v1.3.0 — Surfaceome 1.3

Code release accompanying data release 1.3.0 (10.5281/zenodo.23445521): 5,332 deep-dive records, the genome-wide triage and benchmark TSVs, preset membership, reproducibility replicates and figure source data.

What's Changed

• fix(paper): drop the empty line above the Abstract heading in the PDF by @beccajcarlson in #207
• fix: harden paper comment loading against D1 read-replica lag by @beccajcarlson in #208
• docs: serve the DOI badge from shields.io by @beccajcarlson in #209
• ci: add a weekly floor to the D1 backup; document skipping the LFS payload by @beccajcarlson in #210
• docs: correct two stale claims in the agent guides and say which to read first by @beccajcarlson in #211
• feat(viewer): show paper title, authors and journal for cited references by @beccajcarlson in #221
• fix(paper): colour figure legends by sentence, not by line box by @beccajcarlson in #213
• fix(audit): repair the venn generator's sha pin and a stale provenance path by @beccajcarlson in #214
• feat(audit): Figure 1 becomes an UpSet; the Venn leaves the numbered set by @beccajcarlson in #215
• fix(tools): SURFACE-Bind sites now report which side of the membrane they anchor on by @beccajcarlson in #218
• fix(surface-proteome): repair purge-on-publish and close three API pass-through gaps by @beccajcarlson in #219
• feat(tools): add a cohort-wide purge for the Worker's per-gene caches by @beccajcarlson in #223
• fix(surface-proteome): namespace both cache tiers by the deploy epoch by @beccajcarlson in #222
• fix(viewer): make the whole citation a link and stop the title shouting by @beccajcarlson in #225
• fix(surface-proteome): pin the deploy epoch in cache-key tests by @beccajcarlson in #226
• fix(deps): tighten the sharp override past the libheif advisories by @beccajcarlson in #228
• fix(agents): restore internalization routes in the shared API by @beccajcarlson in #230
• feat(audit): blog Venn with count-scaled labels (co-authored with @ndamania00) by @beccajcarlson in #227
• chore(data): LFS-exempt every per-figure TSV so raw GitHub serves text by @beccajcarlson in #229
• fix(agents): include paper metadata with internalization evidence by @beccajcarlson in #233
• refactor(viewer): label surface reasons by pass count, not "classical" by @beccajcarlson in #236
• docs: reconcile triage_benchmark_v1.md to the benchmark TSV (68/31/48) by @beccajcarlson in #238
• feat(audit): SurfaceGenie SPC vs single-DB comparison on triage benchmark by @beccajcarlson in #237
• feat(agents): extend the pubmed rescue lane to the intracellular buckets by @beccajcarlson in #239
• feat(surface-proteome): backfill n_papers_found on D1-only records; add deep-dive homepage chip by @beccajcarlson in #240
• fix(agents,build): fail on unmeasured topology + five data-destroying sweep bugs by @beccajcarlson in #241
• fix(surface-proteome): gate the low-literature badge on the optimized UniProt cutoff by @beccajcarlson in #244
• fix(viewer): read the low-literature badge from the Worker, drop the duplicate All chip by @beccajcarlson in #245
• feat(surface-proteome): cohort funnel figure + fold the second rescue lane through every figure by @beccajcarlson in #246
• feat(surface-proteome): serve optimized UniProt + CSPA membership everywhere by @beccajcarlson in #247
• fix(agents): stop a cohort paralog release shadowing the global one; second look for every droppable gene by @beccajcarlson in #249
• chore(audit): regenerate every figure on the completed 5,333-record cohort by @beccajcarlson in #248
• fix(viewer): separate triage and deep-dive reason columns, add narrowed pill by @beccajcarlson in #252
• fix(tools): purge the cohort cache surfaces a public-D1 sync stales by @beccajcarlson in #253
• fix(audit): correct S8/S11 figure colours and refresh stale README counts by @beccajcarlson in #254
• fix(audit): label S12's percentage curves, and stop its README describing mock data by @beccajcarlson in #255
• docs(audit): mirror the manuscript figure legends into every gist README by @beccajcarlson in #256
• fix(audit): collapse benchmark replicates on the modal reason, not row order by @beccajcarlson in #257
• feat(audit): figure — which assays established the surface calls, and how often each stood alone by @beccajcarlson in #258
• fix(audit): Figure 5a — x-axis title, tier grouping brackets, uncertain repositioned by @beccajcarlson in #260
• fix(audit): Figure 6 — label the y axes, drop the figure title by @beccajcarlson in #261
• feat(audit): Supp S12 panel b — deep-dive tier composition by literature-size stratum by @beccajcarlson in #262
• fix(audit): Supp S12a — drop the iso-rate diagonals, raise point opacity by @beccajcarlson in #263
• chore(audit): refresh every rendered figure; lower S12a point opacity by @beccajcarlson in #264
• feat(surface-proteome): public record history and numbered data releases by @beccajcarlson in #259
• fix(audit): Figure 4 — give the composite the slug, so by_paper_number ships a PNG by @beccajcarlson in #265
• fix(audit): Figure 4 — stop calling the stage-2 set "zero-database" by @beccajcarlson in #266
• perf(surface-proteome): record-history R2 writes via S3 and batched, throttled D1 by @beccajcarlson in #267
• fix(audit): Figure 4 — break the stage-2 set out by database support by @beccajcarlson in #270
• fix(surface-proteome): never cache or archive a record whose serve-time enrichment failed by @beccajcarlson in #271
• fix(surface-proteome): pace record-history sweeps so they can't overload public D1 by @beccajcarlson in #273
• fix(viewer): keep catalog-header InfoTips legible inside the table scroll box by @beccajcarlson in #274
• fix(viewer): pace the build's API fetches and never bake a degraded record by @beccajcarlson in #275
• perf(surface-proteome): stop full scans on the Worker's hot D1 lookups by @beccajcarlson in #277
• fix(audit): order Figure 3's contextual bars by count by @beccajcarlson in #272
• fix(audit): add the union (>=1 DB) bar to supplementary figure S5 by @beccajcarlson in #276
• chore(audit): refresh Figure 7 with current viewer screenshots by @beccajcarlson in #278
• feat(audit): make Figure 7 reproducible and ship it as PDF + PNG by @beccajcarlson in #280
• fix(surface-proteome): history holds only served revisions; label what each revision changed by @beccajcarlson in #283
• feat(audit): Supplementary Figure 15 and API-only reproducibility replicates by @beccajcarlson in #279
• ci: extend Dependabot to Python (uv) with a 7-day cooldown and grouping by @beccajcarlson in #285
• ci: shared dependency guard and 7-day uv quarantine by @beccajcarlson in #296
• ci: pin the shared dependency guard to a commit hash by @beccajcarlson in #297
• ci(viewer): require the viewer build on every PR and clear its npm audit failures by @beccajcarlson in #299
• ci: Dependabot monthly, majors wait 30 days by @beccajcarlson in #301
• chore(deps): bump the npm-viewer-minor-and-patch group across 1 directory with 6 updates by @dependabot[bot] in #300
• chore(deps): bump the actions group across 1 directory with 4 updates by @dependabot[bot] in #287
• chore(deps): bump sqlite-utils from 3.39 to 4.2.1 by @dependabot[bot] in #292
• ci: ruff outside the Dependabot group; allow the deps-dev title scope by @beccajcarlson in #302
• build(deps): ruff 0.16.9 with an explicit rule set; one ruff for pre-commit and CI by @beccajcarlson in #305
• docs(audit): correct the stale facet totals in the Figure 5 docstring by @beccajcarlson in #282
• fix(audit): clean Figure 7's panel edges and un-clip the last table column by @beccajcarlson in #281
• docs(audit): refresh figure legends and correct stale docstring numbers by @beccajcarlson in #284
• fix(paper): correct the swapped supplementary figures in the build manifest by @beccajcarlson in #310
• fix(audit): rescore Supp S4 against the current benchmark truth by @beccajcarlson in #311
• fix(audit): Supp Fig 9 zero-DB split; legends, READMEs and gists matched to the manuscript by @beccajcarlson in #312
• fix(audit): render figures in Manrope SemiBold on one type scale, without colliding labels by @beccajcarlson in #313
• fix(agents): restore n_papers_found on 19 replayed records and stop the replay helper dropping it by @beccajcarlson in #316
• fix(paper): hyphenated print columns, wrapped identifiers, tidier Supp Table 1, lighter captions by @beccajcarlson in #318
• feat(paper): scroll-reveal motion and load-smoothness for the web edition by @beccajcarlson in #319
• fix(audit): give every Supp S4 panel its own axis titles by @beccajcarlson in #322
• feat(paper): put the legend beside tall figures in the lightbox by @beccajcarlson in #323
• fix(audit): correct figure captions, README prose, and a stale Supp S12 render by @beccajcarlson in #324
• docs(paper): record 58rem as the settled prose measure by @beccajcarlson in #325
• fix(audit): rebuild the surface-evidence assay figure as Supp S13 and renumber S13-S15 to S14-S16 by @beccajcarlson in #326
• fix(viewer): bring dev's tag-site per-gene facts into main's Worker by @beccajcarlson in #327
• feat(viewer): filter the catalog by the method behind each surface call by @beccajcarlson in #328
• feat(audit): show each tier's call confidence under Figure 5a by @beccajcarlson in #329
• fix(viewer): label the revision link "Permanent link" by @beccajcarlson in #331
• docs(audit): match the Figure 6 and Supp S13 gist READMEs to the manuscript legends by @beccajcarlson in #330
• feat(audit): restore the blog gene-card generator, reading live records by @beccajcarlson in #332
• fix(audit): correct Supp S2 model prices and retire the superseded Venn slug by @beccajcarlson in #333
• docs(audit): sync gist READMEs to the manuscript before minting SWHIDs by @beccajcarlson in #334
• fix(viewer): fit the home catalog table to the page and stop its header falling short by @beccajcarlson in #336
• chore(data): record the 95 Schweke homomer PDBs added to R2 by @beccajcarlson in #337
• docs(docs): correct stale pipeline facts in CLAUDE.md, AGENTS.md and README by @beccajcarlson in #335
• fix(audit): Figure 4a database union and Supp S14 HPA denominator by @beccajcarlson in #339
• feat(data): pin orthologs and paralogs to Ensembl Compara 115 and refresh records from D1 by @beccajcarlson in #338
• fix(audit): refresh Figure 6 and Supp S15 from the corrected deterministic records by @beccajcarlson in #340
• feat(data): add topology_ensembl_public for forms with no UniProt proteoform by @beccajcarlson in #308
• fix(audit): Figure 4 trim-card contrast and Figure 5b tier composition by @beccajcarlson in #343
• feat(audit): add Claude 5.5 and Opus 5 to the triage benchmark (S1, S2) by @beccajcarlson in #341
• docs(paper): renumber supplementary figures S1-S4 to match citation order by @beccajcarlson in #344
• docs(data): relabel the reproducibility bundle as Supplementary Figure 16 by @beccajcarlson in #345
• feat(audit): compute the McNemar tests the manuscript reports by @beccajcarlson in #346
• fix(surface-proteome): select catalog rescue rows by run, not prompt variant by @beccajcarlson in #347
• docs(paper): re-export manuscript legends and record re-synced gist SWHIDs by @beccajcarlson in #348
• fix(paper): citation matching, structured JATS, and print-build fixes by @beccajcarlson in #349
• fix(audit): audit Compara release labels, and refresh Fig 6 and S15 data after the record fixes by @beccajcarlson in #350
• fix(viewer): retry a failed Schweke homomer PDB fetch past the browser cache by @beccajcarlson in #351
• chore(audit): record the gists' SWHIDs after re-syncing them to main by @beccajcarlson in #352
• fix(viewer): load experimental structures RCSB only publishes as mmCIF by @beccajcarlson in #356
• test(viewer): audit every gene's 3D structure weekly, and fix the 17 it found by @beccajcarlson in #359
• fix(viewer): read the structure's own DBREF before guessing its numbering by @beccajcarlson in #362
• ci(viewer): run the structure audit weekly, not on every PR by @beccajcarlson in #364
• fix(paper): stamp paper SVGs with their source PDF hash, so CI catches a stale one by @beccajcarlson in #379
• fix(data): add both authors' ORCIDs and full names to every Zenodo record source by @beccajcarlson in #380
• fix(docs): extract every manuscript legend in sync_readme_legends --export by @beccajcarlson in #383
• docs(paper): clarify the lavender bars in Supp Figs 2-3, and sync all 23 legends to the manuscript by @beccajcarlson in #381
• fix(viewer): pin the benchmark matrix and export to the SurfaceBench run by @beccajcarlson in #389
• fix(viewer): repair Markdown brief rendering and gene-page download hints by @beccajcarlson in #388
• fix(viewer): serve the benchmark matrix as the 3-replicate majority, matching the paper by @beccajcarlson in #391
• fix(audit): record the final 1.3.0 figure SWHIDs, and stop the gist sync re-versioning unchanged gists by @beccajcarlson in #387
• fix(data): make the release deposit self-describing and the release procedure explicit by @beccajcarlson in #386
• docs(viewer): sync public API docs, skill and availability page with the live API by @beccajcarlson in #385
• chore(surface-proteome): bump version to 1.3.0 ahead of the release by @beccajcarlson in #382
• fix(agents): keep the search log when a deep dive is replayed or resumed by @beccajcarlson in #393
• fix(data): fill DeepTMHMM's own call on records and in the Worker, and fix two stale API index entries by @beccajcarlson in #384
• fix(data): describe the PubMed rescue as one pass, label every triage row by pass, and add tier and low-lit columns by @beccajcarlson in #395
• feat(viewer): bring dev's serve-time Worker additions onto main, and document them by @beccajcarlson in #396
• fix(viewer): fill DeepTMHMM's call into the stored topology block instead of rebuilding it by @beccajcarlson in #397
• docs(viewer): document which record fields the Worker fills at serve time, and say triage_signal is the first-pass call by @beccajcarlson in #399
• docs(paper): call stage-two triage a PubMed pass in Supp Fig 2 and 3 legends by @beccajcarlson in #400
• fix(ci): stop the D1 backup blocking the live API, and answer 503 while D1 is busy by @beccajcarlson in #401
• fix(paper): restore Figure 7, which rendered blank in the PDF by @beccajcarlson in #404
• docs(data): say the benchmark TSV has no triage_pass column either by @beccajcarlson in #407
• feat(paper): place Figures 3, 5 and 6 so they don't split the text in the PDF by @beccajcarlson in #406
• fix(paper): stop the paper build when any figure renders blank in WeasyPrint by @beccajcarlson in #405

New Contributors

• @dependabot[bot] made their first contribution in #300

Full Changelog: v1.2.0...v1.3.0