infra/paperspec
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
76d76353d9faf1d5464bb25275dcc178c38a6ca5
paperspec/fixtures/records/layer/annotations.jsonl
T
alexmandClaude 76d76353d9 feat: rename to paperspec and add the website 
- Rename manuspec to paperspec everywhere outside pixi.toml: prose, the
  tools, provenance tool names and the fixture key derivations, so every
  fixture and vector is rebuilt.
- Move the namespace addresses under the site, mirroring the repository:
  schema $id https://paperspec.scient.ing/schemas/<file>, the JSON-LD
  context https://paperspec.scient.ing/context/scienting-1.jsonld, and
  term IRIs https://paperspec.scient.ing/vocab#<term>. Format
  identifiers (scienting-*) and URNs (urn:scienting:) are unchanged.
- tools/site.py (standard library only) builds _site/: every file of the
  repository at its own path, each Markdown file rendered as a page with
  sidebar navigation, heading anchors matching the forge's, folder
  listings, a vocabulary page for the context's IRIs, a heading search
  and a 404 page; light and dark themes.
- check.py builds the site and checks that every Markdown file has a
  page, every internal link and fragment resolves, no Markdown is left
  unrendered, and every $id, the context address and the vocabulary IRIs
  are files of the site.
- deploy/: a Caddyfile with the media types and CORS the data needs, and
  a guide; .gitea/workflows/site.yml builds on main and publishes with
  rsync when the SITE_* secrets are set.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-14 21:27:21 -04:00

11 lines
12 KiB
JSON
Raw Blame History

This file contains ambiguous Unicode characters
This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"audience":"novice","format":"text/markdown","kind":"gloss","language":"en","type":"TextualBody","value":"A *harmonic* term treats a bond like a spring: the energy grows with the square of the stretch."},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/jgk1n6dcvwbvw","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"describing","receipt":"pgtc2enctchze","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"sxgcc9h","node_hash":"76e06b4811a688357ac4b912172283463cfaf1b7a1f0795d274fc733a2309ba7","own_hash":"2d7df7b8b233eab6f96d5db0d29c99062aaa94b55cf4e388c49b9995ce7548d5","quote":{"exact":"bond force constant","prefix":"rm{eq}})^2$$ where $K_r$ is the ","suffix":" and $r_\\mathrm{eq}$ the equilib"},"rev":12,"span":[111,130],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"bond force constant","prefix":"rm{eq}})^2$$ where $K_r$ is the ","suffix":" and $r_\\mathrm{eq}$ the equilib","type":"TextQuoteSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"claim-link","pin":"illustrative-pin","role":"states","source":"lode:amber/k-bond","type":"SpecificResource"},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/c9herrt41fcpr","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"linking","receipt":"pgtc2enctchze","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"sxgcc9h","node_hash":"76e06b4811a688357ac4b912172283463cfaf1b7a1f0795d274fc733a2309ba7","own_hash":"2d7df7b8b233eab6f96d5db0d29c99062aaa94b55cf4e388c49b9995ce7548d5","quote":{"exact":"The bond energy is given by $$E_{\\mathrm{bond}} = \\frac{1}{2} K_r (r - r_{\\mathrm{eq}})^2$$ where $K_r$ is the bond force constant and $r_\\mathrm{eq}$ the equilibrium bond length."},"rev":12,"store":"smithlab"},"type":"AnchorSelector"},{"exact":"The bond energy is given by $$E_{\\mathrm{bond}} = \\frac{1}{2} K_r (r - r_{\\mathrm{eq}})^2$$ where $K_r$ is the bond force constant and $r_\\mathrm{eq}$ the equilibrium bond length.","prefix":"","suffix":"","type":"TextQuoteSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"comment","type":"TextualBody","value":"The step size matters more than the text admits."},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/cr683cx7pq7fd","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"commenting","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"eajq93t","node_hash":"42b1de7852cdc68730984fff789fe248ecd5b43198c0e7d671931ff3fe561dc3","own_hash":"4dc28d1ad57c74d044f87264dfbc744ae9d5e9644638db976dbc346361442486","quote":{"exact":"steps of 0.01","prefix":"Each bond was scanned in ","suffix":" Å around its minimum, and the e"},"rev":12,"span":[25,38],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"steps of 0.01","prefix":"Each bond was scanned in ","suffix":" Å around its minimum, and the e","type":"TextQuoteSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"for":"group","kind":"question","type":"TextualBody","value":"Why fit to a scan first and to frequencies second?"},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/a0g73q52t6h2t","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"questioning","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"section","node":"f0tj6ca","node_hash":"8acfa263e93dcee504efbfcd328fb69b81f4d71e97b921fa8da664a541e722ff","own_hash":"c3d50f266b05d7889c001aef16662cecd4e99ac4a2747ec331c1044e6adc8e3e","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"citation-context","reason":"value","reference":"b3g86a4","type":"TextualBody","value":"Cited for the band position; the reference is not in the library.","verdict":"cannot-tell"},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/yaewet6dypvbk","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"assessing","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"f929eq9","node_hash":"cd6cdb032e9b8ab712790b7181f794f6e363b7c4c96888049b59c671c1596369","own_hash":"d5b2ebdc96010fd8fc83abcbec9e5c2340bf766997a485f11f2dae49d0d2dd4c","quote":{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2"},"rev":12,"span":[71,75],"store":"smithlab"},"type":"AnchorSelector"},{"exact":"1595","prefix":" case, with a bending band near ","suffix":" cm⁻¹.2","type":"TextQuoteSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"generator":{"model":"example-model","run":"illustrative-run-1"},"kind":"generated","type":"TextualBody","value":"Two panels: an energy scan and its fit residual."},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:software:example-model","name":"A model (illustrative)","type":"Software"},"id":"urn:scienting:annotation:smithlab/zyjypkh70f089","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"describing","status":"proposed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"figure","node":"ajfvq4s","node_hash":"f76864779843485fa9e2f3cc3cd1c76ad222e1649c56f4cface33bf20b8f33b6","own_hash":"a1e46cb40201a17903dfd6f128db1e707b0e9f5bf45fcc32ec7ca772011edeae","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"exercise":{"exercise":"anchor","format":"scienting-exercise/1","key":{"elements":[{"anchors":[{"context":{"column_path":["Set A","$K_r$ (kcal mol⁻¹ Å⁻²)"],"row_path":["Bond parameters","CT–CT"],"table_label":"Table 1"},"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"cell","node":"nkm3xn5","node_hash":"21f13b21948078f64c564334e5bb180b4495edb25a79ae32aa967986a626f3d5","own_hash":"2937e2a6f14cfebd4ffd20e3d514e5cbbf0626a5c0089b7cbea817ef20782b3d","quote":{"exact":"310.0"},"rev":12,"store":"smithlab"}],"feedback":{"hit":"That is the cell.","miss":"Look in Table 1, row CT–CT."},"points":"1"}]},"prompt":"Find the table cell that gives the Set A bond constant for the CT–CT bond.","rule":{"match":"same-node"}},"kind":"exercise","type":"TextualBody","value":"Find the table cell that gives the Set A bond constant for the CT–CT bond."},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/tj573y8mhap0f","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"assessing","receipt":"pgtc2enctchze","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"table","node":"gm5z4rx","node_hash":"999777484c58cf3646eabb6df3e559369a1b081ec4f337d621dade1bf241f339","own_hash":"b56ce0ab4b480c4c43b11ca2eaca410c60fed73341d53896d509e30eabf54477","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"exercise":{"exercise":"check","format":"scienting-exercise/1","key":{"elements":[{"anchors":[{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"mbtjsqv","node_hash":"97c328c2e2efedd931292eeda806d3e4bad14d67cfcc324537c0d993068cfbfc","own_hash":"c1c6019d21c26d790304f7f7a080e93cf507d0e22ebeec6bf2e7df19a1820b3b","quote":{"exact":"the most common description","prefix":"Harmonic bond terms remain ","suffix":" of covalent stretching in class"},"rev":12,"span":[27,54],"store":"smithlab"}],"points":"1"}],"verdict":{"points":"1","value":"supports"}},"prompt":"Does the cited passage support the claim that harmonic terms are the most common choice?","rule":{"match":"overlap","min_overlap":"0.5"}},"kind":"exercise","type":"TextualBody","value":"Does the cited passage support the claim that harmonic terms are the most common choice?"},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/shn6geqn0rhvs","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"assessing","receipt":"pgtc2enctchze","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"sentence","node":"mbtjsqv","node_hash":"97c328c2e2efedd931292eeda806d3e4bad14d67cfcc324537c0d993068cfbfc","own_hash":"c1c6019d21c26d790304f7f7a080e93cf507d0e22ebeec6bf2e7df19a1820b3b","quote":{"exact":"Harmonic bond terms remain the most common description of covalent stretching in classical force fields.1"},"rev":12,"store":"smithlab"},"type":"AnchorSelector"},{"exact":"Harmonic bond terms remain the most common description of covalent stretching in classical force fields.1","prefix":"","suffix":"","type":"TextQuoteSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"description","language":"en","role":"alt","type":"TextualBody","value":"Energy along the C–C bond stretch (panel a) and the fit residual (panel b)."},"created":"2026-10-11T19:00:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/v5pk0zcbsxa4b","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"describing","receipt":"pgtc2enctchze","status":"confirmed","target":{"selector":[{"anchor":{"doc":"hale2026harmonic","format":"scienting-anchor/1","kind":"figure","node":"ajfvq4s","node_hash":"f76864779843485fa9e2f3cc3cd1c76ad222e1649c56f4cface33bf20b8f33b6","own_hash":"a1e46cb40201a17903dfd6f128db1e707b0e9f5bf45fcc32ec7ca772011edeae","rev":12,"store":"smithlab"},"type":"AnchorSelector"}],"source":"urn:scienting:doc:smithlab/hale2026harmonic","type":"SpecificResource"},"type":"Annotation"}
{"@context":["http://www.w3.org/ns/anno.jsonld","https://paperspec.scient.ing/context/scienting-1.jsonld"],"body":{"kind":"comment","type":"TextualBody","value":"Agreed; see the residual panel."},"created":"2026-10-11T19:05:00Z","creator":{"id":"urn:scienting:key:ana","name":"Ana Example","type":"Person"},"id":"urn:scienting:annotation:smithlab/sfatrthbcfv8a","layer":"urn:scienting:layer:smithlab/kp4m2x7q","motivation":"replying","status":"proposed","target":{"source":"urn:scienting:annotation:smithlab/cr683cx7pq7fd","type":"SpecificResource"},"type":"Annotation"}
Reference in new issue View Git Blame Copy Permalink