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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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[*.py]
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indent_style = space
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indent_size = 4
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max_line_length = 120
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[*.{json,jsonld,sql,md,yml}]
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indent_style = space
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indent_size = 2
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[{vectors,fixtures}/**]
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trim_trailing_whitespace = false
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* text=auto eol=lf
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# Generated data: exact bytes matter, and diffs are by line.
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vectors/** -text diff
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fixtures/** -text diff
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fixtures/**/*.png binary
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# Forgejo and Gitea Actions both read .github/workflows when their own folder is absent.
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name: check
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on: [push, pull_request]
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jobs:
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check:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- name: Second schema validator
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run: python3 -m pip install jsonschema referencing
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- name: Check the repository
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run: python3 tools/check.py
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- name: Lint Markdown
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if: matrix.os == 'ubuntu-latest'
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run: npx --yes markdownlint-cli@0.48.0 '**/*.md'
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__pycache__/
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*.pyc
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.venv/
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*.db
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{
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// One sentence per line makes long lines normal, and tables are wide.
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"MD013": false,
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// The chapters use the same subheadings in different sections.
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"MD024": { "siblings_only": true },
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// Numbered algorithm steps keep their numbers.
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"MD029": { "style": "ordered" },
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"MD033": false
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}
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# Changelog
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Every change to a computed value is a breaking change and needs a major version of the format it touches; see [spec/00-introduction.md](spec/00-introduction.md).
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## 0.1.0
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The first release, written for level 3 so that formats never change as the studio moves up.
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- Chapters 0 to 22, covering every format the design names.
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- 37 JSON Schemas, restricted to a keyword subset that independent validators read alike.
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- Tables for SQLite, Dolt and PostgreSQL, a team store, and the SQLite bundle with FTS5.
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- The JSON-LD context for layers, and registries of formats, rules, stamp rules and stage defaults.
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- Vectors for canonical JSON, normalization, IDs, notation, both projections, offsets, the five values, addresses, keyed hashes, page fingerprints, Merkle roots, signatures, spot-checks, error bounds, alignment, every correction, anchor resolution, rights and grading.
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- Packages for the three M1 fixtures (two sections of a converted chemistry paper with a multi-level-header table, an open-access paper and a short Typst draft), a checks-only export, and a tiny document; records of every other format; and seventeen invalid packages.
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# Code of conduct
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Be kind, assume good faith, and keep discussion about the work.
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Report concerns to the maintainer at `conduct@scient.ing`.
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# Contributing
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## One fix, one test
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Every change to a rule comes with the vector or fixture that shows it.
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Change the oracle in `tools/oracle/` and the chapter together, run `python3 tools/build.py` to regenerate the vectors and fixtures, and commit the regenerated files with the change.
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`python3 tools/check.py` must pass.
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A fixture that breaks something belongs in `fixtures/invalid/`, with the rule it breaks in `expect.json`, built by `tools/build.py` like the others.
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Rule IDs are stable: a rule's meaning never changes, and a retired ID is never reused.
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## Versions
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A change that makes a valid file invalid, or changes any computed value, is breaking: it needs a new major version of the format and a migration in `scienting-core`.
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Adding an optional property, a kind or an enumeration value is a minor change.
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Record each change in [CHANGELOG.md](CHANGELOG.md), and each departure from the design in [DECISIONS.md](DECISIONS.md).
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## Prose
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US English, one sentence per line, so a change to a sentence is a one-line diff.
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Prefer plain words to abbreviations; write "for example", not "e.g.".
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`tools/check.py` lints both, and `markdownlint` checks the Markdown.
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## Data
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||||
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Fixture text is synthetic and dedicated CC0: never copy text from a real paper into this repository.
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Every file is canonical JSON; never edit a generated file by hand.
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# Decisions
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||||
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In the style of Lode's `DECISIONS.md`.
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Each entry says what `spec` 0.1 does where the design leaves a choice open, refines a rule so that two implementations compute the same bytes, or departs from the design's wording.
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Entries marked *provisional* wait for the maintainer; everything else is adopted for 0.1.
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## Refinements and departures
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| ID | Decision | Why |
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||||
| --- | --- | --- |
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| D1 | The repository is `varve-spec`; every identifier inside stays `scienting-*`. | The design keeps product names out of technical identifiers. |
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| D2 | Offsets and quotations index the stored plain projection; `own_hash` and `node_hash` cover stored values exactly, without normalization; only the text values normalize. | When `node_hash` is equal, every offset is still exact, and a renderer slices stored text directly. |
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| D3 | The kind list names `title`, `authors`, `abstract`, `keywords`, `notes`, `acknowledgments`, `appendix`, `figure-note` and `table-note` explicitly. | The design uses them as children but omits them from the list it says refuses all others. |
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| D4 | After its heading, a section's blocks and subsections may interleave. | Papers put text after subsections; the design's "then nested section" would refuse them. |
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| D5 | Simple notation includes `.` and `,`. | Otherwise `$-1.5$` is complex and never agrees with the text "−1.5". |
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| D6 | The strict projection marks `cite`, `xref` and `fnmark` runs with U+FFF9 and U+FFFB. | Citation structure must not vanish: "10" and citation 3 is not "103". The design is silent. |
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| D7 | Outside notation, a hyphen-minus or en dash before a digit becomes U+2212. | The design's "a hyphen before a digit" read for text as well as notation; "10-20" and "10–20" then agree. |
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| D8 | The lossy projection deletes whitespace and dashes rather than collapsing them. | OCR merges and splits words; the key only proposes alignments, so recall matters. |
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| D9 | Container projections join their text leaves with a space; [3.6](spec/03-nodes.md#36-the-plain-projection) defines the leaves. | The design says "concatenated" without a separator or a leaf set. |
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| D10 | Anchors always carry `own_hash`; anchors on containers without content carry their `leaves`. | The relabel rule needs `own_hash` on every anchor, and the "half of the original leaves" rule needs the original leaves. |
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||||
| D11 | Quotations over 200 code points become `exact_hash` and `length`; `prefix` and `suffix` hold at most 32. | The open decision on the cap, adopted provisionally, without losing reattachment of long sentences. *Provisional.* |
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| D12 | When a quote has several hits, `prefix` and `suffix` pick one. | As W3C text-quote selectors do; the design says only "exactly once". |
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||||
| D13 | A tenth operation, `set`, changes one structural attribute; `place_after` positions inserts and moves; `split` trims whitespace at the cut; `merge` joins runs with one space by default. | Spans, roles and header paths are dropped by readings and need a correction; `after` was needed for a hash. |
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||||
| D14 | Applied corrections record `before`, `after`, `path`, `to_path`, `touched`, `created`, `retired` and `from`. | Drift and relabel reattachment become computable from the record, without replaying history. |
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||||
| D15 | Drift's share is touched leaves over current leaves and touched leaves together, four decimals, half up; `high` is strictly above the threshold. | The design gives the idea; this gives one number. |
|
||||
| D16 | A row's `header_path` is not part of any hash. | The design gives rows no content of their own; so a header-path fix does not stale cell anchors. |
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||||
| D17 | Fingerprint text deletes whitespace and control and format characters. | PDF extractors disagree about where they insert spaces. |
|
||||
| D18 | SQL names avoid words reserved in SQLite, PostgreSQL or MySQL: `doc_key`, `work_key`, `idx`, `made_at`, `signer`, `before_hash`, `after_hash`, `ref_node`. | Dolt is MySQL-compatible, and `key`, `index`, `before` and `by` are reserved there. |
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||||
| D19 | The tables store every property of every record, JSON as canonical text, so that unload gives the package back byte for byte, with assets by SHA-256 in `package_files`. | The design requires a byte-identical round trip. |
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||||
| D20 | Keyed hashing: HKDF salts `scienting-team-key/1` and `scienting-page-key/1`, info `scienting-hash/1` or the export's context, `key_id` from a domain-separated SHA-256, and page hashes rather than fingerprints in exports. | The design's open decision on the scheme, made concrete. *Provisional.* |
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||||
| D21 | Receipts may attest F1 to F3, may cover `records` as well as nodes, and are re-issued under a key with `export_of`. | The same mechanism signs annotations and digitizations; plain hashes cannot leave the team. |
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||||
| D22 | Spot-check samples rank node IDs by SHA-256 of the seed and the ID; bounds are one-sided at 95%, reported to six places, rounded up. | One deterministic sample and one string for every implementation. |
|
||||
| D23 | Checks-only packages also omit corrections, suspects, datasets, figure text and CSL records. | Each carries fragments of the text. |
|
||||
| D24 | Fidelity is recorded on leaves only, and F3 comes only from receipts. | A receipt is the only record of a person's check. |
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||||
| D25 | A policy resolves only unknown uses; an expired basis makes every use false. | A team's decision should never silently widen an explicit `false`. |
|
||||
| D26 | Backend conditions are a closed vocabulary, and an unknown answer fails a condition. | A gate that guesses is not a gate. |
|
||||
|
||||
## Still open
|
||||
|
||||
| ID | Decision | Default here | Waits for |
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||||
| --- | --- | --- | --- |
|
||||
| O1 | The roster: `scienting-roster/1` is defined here; Lode already verifies a roster. | This format. | Reconciling with Lode's at M4. |
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||||
| O2 | The manifest's exact field names against `lode-cache/1`. | `{format, doc, key, files: [{path, sha256, size}]}`. | Comparing with Lode's implementation. |
|
||||
| O3 | Package extension and media type. | `.sct.zip`, `application/vnd.scienting.doc+zip`. | The maintainer; fixed forever once shared. |
|
||||
| O4 | Node ID form. | Opaque. | The maintainer. |
|
||||
| O5 | Text normalization for `text_hash`. | NFC and whitespace. | The maintainer; existing Lode extracts keep Lode's rule. |
|
||||
| O6 | Canonical math, stage 2. | Stage 1: complex runs compared by source, run by run. | H4. |
|
||||
| O7 | Quotation cap. | 200 code points. | Counsel and robustness measurements. |
|
||||
| O8 | Drift threshold, spot-check sample, digit rule, target set, receipt scopes, container strictness. | As the design proposes. | The validation tests of the design's 16.1. |
|
||||
| O9 | Stage-to-rights defaults and the combining rule. | As the design proposes, in `registry/stages/`. | Counsel. |
|
||||
| O10 | Stamp-line rules. | Four published patterns and a margin rule. | Pairs of real downloads, kept out of the repository. |
|
||||
| O11 | License of the tools. | Apache-2.0. | The maintainer. |
|
||||
|
||||
## Known limits of 0.1
|
||||
|
||||
- The strict projection removes spaces inside notation but keeps them in text, so `$T = 300$` from LaTeX and "T = 300" from a PDF disagree and become a `word` suspect; M3 should measure how often.
|
||||
- Page fingerprints depend on extracted text lines; the vectors test the function, and the converter and the reader must use extractors that agree on the corpus.
|
||||
- The oracle verifies Ed25519 only; SSH, OpenPGP and Sigstore signatures are specified by reference.
|
||||
- CI executes the SQL on SQLite only; Dolt and PostgreSQL are covered by the portability rules and the reserved-word check, not by execution.
|
||||
- There is no zipped package among the fixtures yet.
|
||||
- Vectors were computed with Unicode 15.0; normalization is stable across versions, but Script and General Category assignments for newly encoded characters are not.
|
||||
+18
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|
||||
# Licenses
|
||||
|
||||
| Paths | License | SPDX |
|
||||
| --- | --- | --- |
|
||||
| `spec/`, `README.md`, `DECISIONS.md`, `CONTRIBUTING.md`, `CHANGELOG.md` and the other prose | Creative Commons Attribution 4.0 International | `CC-BY-4.0` |
|
||||
| `schemas/`, `sql/`, `context/`, `registry/`, `vectors/`, `fixtures/` | Creative Commons Zero 1.0 Universal | `CC0-1.0` |
|
||||
| `tools/` | Apache License 2.0 | `Apache-2.0` |
|
||||
|
||||
The legal texts are at <https://creativecommons.org/licenses/by/4.0/legalcode>, <https://creativecommons.org/publicdomain/zero/1.0/legalcode> and <https://www.apache.org/licenses/LICENSE-2.0>.
|
||||
Before the first public release, add their verbatim texts under `LICENSES/`, as the REUSE specification describes; `reuse download --all` fetches them.
|
||||
|
||||
The license of the tools is an open decision of the design (Apache-2.0 or Prosperity 3.0.0); Apache-2.0 is used here because the tools exist only to check the formats.
|
||||
|
||||
All text in the fixtures is synthetic, written for them.
|
||||
License fields inside fixtures describe fictional works, not the fixtures.
|
||||
The keys in `fixtures/keys/` are public test keys and must never sign anything else.
|
||||
|
||||
Copyright 2026 the Scientific Computing Studio.
|
||||
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|
||||
.PHONY: check quick build lint
|
||||
|
||||
check: lint
|
||||
python3 tools/check.py
|
||||
|
||||
quick:
|
||||
python3 tools/check.py --quick
|
||||
|
||||
build:
|
||||
python3 tools/build.py
|
||||
|
||||
lint:
|
||||
@if command -v markdownlint >/dev/null 2>&1; then markdownlint '**/*.md'; else echo "markdownlint not installed; skipped"; fi
|
||||
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|
||||
# varve-spec
|
||||
|
||||
The specifications of the Scientific Computing Studio's data formats: documents and their packages, anchors, receipts, rights, layers, exercises, datasets, digitizations, views, projects and bundles.
|
||||
This is the repository the design calls `spec`, the baseline every other part implements.
|
||||
|
||||
`spec` defines data, and data outlives code.
|
||||
Every file any part writes is defined here, and a conforming file can be read without the part that wrote it.
|
||||
Formats are named `scienting-<name>/<major>`, never after a product, so a product can be renamed without touching data.
|
||||
|
||||
## What is here
|
||||
|
||||
| Path | Holds |
|
||||
| --- | --- |
|
||||
| [spec/](spec/README.md) | The normative chapters. Start with [spec/00-introduction.md](spec/00-introduction.md). |
|
||||
| [schemas/](schemas/) | JSON Schemas (draft 2020-12) for every file and record. |
|
||||
| [sql/](sql/) | Tables for SQLite, Dolt and PostgreSQL, and the SQLite bundle with full-text search. |
|
||||
| [context/](context/) | The JSON-LD context that makes layers W3C Web Annotations. |
|
||||
| [registry/](registry/) | Formats and media types, validation rule IDs, download-stamp rules and the default stage requirements. |
|
||||
| [vectors/](vectors/README.md) | Test vectors for every computed value. |
|
||||
| [fixtures/](fixtures/README.md) | Valid packages and records, invalid packages with the rule each breaks, and the test keys that signed them. |
|
||||
| [tools/](tools/README.md) | The non-normative oracle that computed the vectors, the builder and the checker. |
|
||||
| [DECISIONS.md](DECISIONS.md) | Where this text refines or departs from the design, and the decisions still open. |
|
||||
|
||||
## Check it
|
||||
|
||||
Python 3.10 or later, with nothing installed:
|
||||
|
||||
```sh
|
||||
python3 tools/check.py
|
||||
```
|
||||
|
||||
It validates every schema, record and package, refuses every invalid package for the stated rule, recomputes every vector, rebuilds the fixtures and vectors and compares them byte for byte, loads every package into SQLite and unloads it byte for byte, and lints the prose.
|
||||
With `jsonschema` installed it also validates every record a second time with that library.
|
||||
`make check` does the same and runs `markdownlint` when it is available.
|
||||
|
||||
## Implement it
|
||||
|
||||
An implementation conforms to the chapters and the vectors.
|
||||
`scienting-core` (Python, standard library only) is the reference implementation of the shared rules, and `core-ts` the browser's; each runs this suite in its CI.
|
||||
The oracle in `tools/` is not a library and is not meant to be imported: it exists so that no vector is typed by hand.
|
||||
|
||||
## Status
|
||||
|
||||
Version 0.1.0.
|
||||
The formats of milestone M1 are `candidate`; datasets, digitizations, views, projects, bundles and the draft formats are `provisional` until their milestones; see [registry/formats.json](registry/formats.json).
|
||||
|
||||
## Licenses
|
||||
|
||||
The chapters and other prose are licensed CC BY 4.0.
|
||||
Schemas, SQL, the JSON-LD context, the registries, the vectors and the fixtures are dedicated to the public domain under CC0 1.0, so anyone may implement the formats.
|
||||
The tools are licensed Apache-2.0.
|
||||
See [LICENSE.md](LICENSE.md).
|
||||
@@ -0,0 +1,42 @@
|
||||
{
|
||||
"@context": {
|
||||
"@version": 1.1,
|
||||
"sct": "https://scient.ing/ns/scienting#",
|
||||
"format": "sct:format",
|
||||
"kind": "sct:kind",
|
||||
"status": "sct:status",
|
||||
"receipt": "sct:receipt",
|
||||
"layer": {
|
||||
"@id": "sct:layer",
|
||||
"@type": "@id"
|
||||
},
|
||||
"audience": "sct:audience",
|
||||
"visibility": "sct:visibility",
|
||||
"purpose": "sct:purpose",
|
||||
"project": "sct:project",
|
||||
"docs": {
|
||||
"@id": "sct:docs",
|
||||
"@container": "@set"
|
||||
},
|
||||
"pin": "sct:pin",
|
||||
"role": "sct:role",
|
||||
"symbol": "sct:symbol",
|
||||
"verdict": "sct:verdict",
|
||||
"reason": "sct:reason",
|
||||
"reference": "sct:reference",
|
||||
"for": "sct:questionFor",
|
||||
"generator": "sct:generatedBy",
|
||||
"exercise": {
|
||||
"@id": "sct:exercise",
|
||||
"@type": "@json"
|
||||
},
|
||||
"anchor": {
|
||||
"@id": "sct:anchor",
|
||||
"@type": "@json"
|
||||
},
|
||||
"AnchorSelector": "sct:AnchorSelector",
|
||||
"rights_use": "sct:rightsUse",
|
||||
"total": "as:totalItems",
|
||||
"as": "https://www.w3.org/ns/activitystreams#"
|
||||
}
|
||||
}
|
||||
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|
||||
# Fixtures
|
||||
|
||||
All text here is synthetic and dedicated CC0; license fields describe fictional works.
|
||||
|
||||
| Path | Is |
|
||||
| --- | --- |
|
||||
| `packages/hale2026harmonic/` | Two sections of a converted chemistry paper, read once with errors and fixed by twelve corrections: a digit, a lost superscript, a missed boundary, a false boundary, a split paragraph, a running head, two labels, a garbled row replaced, a dropped row inserted, and a header span. It has a multi-level-header table, a display equation inside a sentence, a footnote, a figure with figure text and a real image asset, references, legacy aliases, geometry on fingerprinted pages, receipts (one partly invalidated by a correction, one spot-checked clean, one revoked, one suspended), a roster, a reported dataset and derived MathML. |
|
||||
| `packages/hale2026harmonic.checks-only/` | The same document exported to another machine of the team: text withheld, values under the team key in `keys/`. |
|
||||
| `packages/okafor2025open/` | An open-access paper with a JATS witness and a PDF witness, corroborated. |
|
||||
| `packages/smithlab2027charges/` | A short Typst draft that cites sentences of `hale2026harmonic` by address. |
|
||||
| `packages/tiny2026example/` | A small document; the base of the correction vectors and the invalid packages. |
|
||||
| `records/` | A valid record of every other format: anchors (span, leaf, cell, paragraph and keyed), rights, a policy, backends, profiles, a layer with its annotations and receipt, submissions, grades, a project, a digitization with its confirmation and dataset, a view, a QA report, a snapshot and a draft's sentence IDs. |
|
||||
| `invalid/<case>/` | A package that breaks one rule, and `expect.json` naming it. |
|
||||
| `keys/` | The Ed25519 test keys that signed the fixtures, and the checks-only export's team secret. Public; never use them for anything else. |
|
||||
| `src/` | The hand-written sources of the three M1 documents ([src/README.md](src/README.md)). |
|
||||
|
||||
Everything except `src/` is generated by `python3 tools/build.py`; do not edit it by hand.
|
||||
@@ -0,0 +1 @@
|
||||
{"note":"An alias whose node does not exist.","rule":"doc.id.successor"}
|
||||
@@ -0,0 +1 @@
|
||||
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Whitespace-only changes.
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||||
{"note":"Built by hand for the conformance suite; every reading is synthetic.","stages":[{"processor":"local","stage":"hand","tool":"varve-spec tools/build.py"}],"tools":[{"name":"varve-spec tools/build.py","version":"0.1.0"}]}
|
||||
|
||||
@@ -0,0 +1 @@
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||||
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||||
{"label":"1","node":"w1dkdqd","resolution":{"type":"none"}}
|
||||
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||||
{"format":"scienting-roster/1","keys":[{"id":"ana","person":{"name":"Ana Example"},"public":"d157q/XjOTQgq6/mpVl66mZ7PI4TlF1vgywe/1un9ls=","purposes":["sign"],"registered_at":"2026-09-01T00:00:00Z","revoked_at":null,"scheme":"ed25519"},{"id":"ben","person":{"name":"Ben Example"},"public":"Nx+Qb/5CI/CDfhIow84T0vXtUf4mSLsA1qCFud8i7jc=","purposes":["sign"],"registered_at":"2026-09-01T00:00:00Z","revoked_at":null,"scheme":"ed25519"},{"id":"ben-spot","person":{"name":"Ben Example"},"public":"88UkRiHFGoYXvh4Y9/ScWeZwnrlcX3smDr94j7tVh5E=","purposes":["spot-check"],"registered_at":"2026-09-01T00:00:00Z","revoked_at":null,"scheme":"ed25519"},{"id":"cara","person":{"name":"Cara Example"},"public":"MRiP6EKAIULhp5xEiCMKFeGVR0ziXZmGgNYS4C5ed+A=","purposes":["sign"],"registered_at":"2026-09-01T00:00:00Z","revoked_at":null,"scheme":"ed25519"}],"store":"smithlab"}
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||||
@@ -0,0 +1 @@
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||||
{"witnesses":[{"id":"nmfryke","kind":"pdf","media_type":"application/pdf","origin":{"source":"author"},"pages":1,"rights":{"asserted_by":{"by":"ana","evidence":[{"kind":"statement","note":"The team's own draft."}]},"at":"2026-09-15T12:00:00Z","basis":"own-work","format":"scienting-rights/1","license":{"spdx":"CC-BY-4.0"},"uses":{"accessible-copy":true,"ai":{"external/local":true,"external/outside":true,"external/outside-no-retention":true,"external/tenancy":true,"internal/local":true,"internal/outside":true,"internal/outside-no-retention":true,"internal/tenancy":true},"quote-public":true,"read":true,"redistribute":true,"tdm":true},"valid_until":null},"sha256":"fda3f1e9bb3538cd85dcc42281e00fd045f726652664439ce5a15d8489425b21","size":1000}]}
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||||
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||||
{"note":"A line that is valid JSON but not canonical JSON.","rule":"package.file.canonical"}
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||||
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|
||||
{"doc":"scienting-doc/1","files":[{"path":"document.json","sha256":"20a7d6ba83bf42a87e44f3b3f96bfb16ff545b199d82e54d3c17989e465281df","size":555},{"path":"nodes.jsonl","sha256":"9ed0d41facc80ee7213d3d29b17756c9f26780eb3c154680c6f7d7101435f3d8","size":11312},{"path":"provenance.json","sha256":"1d41f5d5bf2bd5e9f4c6d7a4c3ff6e34d9e15a2e9f0004b2d110609f929069b8","size":228},{"path":"receipts.jsonl","sha256":"c5b25e8718f17ac81d34afa6102b2789e2155f6a5462a50f16ab1ba744fbf708","size":2180},{"path":"references.jsonl","sha256":"bb5445037c28bf5fde215b4b831c29327dec6dd88259e2d53aabb995f2fdb98f","size":60},{"path":"roster.json","sha256":"219f5b34ca3a60cbee8233ea0304ad3066df93591ab8f959c80c1122243b1397","size":861},{"path":"witnesses.json","sha256":"83ac4411c2efe65e0f7fc4c9336abbef6977cd32b0f90de029a7f8516afc3e97","size":750}],"format":"scienting-package/1","key":"tiny2026example"}
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||||
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