ('F0', 'F1') ORDER BY seq"):
print(row) print(row)
# Every sentence that cites reference 2: the citation graph is sentence-level. # Every sentence that cites reference 2: the citation graph is sentence-level.
for row in db.execute("SELECT c.sentence FROM citations c JOIN refs r " for row in db.execute("SELECT c.sentence FROM citations c JOIN refs r "
"ON r.doc_key = c.doc_key AND r.node = c.ref_node " "ON r.doc_key = c.doc_key AND r.node = c.ref_node "
"WHERE c.doc_key = 'hale2026harmonic' AND r.label = '2'"): "WHERE c.doc_key = 'hale2026harmonic-damb' AND r.label = '2'"):
print(row) print(row)
# Who signed what. # Who signed what.
@@ -180,26 +180,26 @@ for row in db.execute("SELECT r.signer, r.scope, COUNT(*) FROM receipts r "
# Table 1's body, row by row. # Table 1's body, row by row.
rows = db.execute("SELECT r.id FROM nodes r JOIN nodes b ON b.doc_key = r.doc_key AND b.id = r.parent " rows = db.execute("SELECT r.id FROM nodes r JOIN nodes b ON b.doc_key = r.doc_key AND b.id = r.parent "
"WHERE r.doc_key = 'hale2026harmonic' AND r.kind = 'row' AND b.kind = 'table-body' " "WHERE r.doc_key = 'hale2026harmonic-damb' AND r.kind = 'row' AND b.kind = 'table-body' "
"ORDER BY r.seq").fetchall() "ORDER BY r.seq").fetchall()
for (row,) in rows: for (row,) in rows:
cells = db.execute("SELECT content FROM nodes WHERE doc_key = 'hale2026harmonic' AND parent = ? ORDER BY ord", cells = db.execute("SELECT content FROM nodes WHERE doc_key = 'hale2026harmonic-damb' AND parent = ? ORDER BY ord",
(row,)).fetchall() (row,)).fetchall()
print(" | ".join("".join(r.get("text", "") for r in json.loads(c)) for (c,) in cells)) print(" | ".join("".join(r.get("text", "") for r in json.loads(c)) for (c,) in cells))
``` ```
```text ```text
('e4fkseg', 'F1') ('ec5jc93', 'F1')
('r1gacps', 'F0') ('a4jrz2t', 'F0')
('eajq93t', 'F0') ('xjns57z', 'F0')
('f929eq9',) ('hca6dc5',)
('ana', 'targeted:lode', 3) ('ana', 'targeted:lode', 3)
('ana', 'targeted:lode', 23) ('ana', 'targeted:lode', 23)
('ana', 'section:bzqvbhd', 2) ('ana', 'section:p36k8t6', 2)
('cara', 'page:2', 3) ('cara', 'page:2', 3)
('ana', 'targeted:captions', 3) ('ana', 'targeted:captions', 3)
('ben', 'qa:eqgbbpwb6725v', 10) ('ben', 'qa:y2zw8ctg5s8dp', 10)
('ben', 'qa:gena76nkb6cnc', 3) ('ben', 'qa:gx2s84z9jf9xv', 3)
Bond parameters Bond parameters
CT–CT | 310.0 | 1.526 | 305.2 | 1.5260 CT–CT | 310.0 | 1.526 | 305.2 | 1.5260
CT–HC | 340.0 | 1.090 | 338.7 | 1.0900 CT–HC | 340.0 | 1.090 | 338.7 | 1.0900
@@ -208,7 +208,7 @@ OW–HW | 553.0 | 0.9572 | 548.1 | 0.9570
The first query reads the level the converter recorded, not the final one. The first query reads the level the converter recorded, not the final one.
A receipt is a signed record that a reviewer checked certain nodes against the page. A receipt is a signed record that a reviewer checked certain nodes against the page.
Receipts by `ana` raise `e4fkseg` and `r1gacps` to F3; `eajq93t` stays at F0 because the only receipt that covered it, by `cara`, was revoked. Receipts by `ana` raise `ec5jc93` and `a4jrz2t` to F3; `xjns57z` stays at F0 because the only receipt that covered it, by `cara`, was revoked.
To compute the final level, check each receipt's signature, revocations and spot-checks, as [chapter 8](../spec/08-fidelity.md#82-levels) describes. To compute the final level, check each receipt's signature, revocations and spot-checks, as [chapter 8](../spec/08-fidelity.md#82-levels) describes.
The `scope` column of the third query shows the value `targeted:lode`, which is data in the fixture, copied here exactly as the query prints it. The `scope` column of the third query shows the value `targeted:lode`, which is data in the fixture, copied here exactly as the query prints it.
@@ -239,11 +239,11 @@ This shows what the checks catch.
Change one digit in a fixture and run the checks: Change one digit in a fixture and run the checks:
```sh ```sh
sed -i 's/1718 cm/1719 cm/' fixtures/packages/okafor2025open/nodes.jsonl sed -i 's/1718 cm/1719 cm/' fixtures/packages/okafor2025solvent-acth/nodes.jsonl
pixi run quick pixi run quick
``` ```
The checker reports three failures: the SHA-256 of `nodes.jsonl` no longer matches the manifest, unloading the package from the database no longer gives the same bytes, and the package hash differs after unloading. The checker reports three failures: the SHA-256 of `nodes.jsonl` no longer matches the manifest, unloading the package from the database no longer gives the same bytes, and the package hash differs after unloading.
Restore the file with `git checkout fixtures/packages/okafor2025open/nodes.jsonl`. Restore the file with `git checkout fixtures/packages/okafor2025solvent-acth/nodes.jsonl`.
The broken packages in [fixtures/invalid/](../fixtures/invalid/) are this kind of change, each with the rule it breaks. The broken packages in [fixtures/invalid/](../fixtures/invalid/) are this kind of change, each with the rule it breaks.
`git checkout` restores a tracked file, so run this only in a clone you can reset. `git checkout` restores a tracked file, so run this only in a clone you can reset.
docs/faq.md
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@@ -13,12 +13,18 @@ Every file is JSON or JSON Lines (one JSON value per line), and [spec/](../spec/
## Why not keep using PDFs and page numbers? ## Why not keep using PDFs and page numbers?
A page number names a region, not a statement, and it changes between a preprint and the version of record. A page number names a region, not a statement, and it changes between a preprint and the version of record.
An address names a sentence or a cell by its ID, such as `hale2026harmonic#j06tfhn`. An address names a sentence or a cell by its ID, such as `hale2026harmonic-damb#v3063qv`.
It can add a pin (the first six hex digits of the node's hash) and character offsets, which lets a reader check the address against the exact text ([spec/06 §6.1](../spec/06-anchors.md#61-addresses)). It can add a pin (the first six hex digits of the node's hash) and character offsets, which lets a reader check the address against the exact text ([spec/06 §6.1](../spec/06-anchors.md#61-addresses)).
An ID encodes no page, position or kind. An ID encodes no page, position or kind.
The system mints it once from the document key, kind, text hash and occurrence, then freezes it ([spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids)). The system mints it once from the document key, kind, text hash and occurrence, then freezes it ([spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids)).
## Why does a key end in four odd characters?
`hale2026harmonic-damb` is the paper's key: the citation key a reader would use, then four characters of a hash of its DOI.
Citation keys alone collide, between a preprint and its published version or two papers by one author in one year; the hash settles that, and any tool that knows the DOI can recompute it.
A key is minted once and never recomputed, so a corrected title does not change a key someone has cited ([spec/02 §2.4](../spec/02-model.md#24-work-and-document-keys)).
## Why are numbers stored as strings? ## Why are numbers stored as strings?
Databases and JSON libraries rewrite numbers: `310.0` becomes `310` and `1.5260` becomes `1.526`, and the printed digits are part of what a paper says. Databases and JSON libraries rewrite numbers: `310.0` becomes `310` and `1.5260` becomes `1.526`, and the printed digits are part of what a paper says.
@@ -96,12 +102,12 @@ The full comparison is [docs/comparison.md](comparison.md)
## What is its status and maturity? ## What is its status and maturity?
Version 0.1.0 has 29 formats: 18 are `candidate` and 11 are `provisional`, as [registry/formats.json](../registry/formats.json) lists. Version 0.1.0 has 32 formats: 19 are `candidate` and 13 are `provisional`, as [registry/formats.json](../registry/formats.json) lists.
A `candidate` format is complete, with vectors and fixtures, and ready to implement. A `candidate` format is complete, with vectors and fixtures, and ready to implement.
A `provisional` one is complete and expected to change as implementations gain experience. A `provisional` one is complete and expected to change as implementations gain experience.
The provisional formats are dataset, digitization, view, project, bundle, snapshot, draft-ids, exercise, submission, grade and checklist. The provisional formats are dataset, digitization, view, project, bundle, snapshot, draft-ids, exercise, submission, grade, checklist, log-entry and checkpoint.
The repository holds a reference checker (`tools/check.py`), 21 vector files, five valid packages, one of them also as a zip, and 28 deliberately broken packages ([spec/00 §0.4](../spec/00-introduction.md#04-status), [spec/22](../spec/22-conformance.md)). The repository holds a reference checker (`tools/check.py`), 25 vector files, five valid packages, one of them also as a zip, and 31 deliberately broken packages ([spec/00 §0.4](../spec/00-introduction.md#04-status), [spec/22](../spec/22-conformance.md)).
## What does it not do? ## What does it not do?
docs/glossary.md
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@@ -36,6 +36,10 @@ Checklist
: A record of checking an export, such as accessible HTML, against a named standard, criterion by criterion; it is covered by the receipt of the person who checked. : A record of checking an export, such as accessible HTML, against a named standard, criterion by criterion; it is covered by the receipt of the person who checked.
Format `scienting-checklist/1`, `provisional`. ([8.11](../spec/08-fidelity.md#811-checklists)) Format `scienting-checklist/1`, `provisional`. ([8.11](../spec/08-fidelity.md#811-checklists))
Checkpoint
: A signed note that states a transparency log's size and root hash, which a verifier checks against the last checkpoint it saw.
Format `scienting-checkpoint/1`, `provisional`. ([23.2](../spec/23-log.md#232-checkpoints))
Correction Correction
: An operation on an established document, with its evidence and author; never edited, only appended. ([11](../spec/11-corrections.md)) : An operation on an established document, with its evidence and author; never edited, only appended. ([11](../spec/11-corrections.md))
@@ -45,6 +49,9 @@ Description
Document Document
: The text established for one version of one work, from one or more witnesses, as a tree of nodes. ([2.1](../spec/02-model.md#21-four-objects), [3](../spec/03-nodes.md)) : The text established for one version of one work, from one or more witnesses, as a tree of nodes. ([2.1](../spec/02-model.md#21-four-objects), [3](../spec/03-nodes.md))
Document key
: The work key, with a dotted suffix for any version other than the version of record: `.si` for Supporting Information, `.v2` for a second preprint. ([2.4](../spec/02-model.md#24-work-and-document-keys))
Drift Drift
: The amount that has changed below a container since an anchor on it was made, counted from the corrections: the share of the container's leaves touched by later corrections. : The amount that has changed below a container since an anchor on it was made, counted from the corrections: the share of the container's leaves touched by later corrections.
It is reported as `none`, `low` or `high`, with a default threshold of a quarter. ([6.6](../spec/06-anchors.md#66-drift)) It is reported as `none`, `low` or `high`, with a default threshold of a quarter. ([6.6](../spec/06-anchors.md#66-drift))
@@ -56,10 +63,13 @@ The key is anchors, a verdict, a chain, a value or planted errors, by exercise k
Fidelity level Fidelity level
: How far a leaf's text was checked against its source, from F0 converted to F3 proofread. ([8.1](../spec/08-fidelity.md#81-levels-of-fidelity)) : How far a leaf's text was checked against its source, from F0 converted to F3 proofread. ([8.1](../spec/08-fidelity.md#81-levels-of-fidelity))
History root
: The root of the Merkle tree over a document's corrections, kept in `document.json`, so a consistency proof can show that a later revision extends an earlier one. ([11.5](../spec/11-corrections.md#115-the-history-root))
JATS JATS
: Outside term. : Outside term.
Journal Article Tag Suite, ANSI/NISO Z39.96-2024, an XML format in which publishers and archives exchange journal content ([the NISO page](https://www.niso.org/publications/z3996-2024-jats)). Journal Article Tag Suite, ANSI/NISO Z39.96-2024, an XML format in which publishers and archives exchange journal content ([the NISO page](https://www.niso.org/publications/z3996-2024-jats)).
In paperspec, `jats` is a witness kind: the fixture `okafor2025open` was established from a JATS file and a PDF that agree. In paperspec, `jats` is a witness kind: the fixture `okafor2025solvent-acth` was established from a JATS file and a PDF that agree.
The formats ingest JATS and do not replace it. ([2.3](../spec/02-model.md#23-witnessesjson)) The formats ingest JATS and do not replace it. ([2.3](../spec/02-model.md#23-witnessesjson))
Keyed hash Keyed hash
@@ -101,6 +111,10 @@ Policy
: A project owner's signed decision that settles rights a record leaves unknown. : A project owner's signed decision that settles rights a record leaves unknown.
It never overrides a use the record sets to true or false. ([14.2](../spec/14-rights.md#142-effective-uses)) It never overrides a use the record sets to true or false. ([14.2](../spec/14-rights.md#142-effective-uses))
Proof
: An RFC 9162 inclusion proof that one item was covered by a receipt, or a consistency proof that one history extends another, each a short list of hashes.
Format `scienting-proof/1`. ([8.5](../spec/08-fidelity.md#85-merkle-roots))
Project Project
: A team's curated set of documents, with its members, layers, data, reading paths and drafts. : A team's curated set of documents, with its members, layers, data, reading paths and drafts.
Format `scienting-project/1`, `provisional`. ([20](../spec/20-projects.md)) Format `scienting-project/1`, `provisional`. ([20](../spec/20-projects.md))
@@ -156,6 +170,9 @@ Verdict
Version Version
: One expression of a work: a preprint, the version of record, an erratum, the Supporting Information. ([2.1](../spec/02-model.md#21-four-objects)) : One expression of a work: a preprint, the version of record, an erratum, the Supporting Information. ([2.1](../spec/02-model.md#21-four-objects))
VRF
: A verifiable random function (RFC 9381): a keyed function with exactly one valid proof for each key and input, so that a spot-check seed can be checked but not chosen. ([8.8](../spec/08-fidelity.md#88-spot-checks))
Web Annotation Web Annotation
: Outside term. : Outside term.
The W3C Recommendation of 23 February 2017 for annotations with a body, a target and a motivation ([the W3C model](https://www.w3.org/TR/annotation-model/)). The W3C Recommendation of 23 February 2017 for annotations with a body, a target and a motivation ([the W3C model](https://www.w3.org/TR/annotation-model/)).
@@ -167,3 +184,6 @@ Witness
Work Work
: A piece of scholarship across all its versions. ([2.1](../spec/02-model.md#21-four-objects)) : A piece of scholarship across all its versions. ([2.1](../spec/02-model.md#21-four-objects))
Work key
: A work's permanent name: a Scholar-style citation key, a hyphen, and the first characters of a hash of the work's identity, such as `vaswani2017attention-a241`; minted once and never recomputed. ([2.4](../spec/02-model.md#24-work-and-document-keys))
docs/overview.md
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@@ -26,7 +26,7 @@ The formats supply those three, and they are worth most at the scale of one team
paperspec is a set of file formats for scientific papers that have been converted, split into addressable pieces and checked. paperspec is a set of file formats for scientific papers that have been converted, split into addressable pieces and checked.
The repository is at <https://git.scient.ing/infra/paperspec>. The repository is at <https://git.scient.ing/infra/paperspec>.
It is version 0.1.0 and defines 29 formats; in [registry/formats.json](../registry/formats.json), 18 are `candidate` and 11 are `provisional`. It is version 0.1.0 and defines 32 formats; in [registry/formats.json](../registry/formats.json), 19 are `candidate` and 13 are `provisional`.
## Who it is for ## Who it is for
@@ -51,12 +51,12 @@ It appears inside hashed data and test vectors, and it is separate from the repo
| Folder | Holds | | Folder | Holds |
| --- | --- | | --- | --- |
| [spec/](../spec/README.md) | The specification, in 23 chapters (00 to 22). Normative. | | [spec/](../spec/README.md) | The specification, in 24 chapters (00 to 23). Normative. |
| [schemas/](../schemas/README.md) | 39 JSON (plain-text data format) Schemas for the files and records. | | [schemas/](../schemas/README.md) | 42 JSON (plain-text data format) Schemas for the files and records. |
| [registry/](../registry/README.md) | The list of formats, the rule IDs a checker reports, download-stamp rules, and default rights requirements. | | [registry/](../registry/README.md) | The list of formats, the rule IDs a checker reports, download-stamp rules, and default rights requirements. |
| [tools/](../tools/README.md) | Reference programs: `check.py` checks everything, `build.py` rebuilds the fixtures and vectors, `load.py` loads packages into SQLite, and `oracle/` is a compact implementation of every rule. | | [tools/](../tools/README.md) | Reference programs: `check.py` checks everything, `build.py` rebuilds the fixtures and vectors, `load.py` loads packages into SQLite, and `oracle/` is a compact implementation of every rule. |
| [vectors/](../vectors/README.md) | 21 files of test vectors: inputs and the exact outputs every implementation must compute. | | [vectors/](../vectors/README.md) | 25 files of test vectors: inputs and the exact outputs every implementation must compute. |
| [fixtures/](../fixtures/README.md) | Five valid example packages, one of them also as a zip, 28 deliberately broken ones that each break one named rule, example records, and the test keys that signed them. All text is synthetic. | | [fixtures/](../fixtures/README.md) | Five valid example packages, one of them also as a zip, 31 deliberately broken ones that each break one named rule, example records, and the test keys that signed them. All text is synthetic. |
| [sql/](../sql/README.md) | Tables for SQLite, Dolt and PostgreSQL, and a SQLite bundle with full-text search. | | [sql/](../sql/README.md) | Tables for SQLite, Dolt and PostgreSQL, and a SQLite bundle with full-text search. |
| [context/](../context/README.md) | The JSON-LD context that makes annotation layers W3C Web Annotations. | | [context/](../context/README.md) | The JSON-LD context that makes annotation layers W3C Web Annotations. |
| [docs/](README.md) | Guides, including this page. | | [docs/](README.md) | Guides, including this page. |
@@ -107,7 +107,7 @@ The [specification's reading paths](../spec/README.md) say which chapters each r
A store loads the package into a database. A store loads the package into a database.
A reader renders it with layers of annotations. A reader renders it with layers of annotations.
Anchors (stored references to a sentence, with its hash and a quotation) let a claim, a dataset value or a draft's citation point at a passage. Anchors (stored references to a sentence, with its hash and a quotation) let a claim, a dataset value or a draft's citation point at a passage.
Datasets, drafts, views, projects, exercises and checklists are `provisional` formats. Datasets, drafts, views, projects, exercises, checklists and the transparency log are `provisional` formats.
7. 7.
Check and sign. Check and sign.
People proofread what matters and sign receipts; second reviewers spot-check them. People proofread what matters and sign receipts; second reviewers spot-check them.
docs/rationale.md
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@@ -9,7 +9,7 @@ Implementers find the chapter that defines each rule.
Experts find the cost of each choice and, where a neighboring standard chose differently, how it differs (the full comparison is in [comparison.md](comparison.md)). Experts find the cost of each choice and, where a neighboring standard chose differently, how it differs (the full comparison is in [comparison.md](comparison.md)).
The formats are at version 0.1.0. The formats are at version 0.1.0.
Of the 29 in `registry/formats.json`, 18 are `candidate` and 11 are `provisional`, and the provisional ones are named where they appear. Of the 29 in `registry/formats.json`, 19 are `candidate` and 13 are `provisional`, and the provisional ones are named where they appear.
The repository is paperspec, at <https://git.scient.ing/infra/paperspec>. The repository is paperspec, at <https://git.scient.ing/infra/paperspec>.
The `scienting-` prefix in format names such as `scienting-anchor/1` is the formats' namespace, separate from the repository's name. The `scienting-` prefix in format names such as `scienting-anchor/1` is the formats' namespace, separate from the repository's name.
@@ -36,6 +36,18 @@ The cost is that two conversions that read a sentence differently by one charact
Everything a team builds points at IDs: notes, claims, dataset values, citations in drafts. Everything a team builds points at IDs: notes, claims, dataset values, citations in drafts.
A merge records its successor, a deletion records that there is none, and legacy IDs live on as aliases, all in `ids.jsonl` ([spec/04 §4.3](../spec/04-identity.md#43-permanence-retirement-and-aliases)). A merge records its successor, a deletion records that there is none, and legacy IDs live on as aliases, all in `ids.jsonl` ([spec/04 §4.3](../spec/04-identity.md#43-permanence-retirement-and-aliases)).
### Work keys carry a hash
A citation key such as `vaswani2017attention` is what readers say, and it collides: a preprint and its published version, or two papers by one first author in one year with the same first title word, would share it.
Four characters of a hash of the work's identity, its DOI when it has one, settle the collision and let any tool holding the DOI recompute the key.
The key is minted once and never recomputed, so a corrected title cannot change a name someone has cited; when two works still share four characters, the later one gets six ([spec/02 §2.4](../spec/02-model.md#24-work-and-document-keys)).
The rule is the one the studio's reading-list tool already uses, so a paper keeps its key from the reading list to the store.
### Identifiers are tag URIs
Layers, annotations and documents name themselves with `tag:scient.ing,2026:` URIs (RFC 4151) rather than `urn:` names, because a URN namespace must be registered with IANA and this one is not.
A tag URI needs only a domain and a date, and these identifiers sit inside hashed annotations, so the cheap time to choose was before release.
### Revisions are counted, not timed ### Revisions are counted, not timed
Anchors are made on different machines and packages are imported later, and clocks disagree. Anchors are made on different machines and packages are imported later, and clocks disagree.
@@ -97,6 +109,11 @@ An offset counts Unicode code points, the numbered characters of Unicode, into t
Every stored offset is still exact when `node_hash` is unchanged, and a renderer can slice the stored text without normalizing it first. Every stored offset is still exact when `node_hash` is unchanged, and a renderer can slice the stored text without normalizing it first.
Only the three text values, `text_hash`, `match_hash` and `align_key`, normalize. Only the three text values, `text_hash`, `match_hash` and `align_key`, normalize.
### The character data is pinned to one Unicode version
Normalization and General Categories change between Unicode versions, and both enter every hash.
The chapters pin Unicode 16.0, the reference tools refuse to run on another version, and moving to a later one is a change to every text-hashing format ([spec/01 §1.4](../spec/01-conventions.md#14-text-normalization-for-hashing)).
### Hashes that leave the team are keyed ### Hashes that leave the team are keyed
A plain hash of "310.0" is recovered by hashing guesses, and overlapping anchors can rebuild passages. A plain hash of "310.0" is recovered by hashing guesses, and overlapping anchors can rebuild passages.
@@ -156,6 +173,11 @@ Readings drop spans, roles and header paths, not only words, and those need a co
Drift is computed from the records alone, with no need to replay history, because each record carries `path`, `to_path` and `touched` ([spec/11 §11.3](../spec/11-corrections.md#113-applied-fields)). Drift is computed from the records alone, with no need to replay history, because each record carries `path`, `to_path` and `touched` ([spec/11 §11.3](../spec/11-corrections.md#113-applied-fields)).
### The history has a root
Corrections are append-only in principle, but nothing in a package proved that a later revision extends an earlier one rather than rewriting it.
A Merkle root over the corrections in `document.json`, with RFC 9162 consistency proofs between revisions, does ([spec/11 §11.5](../spec/11-corrections.md#115-the-history-root)).
### Digits need image evidence ### Digits need image evidence
A wrong digit changes a result without looking wrong, so no digit changes without a crop of the page as evidence, and no leaf outside the correction's `touched` list may end up with different digits ([spec/11 §11.4](../spec/11-corrections.md#114-the-gate)). A wrong digit changes a result without looking wrong, so no digit changes without a crop of the page as evidence, and no leaf outside the correction's `touched` list may end up with different digits ([spec/11 §11.4](../spec/11-corrections.md#114-the-gate)).
@@ -182,11 +204,17 @@ The receipt tree follows [RFC 6962](https://www.rfc-editor.org/rfc/rfc6962), who
The specification makes a receipt with no items invalid, where the RFC hashes the empty list ([spec/08 §8.5](../spec/08-fidelity.md#85-merkle-roots)). The specification makes a receipt with no items invalid, where the RFC hashes the empty list ([spec/08 §8.5](../spec/08-fidelity.md#85-merkle-roots)).
The tree is not the one behind `node_hash`, which hashes each node's `own_hash` with its children's `node_hash` values. The tree is not the one behind `node_hash`, which hashes each node's `own_hash` with its children's `node_hash` values.
### Spot-check samples come from a signature nobody can steer ### Spot-check seeds are VRF proofs
A seed the reviewer could influence could be ground until the sample fell on careful work. A seed the reviewer could influence could be ground until the sample fell on careful work, and a seed the checker could vary could be ground by the checker.
The checker's deterministic Ed25519 signature over the receipt is unpredictable to the reviewer and unchoosable by the checker, because the checker's key was registered for spot-checks before the original was signed. An earlier draft used the checker's Ed25519 signature and called it unchoosable because signing is deterministic; that holds only for an honest checker, since a verifier accepts any valid signature and a dishonest one can sign with any nonce.
Anyone can recompute the sample ([spec/08 §8.8](../spec/08-fidelity.md#88-spot-checks)). A verifiable random function (RFC 9381) has exactly one valid proof for a key and an input, which is the property the rule needs, and its keys are ordinary Ed25519 keys, so the roster needs nothing new.
Anyone can verify the proof and recompute the sample ([spec/08 §8.8](../spec/08-fidelity.md#88-spot-checks)).
### A receipt can be proven without being shown
The receipt tree follows RFC 9162 so that an inclusion proof, a dozen hashes, shows a buyer that one cell was proofread without handing over the receipt or the other nodes ([spec/08 §8.5](../spec/08-fidelity.md#85-merkle-roots)).
A transparency log of receipts, revocations and rosters ([spec/23](../spec/23-log.md)) uses the same tree and the checkpoint format transparency logs share, so that a receipt's time and the roster that governed it stop being self-asserted.
### Error rates are reported as bounds ### Error rates are reported as bounds
@@ -270,6 +298,18 @@ These are settled for now, and a future version may revisit them.
| Which drift threshold, spot-check rate and digit rule should teams use? | By default, drift is high above a quarter of the leaves involved, and spot-checks sample 5% of a receipt's nodes, at least ten. The digit rule is `all`, `anchored-sections` or `none`; each is set per project. | | Which drift threshold, spot-check rate and digit rule should teams use? | By default, drift is high above a quarter of the leaves involved, and spot-checks sample 5% of a receipt's nodes, at least ten. The digit rule is `all`, `anchored-sections` or `none`; each is set per project. |
| How should rights combine when a document comes from witnesses held on different bases? | The most restrictive witness governs each use. | | How should rights combine when a document comes from witnesses held on different bases? | The most restrictive witness governs each use. |
## Looking ahead
Choices made so that the formats still serve in the 2030s, and the ones deliberately left open.
- Signature schemes `cose` and `ml-dsa-65` are reserved: COSE so that the IETF's SCITT transparency services can verify receipts, ML-DSA (FIPS 204) for the time Ed25519 is no longer considered safe.
A consumer treats an unimplemented scheme as invalid, so adopting either is a minor version ([spec/08 §8.4](../spec/08-fidelity.md#84-record-hashes-and-signatures)).
- Every hash is SHA-256, and the hashing scheme names only how a value is keyed, not the function.
A hash function change would be a new major version of every format; the formats accept that rather than carrying agility they cannot test.
- Roster keys are named by short keys, not by decentralized identifiers; a `did:key` form could be added as a key property without a new version.
- A correction's author may be a model and its run; a fuller provenance for model output (the model's identity, weights and prompt by hash) is left to the project that first needs it.
- A transparency log is specified but no deployment exists yet; its tile layout is left to the first one ([spec/23](../spec/23-log.md)).
## Known limits ## Known limits
- Notation drops spaces and text keeps them, so `$T = 300$` from a LaTeX source and "T = 300" from a PDF disagree, and become a `word` suspect for review. - Notation drops spaces and text keeps them, so `$T = 300$` from a LaTeX source and "T = 300" from a PDF disagree, and become a `word` suspect for review.
docs/walkthrough.md
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@@ -1,17 +1,17 @@
# Walkthrough: one paper, start to finish # Walkthrough: one paper, start to finish
This guide follows the example paper `hale2026harmonic` from a flawed first reading to a corrected, reviewed and signed document. This guide follows the example paper `hale2026harmonic-damb` from a flawed first reading to a corrected, reviewed and signed document.
The paper is synthetic, written for the fixtures. The paper is synthetic, written for the fixtures.
Its problems are modeled on the failures that the specification's rules address. Its problems are modeled on the failures that the specification's rules address.
Three readers can use the guide, and each gets something different. Three readers can use the guide, and each gets something different.
A newcomer knows what a paper and a citation are, not hashes or JSON, so every term is defined where it first appears. A newcomer knows what a paper and a citation are, not hashes or JSON, so every term is defined where it first appears.
An implementer who will write a reader, writer, converter or checker gets the chapter and test vector for each step. An implementer who will write a reader, writer, converter or checker gets the chapter and test vector for each step.
An expert gets the status: [paperspec](https://git.scient.ing/infra/paperspec) is at version 0.1.0, and each format is `candidate` or `provisional` in [`registry/formats.json`](../registry/formats.json) (18 candidate, 11 provisional). An expert gets the status: [paperspec](https://git.scient.ing/infra/paperspec) is at version 0.1.0, and each format is `candidate` or `provisional` in [`registry/formats.json`](../registry/formats.json) (19 candidate, 13 provisional).
The `scienting-` prefix on format names, as in `scienting-doc/1`, is the formats' namespace. The `scienting-` prefix on format names, as in `scienting-doc/1`, is the formats' namespace.
It has nothing to do with the repository's name. It has nothing to do with the repository's name.
Open [fixtures/packages/hale2026harmonic/](../fixtures/packages/hale2026harmonic/) beside this page, because every ID below is in it. Open [fixtures/packages/hale2026harmonic-damb/](../fixtures/packages/hale2026harmonic-damb/) beside this page, because every ID below is in it.
A package is a folder of files, mostly JSON Lines (`.jsonl`: one JSON record per line). A package is a folder of files, mostly JSON Lines (`.jsonl`: one JSON record per line).
The hand-written source of the first reading is [fixtures/src/hale2026harmonic.json](../fixtures/src/hale2026harmonic.json); no converter ran on it, and [`tools/build.py`](../tools/build.py) expands it into the package. The hand-written source of the first reading is [fixtures/src/hale2026harmonic.json](../fixtures/src/hale2026harmonic.json); no converter ran on it, and [`tools/build.py`](../tools/build.py) expands it into the package.
Each step says what a converter, a person or a checker does. Each step says what a converter, a person or a checker does.
@@ -26,7 +26,7 @@ Whether it allows processing in the team's cloud is unknown.
The publisher stamped the download in the margin with the institution and the time, so two downloads rarely share a SHA-256. The publisher stamped the download in the margin with the institution and the time, so two downloads rarely share a SHA-256.
A page fingerprint avoids the problem of downloads that differ in their stamps. A page fingerprint avoids the problem of downloads that differ in their stamps.
It is a hash of a page's text, size and images after the stamp lines are removed ([spec/07](../spec/07-geometry.md)), and the rules `downloaded-via` and `sharing-guidelines` fired on both pages (see [`pages.jsonl`](../fixtures/packages/hale2026harmonic/pages.jsonl)). It is a hash of a page's text, size and images after the stamp lines are removed ([spec/07](../spec/07-geometry.md)), and the rules `downloaded-via` and `sharing-guidelines` fired on both pages (see [`pages.jsonl`](../fixtures/packages/hale2026harmonic-damb/pages.jsonl)).
Page 101's fingerprint is `6272e6f3…` in this copy, stamped October 11, 2026, and in a second download from another institution, stamped March 2, 2027 ([vectors/fingerprints.jsonl](../vectors/fingerprints.jsonl)). Page 101's fingerprint is `6272e6f3…` in this copy, stamped October 11, 2026, and in a second download from another institution, stamped March 2, 2027 ([vectors/fingerprints.jsonl](../vectors/fingerprints.jsonl)).
## 2. The first reading, with its mistakes ## 2. The first reading, with its mistakes
@@ -57,34 +57,34 @@ Nothing changes until a correction passes the gate ([spec/11](../spec/11-correct
## 3. Twelve corrections ## 3. Twelve corrections
Each fix is appended to [`corrections.jsonl`](../fixtures/packages/hale2026harmonic/corrections.jsonl), numbered, with its evidence (a crop, or a person who read the page), its author (`ana` throughout) and its reason. Each fix is appended to [`corrections.jsonl`](../fixtures/packages/hale2026harmonic-damb/corrections.jsonl), numbered, with its evidence (a crop, or a person who read the page), its author (`ana` throughout) and its reason.
| # | Operation | On | What it did | | # | Operation | On | What it did |
| --- | --- | --- | --- | | --- | --- | --- | --- |
| 1 | `replace` | cell `nkm3xn5` | `3l0.0` to `310.0`. A digit changed, so the gate required a crop, and it has one. | | 1 | `replace` | cell `c20cna6` | `3l0.0` to `310.0`. A digit changed, so the gate required a crop, and it has one. |
| 2 | `replace` | sentence `e4fkseg` | `10-3` to the runs `10` and superscript `−3`. | | 2 | `replace` | sentence `ec5jc93` | `10-3` to the runs `10` and superscript `−3`. |
| 3 | `split` | sentence `e4fkseg` | Split before "Table 1"; the first part keeps `e4fkseg`, the second is new: `r1gacps`. | | 3 | `split` | sentence `ec5jc93` | Split before "Table 1"; the first part keeps `ec5jc93`, the second is new: `a4jrz2t`. |
| 4 | `merge` | sentence `eajq93t` | Joined with `e9rh611`, which is retired with `eajq93t` as its successor. | | 4 | `merge` | sentence `xjns57z` | Joined with `ayea71r`, which is retired with `xjns57z` as its successor. |
| 5 | `merge` | paragraph `zyqr0yc` | Joined with `g44k023`, retired the same way. | | 5 | `merge` | paragraph `gwzbj3s` | Joined with `ncx2v4f`, retired the same way. |
| 6 | `delete` | paragraph `nm7vyzk` | The running head is gone; its IDs are retired with no successor. | | 6 | `delete` | paragraph `v8e4z6z` | The running head is gone; its IDs are retired with no successor. |
| 7 | `relabel` | equation `qn08tj9` | `(l)` to `(1)`. | | 7 | `relabel` | equation `tkxsmts` | `(l)` to `(1)`. |
| 8 | `delete` | row `tfjge3c` | The garbled CT–HC row and its four cells. | | 8 | `delete` | row `rncchma` | The garbled CT–HC row and its four cells. |
| 9 | `insert` | row `fbg2mwq` | The CT–HC row, read again: five new cells. | | 9 | `insert` | row `kx2kz2y` | The CT–HC row, read again: five new cells. |
| 10 | `insert` | row `j0x5twd` | The missing OW–HW row. | | 10 | `insert` | row `ke0jxpn` | The missing OW–HW row. |
| 11 | `set` | cell `vtszvw9` | Set B's `colspan` from 1 to 2. | | 11 | `set` | cell `xyy7x6c` | Set B's `colspan` from 1 to 2. |
| 12 | `relabel` | figure `ajfvq4s` | `Figure l` to `Figure 1`. | | 12 | `relabel` | figure `v7cx6qs` | `Figure l` to `Figure 1`. |
The document is now at revision 12. The document is now at revision 12.
No uncorrected cell, sentence or row changed its ID or its hashes. No uncorrected cell, sentence or row changed its ID or its hashes.
Only corrected nodes and their ancestors got new `node_hash` values; the sentence `sxgcc9h` is one of the ancestors, because it holds the relabeled equation. Only corrected nodes and their ancestors got new `node_hash` values; the sentence `rr20tev` is one of the ancestors, because it holds the relabeled equation.
Inserting a row adds a row node. Inserting a row adds a row node.
The table's own hash (`own_hash`) covers only its label and column definitions, so every other cell, and every value already taken from them, is untouched. The table's own hash (`own_hash`) covers only its label and column definitions, so every other cell, and every value already taken from them, is untouched.
## 4. IDs that never move ## 4. IDs that never move
The sentence about water is still `f929eq9` after twelve corrections, the corrected cell is still `nkm3xn5`, and the sentence that lost its superscript is still `e4fkseg`. The sentence about water is still `hca6dc5` after twelve corrections, the corrected cell is still `c20cna6`, and the sentence that lost its superscript is still `ec5jc93`.
The retired IDs are recorded in [`ids.jsonl`](../fixtures/packages/hale2026harmonic/ids.jsonl), so anything that pointed at them can follow the trail. The retired IDs are recorded in [`ids.jsonl`](../fixtures/packages/hale2026harmonic-damb/ids.jsonl), so anything that pointed at them can follow the trail.
Legacy aliases are recorded there too: `b-p01-text-003`, the ID an older tool gave the water sentence, still leads to `f929eq9`. Legacy aliases are recorded there too: `b-p01-text-003`, the ID an older tool gave the water sentence, still leads to `hca6dc5`.
A fresh conversion of the same input mints the same IDs. A fresh conversion of the same input mints the same IDs.
A reading by a different converter is aligned with this document sentence by sentence ([spec/05 §5.6](../spec/05-hashes.md), pinned by [vectors/alignment.jsonl](../vectors/alignment.jsonl)). A reading by a different converter is aligned with this document sentence by sentence ([spec/05 §5.6](../spec/05-hashes.md), pinned by [vectors/alignment.jsonl](../vectors/alignment.jsonl)).
@@ -116,13 +116,13 @@ The table shows how each anchor resolves at revision 12 ([vectors/resolve.jsonl]
| The water sentence, through the alias `b-p01-text-003` | `current` | The alias leads to the same node. | | The water sentence, through the alias `b-p01-text-003` | `current` | The alias leads to the same node. |
| The cell that read `3l0.0` | `stale` | Its text changed and "3l0.0" is no longer in it; a person must look again. | | The cell that read `3l0.0` | `stale` | Its text changed and "3l0.0" is no longer in it; a person must look again. |
| "treated as zero" | `reattached` | The sentence changed twice, and the quote occurs in it exactly once, so the anchor is re-pinned. | | "treated as zero" | `reattached` | The sentence changed twice, and the quote occurs in it exactly once, so the anchor is re-pinned. |
| "fitted constants" | `stale` | After the split, those words are in the new sentence `r1gacps`, not in `e4fkseg`. | | "fitted constants" | `stale` | After the split, those words are in the new sentence `a4jrz2t`, not in `ec5jc93`. |
| "least squares", in the half-sentence `e9rh611` | `moved` | That ID was merged into `eajq93t`, which still holds the quote. | | "least squares", in the half-sentence `ayea71r` | `moved` | That ID was merged into `xjns57z`, which still holds the quote. |
| The paragraph `g44k023` | `moved` | Merged into `zyqr0yc`, which holds all of its sentences. | | The paragraph `ncx2v4f` | `moved` | Merged into `gwzbj3s`, which holds all of its sentences. |
| The running head | `stale` | Deleted, with no successor. | | The running head | `stale` | Deleted, with no successor. |
| The equation | `reattached` | Only its number changed. | | The equation | `reattached` | Only its number changed. |
| The figure | `reattached` | Only its label changed, by a `relabel`. | | The figure | `reattached` | Only its label changed, by a `relabel`. |
| The CT–HC cell `1.090` in the garbled row | `reattached` | Its row was deleted, and exactly one cell in Table 1 has the same row and column headers and the same text: the new `e0n07n0`. | | The CT–HC cell `1.090` in the garbled row | `reattached` | Its row was deleted, and exactly one cell in Table 1 has the same row and column headers and the same text: the new `b5gd0h1`. |
| Section 2 | `changed-below`, drift high | The section itself is unchanged, and 53% of what it holds or held was touched. | | Section 2 | `changed-below`, drift high | The section itself is unchanged, and 53% of what it holds or held was touched. |
| Table 1 | `changed-below`, drift high | Rows were replaced and added. | | Table 1 | `changed-below`, drift high | Rows were replaced and added. |
| The table body | `changed-below`, drift high | 75% of the cells it holds or held were touched. | | The table body | `changed-below`, drift high | 75% of the cells it holds or held were touched. |
@@ -141,23 +141,23 @@ See [comparison.md](comparison.md).
A receipt is a signed record that a person compared a set of nodes with the page. A receipt is a signed record that a person compared a set of nodes with the page.
It lifts a node to F3, the top fidelity level (F0 is one reading; F1, every doubtful place answered; F2, an independent witness agrees) ([spec/08](../spec/08-fidelity.md)). It lifts a node to F3, the top fidelity level (F0 is one reading; F1, every doubtful place answered; F2, an independent witness agrees) ([spec/08](../spec/08-fidelity.md)).
One signature covers a Merkle tree, a hash over everything reviewed in a sitting, built as in RFC 6962 (a Request for Comments standard; replaced by [RFC 9162](https://www.rfc-editor.org/rfc/rfc9162), which defines the same tree). One signature covers a Merkle tree, a hash over everything reviewed in a sitting, built as in RFC 6962 (a Request for Comments standard; replaced by [RFC 9162](https://www.rfc-editor.org/rfc/rfc9162), which defines the same tree).
The receipts are in [`receipts.jsonl`](../fixtures/packages/hale2026harmonic/receipts.jsonl), and the keys that signed them in [`roster.json`](../fixtures/packages/hale2026harmonic/roster.json). The receipts are in [`receipts.jsonl`](../fixtures/packages/hale2026harmonic-damb/receipts.jsonl), and the keys that signed them in [`roster.json`](../fixtures/packages/hale2026harmonic-damb/roster.json).
- **Before the corrections**, `ana` had signed receipt `c5cx7n4tga6y9` for three cells at revision 0. - **Before the corrections**, `ana` had signed receipt `npc15pn6675z5` for three cells at revision 0.
Two of them never changed, so the receipt still counts for them. Two of them never changed, so the receipt still counts for them.
For the corrected cell it no longer counts, because the cell's hash moved on. For the corrected cell it no longer counts, because the cell's hash moved on.
- After the corrections, `ana` signs `eqgbbpwb6725v` at F3 for 23 nodes: the cells of Table 1's three data rows (15), its four column headers, the equation, and three sentences (`e4fkseg`, `f929eq9` and `sxgcc9h`, the one holding the equation). - After the corrections, `ana` signs `y2zw8ctg5s8dp` at F3 for 23 nodes: the cells of Table 1's three data rows (15), its four column headers, the equation, and three sentences (`ec5jc93`, `hca6dc5` and `rr20tev`, the one holding the equation).
`ben` spot-checks it with receipt `h6yr2ddx6d3ef`. `ben` spot-checks it with receipt `mg18668nzxvap`.
His signature, made with his separate spot-check key `ben-spot`, picks 10 nodes nobody could have chosen, and he finds no errors. His signature, made with his separate spot-check key `ben-spot`, picks 10 nodes nobody could have chosen, and he finds no errors.
- `ana` signs `zaxky8c1y12tc` for two sentences of section 1, including the new `r1gacps`. - `ana` signs `mvjmb94nz7rdh` for two sentences of section 1, including the new `a4jrz2t`.
- `cara` signs `adtrpq41np7sd` for three sentences on page 2, then revokes it herself (`q0yg0w6ygwwxh`) because she had compared them with the crops of another paper. - `cara` signs `q465jpwz8afhe` for three sentences on page 2, then revokes it herself (`pcbhtpwvysgq6`) because she had compared them with the crops of another paper.
Those sentences fall back to their earlier levels, which is why `eajq93t` is still F0. Those sentences fall back to their earlier levels, which is why `xjns57z` is still F0.
- `ana` signs `gena76nkb6cnc` for the figure's three caption sentences. `ben`'s spot-check `tejzs01eqn2ym` finds a missing period in `nmm4md0`, which suspends the receipt until she reviews the sitting again and signs a new one. - `ana` signs `gx2s84z9jf9xv` for the figure's three caption sentences. `ben`'s spot-check `yt70fcc3qm0xb` finds a missing period in `caehhp6`, which suspends the receipt until she reviews the sitting again and signs a new one.
The document's report, in [`document.json`](../fixtures/packages/hale2026harmonic/document.json), counts the result over 45 leaves: 27 at F3, 13 at F2, 4 at F1 and 1 at F0. The document's report, in [`document.json`](../fixtures/packages/hale2026harmonic-damb/document.json), counts the result over 45 leaves: 27 at F3, 13 at F2, 4 at F1 and 1 at F0.
The 27 are the 23 nodes of `eqgbbpwb6725v`, the 2 of `zaxky8c1y12tc`, and 2 of the 3 caption sentences. The 27 are the 23 nodes of `y2zw8ctg5s8dp`, the 2 of `mvjmb94nz7rdh`, and 2 of the 3 caption sentences.
Those two still count because Ben's spot-check is itself a valid receipt, and he compared them with the page and found them right. Those two still count because Ben's spot-check is itself a valid receipt, and he compared them with the page and found them right.
The third, `nmm4md0`, stays at F2: a spot-check never raises a node it found in error ([spec/08 §8.2](../spec/08-fidelity.md#82-levels)). The third, `caehhp6`, stays at F2: a spot-check never raises a node it found in error ([spec/08 §8.2](../spec/08-fidelity.md#82-levels)).
## 7. Data out of the table ## 7. Data out of the table
@@ -171,7 +171,7 @@ The reference checker, [`tools/check.py`](../tools/check.py), confirms each CSV
## 8. Sharing without the text ## 8. Sharing without the text
The team wants to move its notes to another of its own machines without copying the paper there. The team wants to move its notes to another of its own machines without copying the paper there.
[`hale2026harmonic.checks-only`](../fixtures/packages/hale2026harmonic.checks-only/) is the same document with every leaf's text withheld and every hash replaced by an HMAC under the team's key ([spec/12 §12.5](../spec/12-package.md), [spec/05 §5.8](../spec/05-hashes.md)). [`hale2026harmonic-damb.checks-only`](../fixtures/packages/hale2026harmonic-damb.checks-only/) is the same document with every leaf's text withheld and every hash replaced by an HMAC under the team's key ([spec/12 §12.5](../spec/12-package.md), [spec/05 §5.8](../spec/05-hashes.md)).
An HMAC is a hash mixed with a secret key. An HMAC is a hash mixed with a secret key.
Anyone can recover a plain hash of a short text such as "310.0" by hashing guesses; a keyed hash resists that. Anyone can recover a plain hash of a short text such as "310.0" by hashing guesses; a keyed hash resists that.
Corrections, receipts, the roster and the dataset are left out too. Corrections, receipts, the roster and the dataset are left out too.
fixtures/README.md
+6 -1
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@@ -28,7 +28,7 @@ A conforming reader accepts each one and recomputes every hash it contains.
| `packages/hale2026harmonic/` | The main example, followed step by step in [the walkthrough](../docs/walkthrough.md): a chemistry paper that was read once with mistakes and then fixed by twelve corrections. It has a table with two levels of column headers and grouped rows, an equation inside a sentence, a footnote, a figure with text inside its panels and a real image, references, legacy aliases, boxes on fingerprinted pages, receipts in every state (counting, partly invalidated, spot-checked, revoked and suspended), the roster of public keys that checks their signatures, a dataset taken from the table, and derived MathML. | | `packages/hale2026harmonic/` | The main example, followed step by step in [the walkthrough](../docs/walkthrough.md): a chemistry paper that was read once with mistakes and then fixed by twelve corrections. It has a table with two levels of column headers and grouped rows, an equation inside a sentence, a footnote, a figure with text inside its panels and a real image, references, legacy aliases, boxes on fingerprinted pages, receipts in every state (counting, partly invalidated, spot-checked, revoked and suspended), the roster of public keys that checks their signatures, a dataset taken from the table, and derived MathML. |
| `packages/hale2026harmonic.checks-only/` | The same document prepared for sharing within the team: text withheld, every hash an HMAC (a hash computed under a secret key) under the team key. The team key is derived from the team secret in `keys/` ([spec/05](../spec/05-hashes.md), [spec/12 section 12.5](../spec/12-package.md#125-text-policies)). It shows how a team can share its checks on a paywalled paper without sharing the paper. | | `packages/hale2026harmonic.checks-only/` | The same document prepared for sharing within the team: text withheld, every hash an HMAC (a hash computed under a secret key) under the team key. The team key is derived from the team secret in `keys/` ([spec/05](../spec/05-hashes.md), [spec/12 section 12.5](../spec/12-package.md#125-text-policies)). It shows how a team can share its checks on a paywalled paper without sharing the paper. |
| `packages/okafor2025open/` | An open-access paper established from a JATS file (an XML format for journal articles) and a PDF that agree, so every leaf is at fidelity F2, corroborated by an independent witness. | | `packages/okafor2025open/` | An open-access paper established from a JATS file (an XML format for journal articles) and a PDF that agree, so every leaf is at fidelity F2, corroborated by an independent witness. |
| `packages/smithlab2027charges/` | A short draft written in Typst (a typesetting language). One of its sentences holds a cross-reference whose target is the address `hale2026harmonic#r1gacps`, a sentence of the main example. | | `packages/smithlab2027charges/` | A short draft written in Typst (a typesetting language). One of its sentences holds a cross-reference whose target is the address `hale2026harmonic#a4jrz2t`, a sentence of the main example. |
| `packages/tiny2026example/` | A small document, the starting point of the correction vectors (`vectors/corrections.jsonl`) and of every broken package below. | | `packages/tiny2026example/` | A small document, the starting point of the correction vectors (`vectors/corrections.jsonl`) and of every broken package below. |
| `packages/tiny2026example.sct.zip` | The same document as a zipped package, written the way a producer makes a byte-identical archive: entries under one folder named by the key, sorted by path, stored, dated 1980-01-01, with no extra fields ([spec/12 section 12.2](../spec/12-package.md#122-paths)). A reader unpacks it to exactly the folder beside it. | | `packages/tiny2026example.sct.zip` | The same document as a zipped package, written the way a producer makes a byte-identical archive: entries under one folder named by the key, sorted by path, stored, dated 1980-01-01, with no extra fields ([spec/12 section 12.2](../spec/12-package.md#122-paths)). A reader unpacks it to exactly the folder beside it. |
@@ -52,6 +52,8 @@ Each record is a single file, or a folder where a format needs several files.
| `suspect.json` | A doubtful reading raised for review: the converter's reading of an exponent in the main example, before the first correction answered it. | | `suspect.json` | A doubtful reading raised for review: the converter's reading of an exponent in the main example, before the first correction answered it. |
| `qa-report.json` | Reviewer error bounds for a delivery that covers two of the main example's receipts, signed by the team's owner key. | | `qa-report.json` | Reviewer error bounds for a delivery that covers two of the main example's receipts, signed by the team's owner key. |
| `checklist/` | A conformance checklist (`checklist.json`) for an accessible HTML export of the main example, checked against WCAG 2.1 AA criterion by criterion, and the receipt that covers it at its hash (`receipt.json`). The format is `provisional`. | | `checklist/` | A conformance checklist (`checklist.json`) for an accessible HTML export of the main example, checked against WCAG 2.1 AA criterion by criterion, and the receipt that covers it at its hash (`receipt.json`). The format is `provisional`. |
| `proof-inclusion.json`, `proof-consistency.json` | Two RFC 9162 proofs: that one node was covered by the main example's first receipt without showing the rest, and that revision 12 of its correction history extends revision 8 rather than rewriting it. |
| `checkpoint.json` | A signed checkpoint of the team's transparency log over the main example's receipts, revocations and roster, as the parsed form of its signed note. The format is `provisional`. |
| `project.json`, `digitization.json`, `digitization-confirmation.json`, `datasets/`, `view.vl.json`, `snapshot.json`, `draft-ids.jsonl` | A team project; values read off the main example's figure by hand, the receipt that confirms them, and the dataset they yield; a Vega-Lite chart pinned to that dataset; what the draft cites, pinned; and the sentence IDs of the draft's Typst project. These formats are `provisional`. | | `project.json`, `digitization.json`, `digitization-confirmation.json`, `datasets/`, `view.vl.json`, `snapshot.json`, `draft-ids.jsonl` | A team project; values read off the main example's figure by hand, the receipt that confirms them, and the dataset they yield; a Vega-Lite chart pinned to that dataset; what the draft cites, pinned; and the sentence IDs of the draft's Typst project. These formats are `provisional`. |
## Broken packages ## Broken packages
@@ -71,6 +73,9 @@ A conforming implementation refuses every one of them and should report that rul
| `empty-optional-file/` | An optional JSONL file with no records. | `package.file.empty` | | `empty-optional-file/` | An optional JSONL file with no records. | `package.file.empty` |
| `hash-mismatch/` | A node_hash that does not recompute. | `doc.hash.node-hash` | | `hash-mismatch/` | A node_hash that does not recompute. | `doc.hash.node-hash` |
| `heading-not-first/` | A heading must be a section's first child. | `doc.tree.child` | | `heading-not-first/` | A heading must be a section's first child. | `doc.tree.child` |
| `history-wrong/` | document.json's history is not the root over the corrections. | `doc.history` |
| `key-suffix/` | A work key whose hash part is not the hash of the work's DOI. | `doc.key.suffix` |
| `key-work/` | A document key whose suffix is not the version's. | `doc.key.work` |
| `location-unknown-page/` | A location on a page no witness has. | `doc.location.page` | | `location-unknown-page/` | A location on a page no witness has. | `doc.location.page` |
| `manifest-hash/` | A file changed after the manifest was written. | `package.manifest.hash` | | `manifest-hash/` | A file changed after the manifest was written. | `package.manifest.hash` |
| `manifest-key/` | The manifest names another key than document.json. | `package.manifest.key` | | `manifest-key/` | The manifest names another key than document.json. | `package.manifest.key` |
fixtures/invalid/alias-dangling/package/MANIFEST.json
+1 -1
View File
@@ -1 +1 @@
{"doc":"scienting-doc/1","files":[{"path":"document.json","sha256":"20a7d6ba83bf42a87e44f3b3f96bfb16ff545b199d82e54d3c17989e465281df","size":555},{"path":"ids.jsonl","sha256":"1eb53589cd394214dd4ee15be98a3dfbacec5e585a1e655fe2dfeff71a07e19e","size":61},{"path":"nodes.jsonl","sha256":"ffeffbf15cc9fe8182a31ef0bac32c1aef8c7a119706ac1e8a55aad218d0622c","size":11295},{"path":"provenance.json","sha256":"4bc7649bf6d3113f6c72b4016713654f57c8f03069632eabd1e6025c05cb9dac","size":226},{"path":"receipts.jsonl","sha256":"3f610039a8f883356201b63c9ad31afee630ebcbc0cc33bfb989a55716db85f0","size":2180},{"path":"references.jsonl","sha256":"bb5445037c28bf5fde215b4b831c29327dec6dd88259e2d53aabb995f2fdb98f","size":60},{"path":"roster.json","sha256":"4a6d29e8968143a4e19f485741c513245df1de77eec4ef9b3047c71db45cda22","size":924},{"path":"witnesses.json","sha256":"83ac4411c2efe65e0f7fc4c9336abbef6977cd32b0f90de029a7f8516afc3e97","size":750}],"format":"scienting-package/1","key":"tiny2026example"} {"doc":"scienting-doc/1","files":[{"path":"document.json","sha256":"20b269257831ddd1d064586fcee2c4b21c96c0c660bd3b4d0996197724e4b4e7","size":742},{"path":"ids.jsonl","sha256":"1eb53589cd394214dd4ee15be98a3dfbacec5e585a1e655fe2dfeff71a07e19e","size":61},{"path":"nodes.jsonl","sha256":"6ce54e0d837dceb4a2a39c1b2618cc66e16684b93f71b93ab4e6e709a90b0e52","size":11295},{"path":"provenance.json","sha256":"4bc7649bf6d3113f6c72b4016713654f57c8f03069632eabd1e6025c05cb9dac","size":226},{"path":"receipts.jsonl","sha256":"f745067d43480bbd467c5d8f11ff13eec198fac821664894ad8bd90b8b7cf0b3","size":2182},{"path":"references.jsonl","sha256":"59908a8aff6a2d5800747a1f45c6c2943ea1e31e7e1f10b6348967d30f16b87e","size":60},{"path":"roster.json","sha256":"4a6d29e8968143a4e19f485741c513245df1de77eec4ef9b3047c71db45cda22","size":924},{"path":"witnesses.json","sha256":"83ac4411c2efe65e0f7fc4c9336abbef6977cd32b0f90de029a7f8516afc3e97","size":750}],"format":"scienting-package/1","key":"tiny2026tiny-j4qm"}
fixtures/invalid/alias-dangling/package/document.json
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fixtures/invalid/bad-id/package/MANIFEST.json
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fixtures/invalid/bad-id/package/document.json
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fixtures/invalid/counts-wrong/package/document.json
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fixtures/invalid/heading-not-first/package/references.jsonl
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fixtures/invalid/history-wrong/expect.json
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fixtures/invalid/history-wrong/package/MANIFEST.json
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fixtures/invalid/history-wrong/package/document.json
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fixtures/packages/hale2026harmonic.checks-only/provenance.json → fixtures/invalid/history-wrong/package/provenance.json
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fixtures/invalid/history-wrong/package/receipts.jsonl
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fixtures/invalid/history-wrong/package/references.jsonl
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{"label":"1","node":"r3e21zr","resolution":{"type":"none"}}
fixtures/packages/hale2026harmonic/roster.json → fixtures/invalid/history-wrong/package/roster.json
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fixtures/packages/tiny2026example/witnesses.json → fixtures/invalid/history-wrong/package/witnesses.json
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fixtures/invalid/key-suffix/expect.json
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{"note":"A work key whose hash part is not the hash of the work's DOI.","rule":"doc.key.suffix"}
fixtures/invalid/key-suffix/package/MANIFEST.json
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fixtures/invalid/key-suffix/package/document.json
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fixtures/invalid/key-suffix/package/nodes.jsonl
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fixtures/packages/hale2026harmonic/provenance.json → fixtures/invalid/key-suffix/package/provenance.json
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fixtures/invalid/key-suffix/package/receipts.jsonl
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fixtures/invalid/key-suffix/package/references.jsonl
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fixtures/packages/tiny2026example/roster.json → fixtures/invalid/key-suffix/package/roster.json
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fixtures/invalid/key-suffix/package/witnesses.json
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fixtures/invalid/key-work/expect.json
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fixtures/invalid/key-work/package/MANIFEST.json
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fixtures/invalid/key-work/package/document.json
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fixtures/invalid/key-work/package/nodes.jsonl
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fixtures/packages/okafor2025open/provenance.json → fixtures/invalid/key-work/package/provenance.json
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fixtures/invalid/key-work/package/receipts.jsonl
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fixtures/invalid/key-work/package/references.jsonl
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fixtures/invalid/key-work/package/roster.json
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fixtures/invalid/key-work/package/witnesses.json
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fixtures/invalid/location-unknown-page/package/MANIFEST.json
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fixtures/invalid/location-unknown-page/package/document.json
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fixtures/invalid/location-unknown-page/package/locations.jsonl
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fixtures/invalid/location-unknown-page/package/nodes.jsonl
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