paperspec/docs/walkthrough.md

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. The paper is synthetic, written for the fixtures, but everything that happens to it happens to real papers. Open fixtures/packages/hale2026harmonic/ beside this page: every ID below is in it. The hand-written source of the first reading is fixtures/src/hale2026harmonic.json.

1. A PDF arrives

The team downloads the publisher's PDF. It becomes a witness, identified by its SHA-256, with the short ID qptsanv, and a rights record: the library's subscription allows reading, text mining, and AI processing on the team's own machines, until August 31, 2027; 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. Fingerprinting each page removes those lines first (the rules downloaded-via and sharing-guidelines fired on both pages), so page 101's fingerprint is 6272e6f3… in this copy and in a colleague's download stamped a year later. See pages.jsonl.

2. The first reading, with its mistakes

A converter reads the PDF into sections, paragraphs, sentences, a figure, a table, an equation, a footnote and references, and mints a permanent ID for every node. Like every reading, this one has mistakes:

What the reading did	What the page says
A cell read 3l0.0.	310.0, with the digit 1.
A sentence read Values below 10-3 kcal mol⁻¹….	A superscript: 10⁻³.
Two sentences ran together: "…treated as zero. Table 1 lists…".	Two sentences.
One sentence was cut in two at a line break: "…and the energies were" and "fitted by least squares."	One sentence.
A paragraph was split at a column break.	One paragraph.
The running head "J. Example Chem. 2026, 14, 101–109" became a paragraph.	A running head, not text.
The equation's number read (l) and the figure's Figure l.	(1) and Figure 1.
The CT–HC row merged two cells into "338.7 1.0900".	Two cells.
The OW–HW row was missing.	It is there.
"Set B" spanned one column.	It spans two.

The doubtful places become suspects with crops of the page, for a person to answer. The converter does not guess, and nothing changes until a correction passes the gate.

3. Twelve corrections

Each fix is appended to corrections.jsonl, numbered, with its evidence, its author and its reason.

#	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.
2	replace	sentence e4fkseg	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.
4	merge	sentence eajq93t	Joined with e9rh611, which is retired with eajq93t as its successor.
5	merge	paragraph zyqr0yc	Joined with g44k023, retired the same way.
6	delete	paragraph nm7vyzk	The running head is gone; its IDs are retired with no successor.
7	relabel	equation qn08tj9	(l) to (1).
8	delete	row tfjge3c	The garbled CT–HC row and its four cells.
9	insert	row fbg2mwq	The CT–HC row, read again: five new cells.
10	insert	row j0x5twd	The missing OW–HW row.
11	set	cell vtszvw9	Set B's colspan from 1 to 2.
12	relabel	figure ajfvq4s	Figure l to Figure 1.

The document is now at revision 12. Notice what did not happen: no other cell, sentence or row changed its ID or its hashes. Inserting a row adds a row node; the table's 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

After twelve corrections, the sentence about water is still f929eq9, the corrected cell is still nkm3xn5, and the sentence that lost its superscript is still e4fkseg. The retired IDs are recorded in ids.jsonl, so anything that pointed at them can follow the trail. So is a legacy alias: b-p01-text-003, the ID an older tool gave the water sentence, still leads to f929eq9.

If a better converter comes along next year, its reading is aligned with this document sentence by sentence; every sentence it reads the same way keeps its ID, and every difference becomes a suspect rather than a silent change.

5. What happened to the notes

Before any correction, at revision 0, the team had already made seventeen anchors: notes, extracts and citations pointing into the first reading. Here is how each resolves at revision 12 (vectors/resolve.jsonl records them all).

Anchor on	Result	Why
"H$_2$O" in the water sentence	current	Nothing in that sentence changed.
The cell 1.5260	current	Untouched, though its table changed around it.
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, which is right, because the number changed.
"treated as zero"	reattached	The sentence changed twice, but 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.
"least squares", in the half-sentence e9rh611	moved	That ID was merged into eajq93t, which still holds the quote.
The paragraph g44k023	moved	Merged into zyqr0yc, which holds all of its sentences.
The running head	stale	Deleted, with no successor.
The equation	reattached	Only its number changed.
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, but exactly one cell in Table 1 has the same row and column headers and the same text: the new e0n07n0.
Section 2	changed-below, drift high	The section itself is unchanged, but 53% of what is in it was touched.
Table 1	changed-below, drift high	Rows were replaced and added.
The table body	changed-below, drift high	75% of its cells were touched.
The paragraph whose broken sentence was rejoined	changed-below, drift high	Two of the three sentences it has held were touched.
The CT–CT row	changed-below, drift low	One of its five cells was corrected.

A reader shows each note accordingly, and a Lode check, which is about exact words, accepts only current, moved and reattached.

6. Review and signatures

Now people check what matters. The receipts are in receipts.jsonl, and the keys that signed them in roster.json.

• Before the corrections, ana had signed receipt c5cx7n4tga6y9 for three cells at revision 0. Two of them never changed, so the receipt still counts for them; for the corrected cell it no longer does, because its hash moved on.
• After the corrections, ana signs eqgbbpwb6725v at F3 for 23 nodes: the cells of Table 1's three data rows, its four column headers, the equation and the sentences around it. ben spot-checks it with receipt p38t0s91trb6j: his signature over the receipt 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.
• cara signs adtrpq41np7sd for three sentences on page 2, then revokes it herself (q0yg0w6ygwwxh): 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.
• ana signs gena76nkb6cnc for the figure's caption; ben's spot-check qab588b6xy94y finds a missing period in nmm4md0, which suspends the receipt until she reviews the sitting again.

The document's report, in document.json, counts the result: 28 leaves at F3, 12 at F2, 4 at F1 and 1 at F0.

7. Data out of the table

Table 1 becomes a dataset, ds-hale-bond-params, inside the package. Its CSV keeps every digit as printed (1.526 and 1.5260 stay different), and every value has an anchor to the cell that prints it, so a claim that rests on a value can show the cell. All twelve value anchors resolve as current; the checker confirms each CSV value equals its cell's text.

8. Sharing without the text

The team wants to share its notes with a collaborator's machine but not the paper. 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. IDs, labels, pages and boxes survive, so annotations still land in the right place; only someone holding the key and the text can check the values.

9. Your turn

The examples show how to recompute one of these hashes with sha256sum, print the outline with a few lines of Python, and load the whole package into SQLite to query it.