feature/SOF-8014-1 Update: index §1.2 by publication, one row each - #399
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Rename "Reproducing Published Structures" to "Reproducing Publications" and give each
publication one row carrying both the structure it builds and the properties calculated
from it, instead of a second row per simulation. 24 rows, 22 publications.
The per-publication model already existed in tutorials/materials/specific/overview.md
(**Structure** / **Properties** / **DOI**, with "Coming Soon" where no simulation page
exists yet); this brings the flat table into line with it rather than inventing a second
convention. Property names follow §2.1's existing vocabulary in this same file — "Band gap",
"Density of states" — not overview.md's prose, and the index states the headline properties
rather than restating the tutorial's full list.
Also wires up the footnotes. index-guide.md defined [^1]-[^22] — one DOI per publication —
and nothing referenced any of them: the built page had 22 fn: list items and 0 fnref:
markers, so the citations rendered as an unlabelled list with no way to tell which row each
belonged to. Every Reference cell now carries its [^N]. Row order is unchanged from the old
table, which is the order the footnotes were numbered in, so the definitions are untouched.
The legacy site keeps its own name for this section ("Reproducing Specific Manuscripts", in
both mkdocs.yml and tutorials/overview.md). Those two are a hand-maintained duplicate of the
same 22 links and they agree with each other; renaming one without the other puts two names
on one rendered page. Converging all four surfaces — better still, generating the duplicate
list — is its own change, filed in plan/log/findings.md.
Anchor changes: #12-reproducing-published-structures -> #12-reproducing-publications.
Nothing in the repo links to the old one. A fragment is never sent to the server, so no
redirect can act on it; external inbound links to the old anchor will land on the page.
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Matches the 45 other [Link] cells in this file — §1.1 and §2.1 both use a constant label per link column rather than a per-row verb.
timurbazhirov
approved these changes
Aug 26, 2026
The Material name is now the link to the structure tutorial, so the cell says what the structure is instead of saying "Link". Five columns become four, which also takes the widest table in this file back down to the width of its neighbours.
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§1.2 of the guide index listed a publication's structure and its simulation as two table rows, distinguished only by a parenthetical, repeating the reference and the structure type and naming no property. This gives each publication one row:
Reference | Structure Type | Material | Structure | Properties24 rows → 22 publications. The section is renamed Reproducing Publications, since it indexes simulations now and not only structures.
The model is not new.
tutorials/materials/specific/overview.mdalready does exactly this per entry —**Structure**/**Properties**/**DOI**, with "Coming Soon" where no simulation tutorial exists. This brings the flat table into line with it rather than inventing a second convention. Property names follow §2.1's existing vocabulary in the same file rather thanoverview.md's prose, with the full list one click away in the tutorial.It also wires up 22 orphaned citations.
index-guide.mddefined[^1]–[^22], one DOI per publication, and nothing in the page referenced any of them — so they rendered as an unlabelled list at the page foot with no way to tell which row each belonged to. mkdocs has been reporting this on every build:mainlogs 22footnote that is never referencedINFO lines, this branch logs 0. Row order is unchanged from the old table, which is the order the footnotes were numbered in, so the 22 definition lines are untouched.Two deliberate non-changes
1. The anchor breaks.
#12-reproducing-published-structures→#12-reproducing-publications. Nothing in the repo links to the old one. A URL fragment is never sent to the server, so no redirect can act on it andscripts/links/check-links.pyis fragment-blind — an external inbound link lands on the page at the wrong scroll position rather than 404ing.2. The legacy site keeps its own name.
/guide/now says Reproducing Publications while/says Reproducing Specific Manuscripts (mkdocs.yml:153andlang/en/docs/tutorials/overview.md:76, which agree with each other and are untouched here). Those two are a hand-maintained duplicate of the same 22 links; renaming one without the other puts two names on one rendered page. Converging all four surfaces means hand-copying the list that #279 asked to have generated, so it is deliberately left for that change. This is the one call that could reasonably go the other way — the four-file version is the better end state if the extra scope is wanted.Gate
Both site builds exit 0 with warning sets identical to
main(guide and legacy, compared sorted — the two mkdocs-bibtex config warnings emit in nondeterministic order). Full eight-site build pluscheck-links.py: Checked 331474 internal links. No broken internal links found.Manual checks
Merging accepts anything unticked.
Propertiescells is the thing to look at.#12-reproducing-publicationsresolves on the preview, and the old anchor lands on the page rather than 404ing. Nothing automated catches this.[^N]lands on that row's own paper. All 22 verified unchanged againstmain— but the mapping was inherited frommain, so whether each DOI is the right paper for that author has never been checked by anyone..md-typeset__scrollwrap{overflow-x:auto}, same as §2.1's existing 5-column table) — a look-once, not a risk.