Deploy publications PDF hotfixes#229
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PR #225 introduced TWO new research notes (Natarajan RN-032 and Reading-PROMETHEUS RN-033) but only bumped the Site Atlas collection_counts by one (81 → 82). The Jekyll deploy then failed at the Site Atlas collection-count gate: Site Atlas collection count check failed: - publications_artifacts: expected 82, observed 83 Bumping both occurrences of: - publications_artifacts.expected_item_count: 82 → 83 - publications_artifacts.grouping[research_notes].expected_item_count: 10 → 11 Both occurrences appear because the JSON carries the collection schema in two sections (collection_index + collections); both must be kept in sync. After this fix: - publications_artifacts: expected 83, observed 83 (match) - research_notes: expected 11, observed 11 (match) - The /publications/research-notes/reading-prometheus-through-tau/ landing page + PDF asset become reachable on the live site. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Back-fill the public Research Note landing page with the minted OSF DOI: - Frontmatter: add doi, doi_url, osf_url, osf_short_id. - external_links: prepend the OSF deposit link. - right_rail.related: insert "OSF deposit (DOI)" link right after the PDF link. - editorial.citation_note: replace the "DOI is currently pending OSF mint" wording with the actual citable DOI and note that this is the first Panta Rhei Research note minted on OSF. The site's central authors registry already injected the real ORCIDs into the rendered citation_author_orcid meta tags (0009-0007-0718-1042 for Thorsten; 0009-0007-3495-7416 for Anna-Sophie), so no ORCID change needed on the landing page itself. Google Scholar's citation_doi meta tag will populate from the corpus rn033.scholar.citation_doi field on the next Jekyll build. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…on_doi on rn031–rn033
Pulls in the newly-refreshed corpus/exports/public/publications.{yml,json,ndjson,csv}
projection (corpus PR feat/wave-sigma-1-publications-export-refresh) into
the site's Jekyll-side mirror. Restores entry-count parity with the corpus
source-of-truth (94 records — was 86; the 89 corpus exports plus the
publications-catalog overlay of 5 anchor/legacy entries) and most importantly
adds rn033, rn032, rn031 to the mirror.
Why this matters: _includes/scholar-citation-meta.html matches each landing
page's URL against corpus_publication.canonical_url to decide whether to
emit Scholar/Dublin-Core meta tags (citation_doi, citation_title, DC.creator,
DC.identifier, …). When the lookup fails, the include's emission guards
silently skip — so research-note pages without a mirror entry could not
be indexed by Google Scholar with a citable DOI. This is the post-mint
half of the RN-033 OSF DOI back-fill landing on the public site.
Concrete effects after deploy:
- /publications/research-notes/reading-prometheus-through-tau/ (rn033)
will emit <meta name="citation_doi" content="10.17605/OSF.IO/76CZR">
for the first time.
- /publications/research-notes/natarajan-cluster-dichotomy-categorical/
(rn032) will emit <meta name="citation_doi" content="10.5281/zenodo.20251191">
— fixing a pre-existing systemic gap where the Zenodo DOI was minted
but never surfaced in Scholar metadata.
- /publications/research-notes/when-search-becomes-structure/ (rn031)
intentionally does NOT emit citation_doi (no DOI minted yet,
metadata_pending=true) — the include's guards correctly handle this.
Mirror refresh produced by:
cd site && python3 scripts/sync_corpus_public_exports.py --scope publications
Diff is purely data-layer; no template, layout, include, or stylesheet
changes. The +/- line counts look large because YAML/JSON re-serialization
re-emits adjacent fields whose ordering was last fixed by a prior sync
run; the meaningful change is the +5 rn-entry inclusion (rn031, rn032,
rn033) plus minor field-set additions on existing records.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…DOI 10.17605/OSF.IO/BFRX3 across site
Programme-wide migration from Zenodo to OSF as primary DOI platform.
Triggered 2026-05-17 by Zenodo disabling the programme account following
an incorrect spam classification; chair-authority decision.
This commit refreshes the site-side representation of the natarajan
cluster-dichotomy research note (RN-032) to point at the new OSF deposit
(10.17605/OSF.IO/BFRX3) bit-perfect with the rebuilt PDF artifact, and
deprecates the now-unresolvable Zenodo references across the corpus-side
mirror data files.
Updated files:
- _research_notes/2026-05-17-natarajan-cluster-dichotomy-categorical.md
Jekyll front-matter: doi / doi_url -> OSF; zenodo_url -> osf_url;
external_links and right_rail label "Zenodo DOI" -> "OSF DOI";
citation_note and prose body OSF deposit reference.
- _changelog/2026-05-17-natarajan-cluster-dichotomy-categorical-research-note.md
summary_short, OSF deposit line, new sha256, right_rail OSF label;
includes one-sentence disclosure of the Zenodo->OSF migration history.
- assets/pdfs/research-notes/research-note-2026-05-17-natarajan-cluster-dichotomy-categorical.pdf
Replaced with rebuilt 204005-byte PDF (was 204221 bytes; smaller
because Zenodo->OSF text swap is shorter). New sha256:
5c071652381341c820fc81e6a7fc864f54f7d29c935a98d322b4c14dc4f70a69
Bit-identical with the publications mirror (cross-repo integrity).
- _data/corpus/latest_publications.yml + _data/corpus/publications.yml
Corpus-projection mirrors: identifiers + external_links + citation +
scholar + integrity blocks refreshed with OSF DOI + new hashes.
- assets/data/publications/{publications,latest-publications}.{json,ndjson}
Downstream JSON/NDJSON exports refreshed with OSF DOI + new hashes.
Verification:
- 0 residual non-deprecation Zenodo references in site/.
- citation_doi meta-tag will render as 10.17605/OSF.IO/BFRX3 on the
/publications/research-notes/natarajan-cluster-dichotomy-categorical/
page when Jekyll rebuilds.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Pulls in the refreshed corpus/exports/public/publications.* projection (corpus PR feat/wave-sigma-2-natarajan-publications-refresh) into the site's Jekyll mirror. After deploy: - /publications/research-notes/natarajan-cluster-dichotomy-categorical/ will emit <meta name="citation_doi" content="10.17605/OSF.IO/BFRX3"> instead of the deprecated 10.5281/zenodo.20251191. The Dublin-Core <meta name="DC.identifier"> tag also updates to the OSF DOI URL. Diff is pure data-layer (no template / include / layout changes). Identical mechanism to Wave Σ₁ — the canonical sync_corpus_public_exports.py --scope publications path. Site landing-page frontmatter for natarajan (in _research_notes/) was already updated by the chair pre-this-commit with the OSF DOI; this commit completes the propagation through the Scholar-tag rendering path. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…outreach wiring Promote RN-031 from RC1 to RC2 after the 5-referee internal peer-review panel (MAJOR-tilt verdict, 12 HIGH-priority fixes applied). Retitle from "When Search Becomes Structure" to "When Witness Search Becomes Address Construction" to foreground the address-construction reading. Mint OSF DOI 10.17605/OSF.IO/HPZSN as the canonical citable deposit. Cross-link the companion 100-step Construction Spine whitepaper at OSF DOI 10.17605/OSF.IO/6GJ9K. Cross-link the Wolfram anchor essay at DOI 10.31855/be91a2c3-b2c. URL slug `when-search-becomes-structure` retained for permalink stability; the slogan-style RC1 title preserved in search_keywords for backward-compat search. Files: - _research_notes/2026-05-17-when-search-becomes-structure.md (frontmatter expanded: title, doi, doi_url, osf_url, osf_short_id, companion_doi, anchor_paper_doi, RC2 status, expanded abstract with panel + RC2 changes, expanded keywords for Hopkins-Bousfield + barriers + ZFC-horizon, pdf_legacy with RC1 preserved as historical artefact, new "What changed in RC2" section). - _changelog/2026-05-18-when-witness-search-becomes-address-construction-rc2.md (new changelog entry documenting retitle + DOI mint + 12 HIGH fixes). - assets/pdfs/research-notes/research-note-2026-05-18-when-search-becomes-structure-rc2.pdf (246970 bytes, sha256 2448de5e3600ef02c27b6d87d6546e85938c4438fa27317c77802a7d082c4ec2). Part of Wave Sigma_2 Zenodo->OSF migration. Sister commits in publications/, corpus/, atlas/ wave-sigma-2 sprint folder. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…605/OSF.IO/SBPD6 back-fill (rn007)
Phase B back-fill for the third programme OSF mint. Refresh the site-side
representation of the aesthetic-topology research note (rn007) to point at
the new OSF deposit (10.17605/OSF.IO/SBPD6) bit-perfect with the rebuilt
PDF artifact.
Files updated:
- _research_notes/2026-05-15-aesthetic-topology-pre-symbolic-readout.md:
Jekyll front-matter — doi / doi_url / osf_url populated; external_links
extended with OSF deposit (v0.9 RC) entry.
- assets/pdfs/research-notes/research-note-2026-05-15-aesthetic-topology-
pre-symbolic-readout-v0-9-rc.pdf:
Replaced with rebuilt 180493-byte PDF; sha256
b80cf2f401db16f6f955bee92b09a2235974824382e38402032d2785687862a2.
Bit-identical with the publications mirror.
- _data/corpus/{latest_publications.yml, publications.yml}:
rn007 entry refreshed (identifiers + osf_url + scholar.citation_doi +
integrity sha256 + sha512 + bytes).
- assets/data/publications/{publications, latest-publications}.{json,ndjson}:
Downstream JSON/NDJSON exports refreshed with OSF DOI + new hashes.
Verification: 0 residual placeholder DOI references for rn007 in site/.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…ed 'doi:' in scholar block) Follow-up fix to ffdaca7. The corpus-projection YAML files carried an 'H.17605/OSF.IO/SBPD6' fragment introduced by a regex pass during the Phase B back-fill, which the previous commit fixed by inserting ' doi:' prefix. However, the SECOND occurrence (inside the scholar: block, replacing what should have been 'citation_doi:') was also fixed to 'doi:' instead of the correct 'citation_doi:'. This commit corrects the scholar.citation_doi label for the rn007 (aesthetic-topology) entry in both corpus-mirror YAML files. Both files now have: - identifiers.doi: 10.17605/OSF.IO/SBPD6 - scholar.citation_doi: 10.17605/OSF.IO/SBPD6 Verified by yaml.safe_load + structured dict access. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
![github-code-quality[bot]](https://avatars.githubusercontent.com/u/9919?s=60&v=4){kind=small}
| import json | ||
| import re | ||
| import subprocess | ||
| import sys |
…arajan-mirror-refresh # Conflicts: # _data/corpus/latest_publications.yml # _data/corpus/publications.yml # assets/data/publications/latest-publications.csv # assets/data/publications/latest-publications.json # assets/data/publications/latest-publications.ndjson # assets/data/publications/publications.csv # assets/data/publications/publications.json # assets/data/publications/publications.ndjson
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Deploys the publications-lane PDF hotfixes for RN031 and RN033.\n\nIncludes:\n- publishes the RN031 PDF asset already referenced by the live metadata;\n- rebuilds/replaces the RN033 PDF with visible OSF DOI 10.17605/OSF.IO/76CZR and PDF metadata;\n- refreshes publication projections and citation metadata;\n- adds publications-lane audit tooling and regenerated prrp.site route worker data from the prior audit pass.\n\nQA:\n- Jekyll build passes;\n- Pagefind build passes;\n- publications audit: 96 records, 0 errors, 0 warnings;\n- focused RN031/RN033 _site checks pass;\n- smoke-test, registry verify, MathML test, headers test pass;\n- link-check passes;\n- git diff --check passes.