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WUBING2023/PaperSpine

PaperSpine5 — local-first, evidence-bound paper research, writing, figures, review and delivery. Download: https://wubing2023.github.io/PaperSpine/v5/

Claude CodeResearchWriting

History

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paperspine5/core/02_PaperFigure/02_paperFig_skill/SKILL.md

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View on GitHubAdd to my skills

Verified commit 42312b8d9c76ab25990cddfd76e3622276854118

git clone --filter=blob:none --no-checkout https://github.com/WUBING2023/PaperSpine.git .hotskills/wubing2023-paperspine && git -C .hotskills/wubing2023-paperspine checkout --detach 42312b8d9c76ab25990cddfd76e3622276854118 # Copy each selected skill directory from .hotskills/wubing2023-paperspine into .claude/skills/<skill-name>/
6.2kGitHub stars
81stars in 7 days
7skills in this repository
2commits in 30 days

Heat

6.7
  • Star growth, last 7 daysAhead of 87% of tracked repositories
  • Star growth, last 24 hoursAhead of 84% of tracked repositories
  • Rank movement, last 7 daysAhead of 58% of tracked repositories
  • Commits, last 30 daysAhead of 60% of tracked repositories
  • Accounts asking about it through MCP, last 7 daysNot available
  • Hot votes this weekAhead of 0% of tracked repositories

Heat never changes the order by stars, and sponsorship never touches it. How heat works

Stars over time

Aug 2, 2026Nov 6, 20266,215

Individual skills in this repository

How it works

paper-spine

When your agent uses it

Research, write, review and deliver evidence-bound papers in one task, with user choices, real files, editable outputs and same-task revision.

What it loads into context

Frontmatter

46 tokens

Always available to the agent

SKILL.md

4,489 tokens

When the skill is activated

Reference documents

127,179 tokens

Loaded on request

Token counts are estimates. Scripts run separately; they are not counted as reference context.

The playbook

  1. Authority and boundaries
  2. Update once on invocation, then continue the paper
  3. Start, configure and continue the current paper
  4. Work continuously within the confirmed scope
  5. Scientific work and expected results
  6. Quality rules that always remain active
  7. Completion contract

Scripts executed separately

  • scripts/_paper_spine_utils.py
  • scripts/adaptive_shadow.py
  • scripts/artifact_check.py
  • scripts/asset_selection.py
  • scripts/author_voice_check.py
  • scripts/citation_bank_check.py
  • scripts/citation_quality_audit.py
  • scripts/citation_verification_en.py
  • scripts/citation_verification_zh.py
  • scripts/contribution_check.py
  • scripts/evidence_grounded_review.py
  • scripts/execution_receipt.py
  • scripts/figure_comparison.py
  • scripts/figure_reference_check.py
  • scripts/figure_story_check.py
  • scripts/humanize_check.py
  • scripts/intake_wizard.py
  • scripts/integrity_audit.py
  • scripts/latex_guard.py
  • scripts/launch_paperspine_ui.ps1
  • scripts/launch_paperspine_ui.sh
  • scripts/manuscript_export.py
  • scripts/manuscript_refs.lua
  • scripts/material_inventory.py
  • scripts/metadata_readiness_check.py
  • scripts/open_release.py
  • scripts/paperspine5_web.py
  • scripts/paperspine_methods.py
  • scripts/paperspine_public_client.py
  • scripts/paperspine_stable_update.py
  • scripts/paperspine_update.py
  • scripts/preserve_figure_revision.py
  • scripts/progress_check.py
  • scripts/publication_cycle.py
  • scripts/publication_surface_check.py
  • scripts/reference_inventory.py
  • scripts/respond_check.py
  • scripts/results_validation_check.py
  • scripts/reviewer_audit_check.py
  • scripts/revision_audit.py
  • scripts/scientific_evidence_check.py
  • scripts/section_economy_check.py
  • scripts/skill_discovery_migration.py
  • scripts/structured_review.py
  • scripts/style_metrics.py
  • scripts/submission_check.py
  • scripts/supplement_evidence_index.py
  • scripts/translate_guard.py
  • scripts/usage_ledger.py
  • scripts/visual_readiness_check.py
  • scripts/word_guard.py
  • scripts/word_surface_repair.py

Files

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Read SKILL.md

# PaperSpine Orchestrator

Before paper production or resume, read [paper-spine-production-protocol.md](references/paper-spine-production-protocol.md). It is the operational 17-step handoff for the methods below.

The current host Agent performs research, citation checking, interpretation,
writing, figures and revision, and arranges independent review. Web, local files
and small scripts support interaction, persistence, rendering and delivery.

When configuration is missing, launch the intake UI automatically before inspecting
materials; do not hand-write configuration or silently choose a paper root.
For a visible launcher action, use `require_escalated` as required by the host.
After the update preflight below, launch is the first paper-production action when configuration is missing.

**Product outcome:** an evidence-bound, coherent paper with informative figures,
View the complete source on GitHub

Skills included

  • paper-spine
  • paper-spine
  • paper-spine
  • paper-spine
  • paper-spine
  • paperFig
  • paper-spine

Repository facts

License
MIT
Created
May 17, 2026
Last pushed
Oct 14, 2026
Forks
249
Open issues
1
Project activity
Active

Rank over the last 12 weeks

Now #240 · best #211 · down 16 in 30 days

  1. #233 on Oct 29
  2. #236 on Oct 30
  3. #237 on Oct 31
  4. #236 from Nov 1 to Nov 2
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  6. #240 since Nov 6
61 earlier periods
  1. #204 on Aug 2
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Before you install

Network or broad shell

Automated signals, not a guarantee

Checked Nov 2, 2026

Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.

Show 38 notes
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Show all 1,692 signals by file

.claude-plugin/marketplace.json

  • Network accessline 1
    {   "$schema": "https://anthropic.com/claude-code/marketplace.schema.json",
  • Network accessline 2
    "$schema": "https://anthropic.com/claude-code/marketplace.schema.json",
  • Network accessline 5
    "owner": {     "name": "WUBING2023",     "url": "https://github.com/WUBING2023"
  • Network accessline 6
    "name": "WUBING2023",     "url": "https://github.com/WUBING2023"   },
  • Network accessline 7
    "url": "https://github.com/WUBING2023"
  • Network accessline 14
    "version": "4.0.1",       "category": "writing",       "homepage": "https://github.com/WUBING2023/PaperSpine",
  • Network accessline 15
    "category": "writing",       "homepage": "https://github.com/WUBING2023/PaperSpine",       "skills": [
  • Network accessline 16
    "homepage": "https://github.com/WUBING2023/PaperSpine",

.claude-plugin/plugin.json

  • Network accessline 1
    {   "$schema": "https://anthropic.com/claude-code/plugin.schema.json",
  • Network accessline 2
    "$schema": "https://anthropic.com/claude-code/plugin.schema.json",
  • Network accessline 6
    "author": {     "name": "WUBING2023",     "url": "https://github.com/WUBING2023"
  • Network accessline 7
    "name": "WUBING2023",     "url": "https://github.com/WUBING2023"   },
  • Network accessline 8
    "url": "https://github.com/WUBING2023"
  • Network accessline 9
    },   "repository": "https://github.com/WUBING2023/PaperSpine",   "license": "MIT",
  • Network accessline 10
    "repository": "https://github.com/WUBING2023/PaperSpine",

dist/claude/skills/paper-spine/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

dist/claude/skills/paper-spine/references/contracts/author-voice-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

dist/claude/skills/paper-spine/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

dist/claude/skills/paper-spine/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

dist/claude/skills/paper-spine/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

dist/claude/skills/paper-spine/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

dist/claude/skills/paper-spine/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

dist/claude/skills/paper-spine/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

dist/claude/skills/paper-spine/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/claude/skills/paper-spine/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

dist/claude/skills/paper-spine/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

dist/claude/skills/paper-spine/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
  • Network accessline 289
    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

dist/claude/skills/paper-spine/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

dist/claude/skills/paper-spine/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

dist/claude/skills/paper-spine/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

dist/claude/skills/paper-spine/scripts/_paper_spine_utils.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/adaptive_shadow.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/artifact_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/asset_selection.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/author_voice_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/citation_bank_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/citation_quality_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 38
    ARXIV_RE = re.compile(r"\barxiv\s*:?\s*(\d{4}\.\d{4,5}(?:v\d+)?)\b", re.IGNORECASE) URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 39
    URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/" SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 40
    CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 41
    SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 42
    USER_AGENT = "PaperSpine/3.0 (citation-quality; https://github.com/WUBING2023/PaperSpine)"

dist/claude/skills/paper-spine/scripts/citation_verification_en.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 29
    CROSSREF_QUERY_URL = "https://api.crossref.org/works"
  • Network accessline 185
    Extracted as a module-level function so tests can mock it without     touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 186
    touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 189
    req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
  • Network accessline 190
    try:         with urllib.request.urlopen(req, timeout=timeout) as resp:             return json.loads(resp.read().decode("utf-8"))  # type: ignore[no-any-return]
  • Network accessline 191
    with urllib.request.urlopen(req, timeout=timeout) as resp:
  • Network accessline 460
    doi_url = f"{CROSSREF_QUERY_URL}/{urllib.parse.quote(doi, safe='')}"             data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 461
    data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 514
    f"{urllib.parse.urlencode({'query.bibliographic': bib_query[:200], 'rows': 3})}"             )             data = fetch(bib_url)  # type: ignore[call-arg]
  • Network accessline 516
    data = fetch(bib_url)  # type: ignore[call-arg]

dist/claude/skills/paper-spine/scripts/citation_verification_zh.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 24
    USER_AGENT = "PaperSpine/3.0 (citation-zh; https://github.com/WUBING2023/PaperSpine)"
  • Network accessline 97
    def verify_doi(doi: str) -> bool:     try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})
  • Network accessline 98
    try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:
  • Network accessline 99
    req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:             return resp.status == 200

dist/claude/skills/paper-spine/scripts/contribution_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/evidence_grounded_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/execution_receipt.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/figure_comparison.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/figure_reference_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/figure_story_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/humanize_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/intake_wizard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 274
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/integrity_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/latex_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/launch_paperspine_ui.ps1

  • Executable scriptline 1
    Executable file

dist/claude/skills/paper-spine/scripts/launch_paperspine_ui.sh

  • Executable scriptline 1
    #!/usr/bin/env bash

dist/claude/skills/paper-spine/scripts/manuscript_export.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/manuscript_refs.lua

  • Executable scriptline 1
    Executable file

dist/claude/skills/paper-spine/scripts/material_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/metadata_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/open_release.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 37
    [Credential-related source omitted]
  • Access to secretsline 41
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/paperspine5_web.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 29
    [Credential-related source omitted]
  • Access to secretsline 200
    [Credential-related source omitted]
  • Access to secretsline 201
    [Credential-related source omitted]
  • Access to secretsline 411
    [Credential-related source omitted]
  • Access to secretsline 516
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/paperspine_methods.py

  • Executable scriptline 1
    Executable file

dist/claude/skills/paper-spine/scripts/paperspine_public_client.py

  • Executable scriptline 1
    Executable file
  • Access to secretsline 41
    [Credential-related source omitted]
  • Access to secretsline 45
    [Credential-related source omitted]
  • Access to secretsline 78
    [Credential-related source omitted]
  • Access to secretsline 142
    [Credential-related source omitted]
  • Network accessline 228
    with urlopen(f'http://127.0.0.1:{port}/api/v1/session', timeout=2) as response:
  • Access to secretsline 335
    [Credential-related source omitted]
  • Network accessline 382
    kernel.close()         raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Network accessline 383
    raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',         'port': server.server_
  • Network accessline 384
    _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Access to secretsline 533
    [Credential-related source omitted]
  • Access to secretsline 562
    [Credential-related source omitted]
  • Access to secretsline 655
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/paperspine_stable_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 208
    def fetch(source, target, limit=LIMIT):
  • Network accessline 230
    scratch.mkdir(parents=True, exist_ok=True)     downloaded = scratch / "source"     fetch(source, downloaded)
  • Network accessline 231
    downloaded = scratch / "source"     fetch(source, downloaded)     channel = None
  • Network accessline 232
    fetch(source, downloaded)
  • Network accessline 235
    channel = read(downloaded)         bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 236
    bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")         expected = bundle["sha256"]
  • Network accessline 237
    fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 254
    with tempfile.TemporaryDirectory(prefix="paperspine-check-") as temporary:             metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)
  • Network accessline 255
    metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)             if zipfile.is_zipfile(metadata):
  • Network accessline 256
    fetch(source, metadata, limit=2 * 1024 * 1024)
  • Access to secretsline 455
    [Credential-related source omitted]
  • Access to secretsline 628
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/paperspine_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 26
    DEFAULT_MANIFEST_URL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 27
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 28
    ) DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 29
    DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json" )
  • Network accessline 30
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 33
    DEFAULT_ARCHIVE_URL = "https://github.com/WUBING2023/PaperSpine/archive/refs/tags/v4.0.0.zip"
  • Access to secretsline 129
    [Credential-related source omitted]
  • Network accessline 291
    def load_manifest_from_url(url: str) -> dict[str, Any]:     try:         with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 292
    try:         with urllib.request.urlopen(url, timeout=20) as response:             body = response.read().decode("utf-8")
  • Network accessline 293
    with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 313
    archive_path = temp_dir / "paperspine-update.zip"     try:         with urllib.request.urlopen(url, timeout=60) as response:
  • Network accessline 314
    try:         with urllib.request.urlopen(url, timeout=60) as response:             archive_path.write_bytes(response.read())
  • Network accessline 315
    with urllib.request.urlopen(url, timeout=60) as response:
  • Access to secretsline 440
    [Credential-related source omitted]
  • Access to secretsline 443
    [Credential-related source omitted]
  • Access to secretsline 445
    [Credential-related source omitted]
  • Access to secretsline 446
    [Credential-related source omitted]
  • Access to secretsline 448
    [Credential-related source omitted]
  • Access to secretsline 451
    [Credential-related source omitted]
  • Access to secretsline 601
    [Credential-related source omitted]

dist/claude/skills/paper-spine/scripts/preserve_figure_revision.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/progress_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/publication_cycle.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/publication_surface_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 269
    def _docx(path: Path) -> list[_Text]:     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 270
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 271
    "r": "http://schemas.openxmlformats.org/officeDocument/2006/relationships"}

dist/claude/skills/paper-spine/scripts/reference_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/respond_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/results_validation_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/reviewer_audit_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/revision_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/scientific_evidence_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/section_economy_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/skill_discovery_migration.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/structured_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/style_metrics.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/submission_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 65
    A4_HEIGHT_TWIPS = "16838" DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 66
    DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" W = f"{{{W_NS}}}"
  • Network accessline 67
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

dist/claude/skills/paper-spine/scripts/supplement_evidence_index.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/translate_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 514
    except (zipfile.BadZipFile, ElementTree.ParseError, OSError):         return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 515
    return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 516
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}

dist/claude/skills/paper-spine/scripts/usage_ledger.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/visual_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/claude/skills/paper-spine/scripts/word_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 172
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 173
    A_NS = "http://schemas.openxmlformats.org/drawingml/2006/main"
  • Network accessline 174
    WP_NS = "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing"
  • Network accessline 175
    PIC_NS = "http://schemas.openxmlformats.org/drawingml/2006/picture"
  • Network accessline 176
    R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"
  • Network accessline 177
    PACKAGE_NS = "http://schemas.openxmlformats.org/package/2006/relationships"
  • Network accessline 481
    def extract_text(document_xml: bytes) -> tuple[str, int]:     root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 482
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 483
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 506
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 507
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 968
    if root.getroottree().docinfo.doctype:         raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 969
    raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"     qname_lists = {f"{{{mc}}}{name}" for name in (
  • Network accessline 970
    mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 1118
    if anchor and not node.get("{http://schemas.openxmlformats.org/officeDocument/2006/relationships}id") and anchor.lower() != "_top" and anchor not in bookmarks:

dist/claude/skills/paper-spine/scripts/word_surface_repair.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

dist/codex/skills/paper-spine/references/contracts/author-voice-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

dist/codex/skills/paper-spine/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

dist/codex/skills/paper-spine/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

dist/codex/skills/paper-spine/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

dist/codex/skills/paper-spine/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

dist/codex/skills/paper-spine/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

dist/codex/skills/paper-spine/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

dist/codex/skills/paper-spine/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/codex/skills/paper-spine/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

dist/codex/skills/paper-spine/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

dist/codex/skills/paper-spine/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
  • Network accessline 289
    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

dist/codex/skills/paper-spine/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

dist/codex/skills/paper-spine/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

dist/codex/skills/paper-spine/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

dist/codex/skills/paper-spine/scripts/_paper_spine_utils.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/adaptive_shadow.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/artifact_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/asset_selection.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/author_voice_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/citation_bank_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/citation_quality_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 38
    ARXIV_RE = re.compile(r"\barxiv\s*:?\s*(\d{4}\.\d{4,5}(?:v\d+)?)\b", re.IGNORECASE) URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 39
    URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/" SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 40
    CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 41
    SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 42
    USER_AGENT = "PaperSpine/3.0 (citation-quality; https://github.com/WUBING2023/PaperSpine)"

dist/codex/skills/paper-spine/scripts/citation_verification_en.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 29
    CROSSREF_QUERY_URL = "https://api.crossref.org/works"
  • Network accessline 185
    Extracted as a module-level function so tests can mock it without     touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 186
    touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 189
    req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
  • Network accessline 190
    try:         with urllib.request.urlopen(req, timeout=timeout) as resp:             return json.loads(resp.read().decode("utf-8"))  # type: ignore[no-any-return]
  • Network accessline 191
    with urllib.request.urlopen(req, timeout=timeout) as resp:
  • Network accessline 460
    doi_url = f"{CROSSREF_QUERY_URL}/{urllib.parse.quote(doi, safe='')}"             data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 461
    data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 514
    f"{urllib.parse.urlencode({'query.bibliographic': bib_query[:200], 'rows': 3})}"             )             data = fetch(bib_url)  # type: ignore[call-arg]
  • Network accessline 516
    data = fetch(bib_url)  # type: ignore[call-arg]

dist/codex/skills/paper-spine/scripts/citation_verification_zh.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 24
    USER_AGENT = "PaperSpine/3.0 (citation-zh; https://github.com/WUBING2023/PaperSpine)"
  • Network accessline 97
    def verify_doi(doi: str) -> bool:     try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})
  • Network accessline 98
    try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:
  • Network accessline 99
    req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:             return resp.status == 200

dist/codex/skills/paper-spine/scripts/contribution_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/evidence_grounded_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/execution_receipt.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/figure_comparison.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/figure_reference_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/figure_story_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/humanize_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/intake_wizard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 274
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/integrity_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/latex_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/launch_paperspine_ui.ps1

  • Executable scriptline 1
    Executable file

dist/codex/skills/paper-spine/scripts/launch_paperspine_ui.sh

  • Executable scriptline 1
    #!/usr/bin/env bash

dist/codex/skills/paper-spine/scripts/manuscript_export.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/manuscript_refs.lua

  • Executable scriptline 1
    Executable file

dist/codex/skills/paper-spine/scripts/material_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/metadata_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/open_release.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 37
    [Credential-related source omitted]
  • Access to secretsline 41
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/paperspine5_web.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 29
    [Credential-related source omitted]
  • Access to secretsline 200
    [Credential-related source omitted]
  • Access to secretsline 201
    [Credential-related source omitted]
  • Access to secretsline 411
    [Credential-related source omitted]
  • Access to secretsline 516
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/paperspine_methods.py

  • Executable scriptline 1
    Executable file

dist/codex/skills/paper-spine/scripts/paperspine_public_client.py

  • Executable scriptline 1
    Executable file
  • Access to secretsline 41
    [Credential-related source omitted]
  • Access to secretsline 45
    [Credential-related source omitted]
  • Access to secretsline 78
    [Credential-related source omitted]
  • Access to secretsline 142
    [Credential-related source omitted]
  • Network accessline 228
    with urlopen(f'http://127.0.0.1:{port}/api/v1/session', timeout=2) as response:
  • Access to secretsline 335
    [Credential-related source omitted]
  • Network accessline 382
    kernel.close()         raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Network accessline 383
    raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',         'port': server.server_
  • Network accessline 384
    _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Access to secretsline 533
    [Credential-related source omitted]
  • Access to secretsline 562
    [Credential-related source omitted]
  • Access to secretsline 655
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/paperspine_stable_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 208
    def fetch(source, target, limit=LIMIT):
  • Network accessline 230
    scratch.mkdir(parents=True, exist_ok=True)     downloaded = scratch / "source"     fetch(source, downloaded)
  • Network accessline 231
    downloaded = scratch / "source"     fetch(source, downloaded)     channel = None
  • Network accessline 232
    fetch(source, downloaded)
  • Network accessline 235
    channel = read(downloaded)         bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 236
    bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")         expected = bundle["sha256"]
  • Network accessline 237
    fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 254
    with tempfile.TemporaryDirectory(prefix="paperspine-check-") as temporary:             metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)
  • Network accessline 255
    metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)             if zipfile.is_zipfile(metadata):
  • Network accessline 256
    fetch(source, metadata, limit=2 * 1024 * 1024)
  • Access to secretsline 455
    [Credential-related source omitted]
  • Access to secretsline 628
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/paperspine_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 26
    DEFAULT_MANIFEST_URL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 27
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 28
    ) DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 29
    DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json" )
  • Network accessline 30
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 33
    DEFAULT_ARCHIVE_URL = "https://github.com/WUBING2023/PaperSpine/archive/refs/tags/v4.0.0.zip"
  • Access to secretsline 129
    [Credential-related source omitted]
  • Network accessline 291
    def load_manifest_from_url(url: str) -> dict[str, Any]:     try:         with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 292
    try:         with urllib.request.urlopen(url, timeout=20) as response:             body = response.read().decode("utf-8")
  • Network accessline 293
    with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 313
    archive_path = temp_dir / "paperspine-update.zip"     try:         with urllib.request.urlopen(url, timeout=60) as response:
  • Network accessline 314
    try:         with urllib.request.urlopen(url, timeout=60) as response:             archive_path.write_bytes(response.read())
  • Network accessline 315
    with urllib.request.urlopen(url, timeout=60) as response:
  • Access to secretsline 440
    [Credential-related source omitted]
  • Access to secretsline 443
    [Credential-related source omitted]
  • Access to secretsline 445
    [Credential-related source omitted]
  • Access to secretsline 446
    [Credential-related source omitted]
  • Access to secretsline 448
    [Credential-related source omitted]
  • Access to secretsline 451
    [Credential-related source omitted]
  • Access to secretsline 601
    [Credential-related source omitted]

dist/codex/skills/paper-spine/scripts/preserve_figure_revision.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/progress_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/publication_cycle.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/publication_surface_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 269
    def _docx(path: Path) -> list[_Text]:     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 270
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 271
    "r": "http://schemas.openxmlformats.org/officeDocument/2006/relationships"}

dist/codex/skills/paper-spine/scripts/reference_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/respond_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/results_validation_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/reviewer_audit_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/revision_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/scientific_evidence_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/section_economy_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/skill_discovery_migration.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/structured_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/style_metrics.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/submission_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 65
    A4_HEIGHT_TWIPS = "16838" DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 66
    DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" W = f"{{{W_NS}}}"
  • Network accessline 67
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

dist/codex/skills/paper-spine/scripts/supplement_evidence_index.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/translate_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 514
    except (zipfile.BadZipFile, ElementTree.ParseError, OSError):         return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 515
    return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 516
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}

dist/codex/skills/paper-spine/scripts/usage_ledger.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/visual_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/codex/skills/paper-spine/scripts/word_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 172
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 173
    A_NS = "http://schemas.openxmlformats.org/drawingml/2006/main"
  • Network accessline 174
    WP_NS = "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing"
  • Network accessline 175
    PIC_NS = "http://schemas.openxmlformats.org/drawingml/2006/picture"
  • Network accessline 176
    R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"
  • Network accessline 177
    PACKAGE_NS = "http://schemas.openxmlformats.org/package/2006/relationships"
  • Network accessline 481
    def extract_text(document_xml: bytes) -> tuple[str, int]:     root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 482
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 483
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 506
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 507
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 968
    if root.getroottree().docinfo.doctype:         raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 969
    raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"     qname_lists = {f"{{{mc}}}{name}" for name in (
  • Network accessline 970
    mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 1118
    if anchor and not node.get("{http://schemas.openxmlformats.org/officeDocument/2006/relationships}id") and anchor.lower() != "_top" and anchor not in bookmarks:

dist/codex/skills/paper-spine/scripts/word_surface_repair.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/author-voice-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

dist/hermes/skills/academic-writing/paper-spine/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
  • Network accessline 289
    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

dist/hermes/skills/academic-writing/paper-spine/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

dist/hermes/skills/academic-writing/paper-spine/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

dist/hermes/skills/academic-writing/paper-spine/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

dist/hermes/skills/academic-writing/paper-spine/scripts/_paper_spine_utils.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/adaptive_shadow.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/artifact_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/asset_selection.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/author_voice_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/citation_bank_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/citation_quality_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 38
    ARXIV_RE = re.compile(r"\barxiv\s*:?\s*(\d{4}\.\d{4,5}(?:v\d+)?)\b", re.IGNORECASE) URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 39
    URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/" SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 40
    CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 41
    SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 42
    USER_AGENT = "PaperSpine/3.0 (citation-quality; https://github.com/WUBING2023/PaperSpine)"

dist/hermes/skills/academic-writing/paper-spine/scripts/citation_verification_en.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 29
    CROSSREF_QUERY_URL = "https://api.crossref.org/works"
  • Network accessline 185
    Extracted as a module-level function so tests can mock it without     touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 186
    touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 189
    req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
  • Network accessline 190
    try:         with urllib.request.urlopen(req, timeout=timeout) as resp:             return json.loads(resp.read().decode("utf-8"))  # type: ignore[no-any-return]
  • Network accessline 191
    with urllib.request.urlopen(req, timeout=timeout) as resp:
  • Network accessline 460
    doi_url = f"{CROSSREF_QUERY_URL}/{urllib.parse.quote(doi, safe='')}"             data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 461
    data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 514
    f"{urllib.parse.urlencode({'query.bibliographic': bib_query[:200], 'rows': 3})}"             )             data = fetch(bib_url)  # type: ignore[call-arg]
  • Network accessline 516
    data = fetch(bib_url)  # type: ignore[call-arg]

dist/hermes/skills/academic-writing/paper-spine/scripts/citation_verification_zh.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 24
    USER_AGENT = "PaperSpine/3.0 (citation-zh; https://github.com/WUBING2023/PaperSpine)"
  • Network accessline 97
    def verify_doi(doi: str) -> bool:     try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})
  • Network accessline 98
    try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:
  • Network accessline 99
    req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:             return resp.status == 200

dist/hermes/skills/academic-writing/paper-spine/scripts/contribution_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/evidence_grounded_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/execution_receipt.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/figure_comparison.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/figure_reference_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/figure_story_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/humanize_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/intake_wizard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 274
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/integrity_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/latex_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/launch_paperspine_ui.ps1

  • Executable scriptline 1
    Executable file

dist/hermes/skills/academic-writing/paper-spine/scripts/launch_paperspine_ui.sh

  • Executable scriptline 1
    #!/usr/bin/env bash

dist/hermes/skills/academic-writing/paper-spine/scripts/manuscript_export.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/manuscript_refs.lua

  • Executable scriptline 1
    Executable file

dist/hermes/skills/academic-writing/paper-spine/scripts/material_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/metadata_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/open_release.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 37
    [Credential-related source omitted]
  • Access to secretsline 41
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/paperspine5_web.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 29
    [Credential-related source omitted]
  • Access to secretsline 200
    [Credential-related source omitted]
  • Access to secretsline 201
    [Credential-related source omitted]
  • Access to secretsline 411
    [Credential-related source omitted]
  • Access to secretsline 516
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/paperspine_methods.py

  • Executable scriptline 1
    Executable file

dist/hermes/skills/academic-writing/paper-spine/scripts/paperspine_public_client.py

  • Executable scriptline 1
    Executable file
  • Access to secretsline 41
    [Credential-related source omitted]
  • Access to secretsline 45
    [Credential-related source omitted]
  • Access to secretsline 78
    [Credential-related source omitted]
  • Access to secretsline 142
    [Credential-related source omitted]
  • Network accessline 228
    with urlopen(f'http://127.0.0.1:{port}/api/v1/session', timeout=2) as response:
  • Access to secretsline 335
    [Credential-related source omitted]
  • Network accessline 382
    kernel.close()         raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Network accessline 383
    raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',         'port': server.server_
  • Network accessline 384
    _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Access to secretsline 533
    [Credential-related source omitted]
  • Access to secretsline 562
    [Credential-related source omitted]
  • Access to secretsline 655
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/paperspine_stable_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 208
    def fetch(source, target, limit=LIMIT):
  • Network accessline 230
    scratch.mkdir(parents=True, exist_ok=True)     downloaded = scratch / "source"     fetch(source, downloaded)
  • Network accessline 231
    downloaded = scratch / "source"     fetch(source, downloaded)     channel = None
  • Network accessline 232
    fetch(source, downloaded)
  • Network accessline 235
    channel = read(downloaded)         bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 236
    bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")         expected = bundle["sha256"]
  • Network accessline 237
    fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 254
    with tempfile.TemporaryDirectory(prefix="paperspine-check-") as temporary:             metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)
  • Network accessline 255
    metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)             if zipfile.is_zipfile(metadata):
  • Network accessline 256
    fetch(source, metadata, limit=2 * 1024 * 1024)
  • Access to secretsline 455
    [Credential-related source omitted]
  • Access to secretsline 628
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/paperspine_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 26
    DEFAULT_MANIFEST_URL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 27
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 28
    ) DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 29
    DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json" )
  • Network accessline 30
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 33
    DEFAULT_ARCHIVE_URL = "https://github.com/WUBING2023/PaperSpine/archive/refs/tags/v4.0.0.zip"
  • Access to secretsline 129
    [Credential-related source omitted]
  • Network accessline 291
    def load_manifest_from_url(url: str) -> dict[str, Any]:     try:         with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 292
    try:         with urllib.request.urlopen(url, timeout=20) as response:             body = response.read().decode("utf-8")
  • Network accessline 293
    with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 313
    archive_path = temp_dir / "paperspine-update.zip"     try:         with urllib.request.urlopen(url, timeout=60) as response:
  • Network accessline 314
    try:         with urllib.request.urlopen(url, timeout=60) as response:             archive_path.write_bytes(response.read())
  • Network accessline 315
    with urllib.request.urlopen(url, timeout=60) as response:
  • Access to secretsline 440
    [Credential-related source omitted]
  • Access to secretsline 443
    [Credential-related source omitted]
  • Access to secretsline 445
    [Credential-related source omitted]
  • Access to secretsline 446
    [Credential-related source omitted]
  • Access to secretsline 448
    [Credential-related source omitted]
  • Access to secretsline 451
    [Credential-related source omitted]
  • Access to secretsline 601
    [Credential-related source omitted]

dist/hermes/skills/academic-writing/paper-spine/scripts/preserve_figure_revision.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/progress_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/publication_cycle.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/publication_surface_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 269
    def _docx(path: Path) -> list[_Text]:     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 270
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 271
    "r": "http://schemas.openxmlformats.org/officeDocument/2006/relationships"}

dist/hermes/skills/academic-writing/paper-spine/scripts/reference_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/respond_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/results_validation_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/reviewer_audit_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/revision_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/scientific_evidence_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/section_economy_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/skill_discovery_migration.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/structured_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/style_metrics.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/submission_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 65
    A4_HEIGHT_TWIPS = "16838" DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 66
    DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" W = f"{{{W_NS}}}"
  • Network accessline 67
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

dist/hermes/skills/academic-writing/paper-spine/scripts/supplement_evidence_index.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/translate_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 514
    except (zipfile.BadZipFile, ElementTree.ParseError, OSError):         return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 515
    return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 516
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}

dist/hermes/skills/academic-writing/paper-spine/scripts/usage_ledger.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/visual_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/hermes/skills/academic-writing/paper-spine/scripts/word_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 172
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 173
    A_NS = "http://schemas.openxmlformats.org/drawingml/2006/main"
  • Network accessline 174
    WP_NS = "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing"
  • Network accessline 175
    PIC_NS = "http://schemas.openxmlformats.org/drawingml/2006/picture"
  • Network accessline 176
    R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"
  • Network accessline 177
    PACKAGE_NS = "http://schemas.openxmlformats.org/package/2006/relationships"
  • Network accessline 481
    def extract_text(document_xml: bytes) -> tuple[str, int]:     root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 482
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 483
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 506
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 507
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 968
    if root.getroottree().docinfo.doctype:         raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 969
    raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"     qname_lists = {f"{{{mc}}}{name}" for name in (
  • Network accessline 970
    mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 1118
    if anchor and not node.get("{http://schemas.openxmlformats.org/officeDocument/2006/relationships}id") and anchor.lower() != "_top" and anchor not in bookmarks:

dist/hermes/skills/academic-writing/paper-spine/scripts/word_surface_repair.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/author-voice-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

dist/openclaw/skills/paper-spine/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

dist/openclaw/skills/paper-spine/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

dist/openclaw/skills/paper-spine/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
  • Network accessline 289
    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

dist/openclaw/skills/paper-spine/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

dist/openclaw/skills/paper-spine/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

dist/openclaw/skills/paper-spine/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

dist/openclaw/skills/paper-spine/scripts/_paper_spine_utils.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/adaptive_shadow.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/artifact_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/asset_selection.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/author_voice_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/citation_bank_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/citation_quality_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 38
    ARXIV_RE = re.compile(r"\barxiv\s*:?\s*(\d{4}\.\d{4,5}(?:v\d+)?)\b", re.IGNORECASE) URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 39
    URL_RE = re.compile(r"https?://[^\s)\]]+", re.IGNORECASE) CROSSREF_URL = "https://api.crossref.org/works/" SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 40
    CROSSREF_URL = "https://api.crossref.org/works/"
  • Network accessline 41
    SEMANTIC_SCHOLAR_URL = "https://api.semanticscholar.org/graph/v1/paper/DOI:"
  • Network accessline 42
    USER_AGENT = "PaperSpine/3.0 (citation-quality; https://github.com/WUBING2023/PaperSpine)"

dist/openclaw/skills/paper-spine/scripts/citation_verification_en.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 29
    CROSSREF_QUERY_URL = "https://api.crossref.org/works"
  • Network accessline 185
    Extracted as a module-level function so tests can mock it without     touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 186
    touching ``urllib.request.urlopen`` internals.  Returns the parsed
  • Network accessline 189
    req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT})
  • Network accessline 190
    try:         with urllib.request.urlopen(req, timeout=timeout) as resp:             return json.loads(resp.read().decode("utf-8"))  # type: ignore[no-any-return]
  • Network accessline 191
    with urllib.request.urlopen(req, timeout=timeout) as resp:
  • Network accessline 460
    doi_url = f"{CROSSREF_QUERY_URL}/{urllib.parse.quote(doi, safe='')}"             data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 461
    data = fetch(doi_url)  # type: ignore[call-arg]
  • Network accessline 514
    f"{urllib.parse.urlencode({'query.bibliographic': bib_query[:200], 'rows': 3})}"             )             data = fetch(bib_url)  # type: ignore[call-arg]
  • Network accessline 516
    data = fetch(bib_url)  # type: ignore[call-arg]

dist/openclaw/skills/paper-spine/scripts/citation_verification_zh.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 24
    USER_AGENT = "PaperSpine/3.0 (citation-zh; https://github.com/WUBING2023/PaperSpine)"
  • Network accessline 97
    def verify_doi(doi: str) -> bool:     try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})
  • Network accessline 98
    try:         req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:
  • Network accessline 99
    req = Request(f"https://api.crossref.org/works/{doi}", headers={"User-Agent": USER_AGENT})         with urlopen(req, timeout=15) as resp:             return resp.status == 200

dist/openclaw/skills/paper-spine/scripts/contribution_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/evidence_grounded_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/execution_receipt.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/figure_comparison.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/figure_reference_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/figure_story_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/humanize_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/intake_wizard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 274
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/integrity_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/latex_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/launch_paperspine_ui.ps1

  • Executable scriptline 1
    Executable file

dist/openclaw/skills/paper-spine/scripts/launch_paperspine_ui.sh

  • Executable scriptline 1
    #!/usr/bin/env bash

dist/openclaw/skills/paper-spine/scripts/manuscript_export.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/manuscript_refs.lua

  • Executable scriptline 1
    Executable file

dist/openclaw/skills/paper-spine/scripts/material_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/metadata_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/open_release.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 37
    [Credential-related source omitted]
  • Access to secretsline 41
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/paperspine5_web.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Access to secretsline 29
    [Credential-related source omitted]
  • Access to secretsline 200
    [Credential-related source omitted]
  • Access to secretsline 201
    [Credential-related source omitted]
  • Access to secretsline 411
    [Credential-related source omitted]
  • Access to secretsline 516
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/paperspine_methods.py

  • Executable scriptline 1
    Executable file

dist/openclaw/skills/paper-spine/scripts/paperspine_public_client.py

  • Executable scriptline 1
    Executable file
  • Access to secretsline 41
    [Credential-related source omitted]
  • Access to secretsline 45
    [Credential-related source omitted]
  • Access to secretsline 78
    [Credential-related source omitted]
  • Access to secretsline 142
    [Credential-related source omitted]
  • Network accessline 228
    with urlopen(f'http://127.0.0.1:{port}/api/v1/session', timeout=2) as response:
  • Access to secretsline 335
    [Credential-related source omitted]
  • Network accessline 382
    kernel.close()         raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Network accessline 383
    raise RuntimeError('Product code changed during Web startup; retry this same profile after the update finishes.')     _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',         'port': server.server_
  • Network accessline 384
    _write_json(Path(job['ready_file']), {'address': f'http://127.0.0.1:{server.server_port}/',
  • Access to secretsline 533
    [Credential-related source omitted]
  • Access to secretsline 562
    [Credential-related source omitted]
  • Access to secretsline 655
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/paperspine_stable_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 208
    def fetch(source, target, limit=LIMIT):
  • Network accessline 230
    scratch.mkdir(parents=True, exist_ok=True)     downloaded = scratch / "source"     fetch(source, downloaded)
  • Network accessline 231
    downloaded = scratch / "source"     fetch(source, downloaded)     channel = None
  • Network accessline 232
    fetch(source, downloaded)
  • Network accessline 235
    channel = read(downloaded)         bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 236
    bundle = select_bundle(channel)         fetch(bundle_reference(source, bundle), scratch / "bundle.zip")         expected = bundle["sha256"]
  • Network accessline 237
    fetch(bundle_reference(source, bundle), scratch / "bundle.zip")
  • Network accessline 254
    with tempfile.TemporaryDirectory(prefix="paperspine-check-") as temporary:             metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)
  • Network accessline 255
    metadata = Path(temporary) / "channel.json"             fetch(source, metadata, limit=2 * 1024 * 1024)             if zipfile.is_zipfile(metadata):
  • Network accessline 256
    fetch(source, metadata, limit=2 * 1024 * 1024)
  • Access to secretsline 455
    [Credential-related source omitted]
  • Access to secretsline 628
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/paperspine_update.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 26
    DEFAULT_MANIFEST_URL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 27
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/dist/paperspine_version.json"
  • Network accessline 28
    ) DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 29
    DEFAULT_STABLE_CHANNEL = (     "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json" )
  • Network accessline 30
    "https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json"
  • Network accessline 33
    DEFAULT_ARCHIVE_URL = "https://github.com/WUBING2023/PaperSpine/archive/refs/tags/v4.0.0.zip"
  • Access to secretsline 129
    [Credential-related source omitted]
  • Network accessline 291
    def load_manifest_from_url(url: str) -> dict[str, Any]:     try:         with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 292
    try:         with urllib.request.urlopen(url, timeout=20) as response:             body = response.read().decode("utf-8")
  • Network accessline 293
    with urllib.request.urlopen(url, timeout=20) as response:
  • Network accessline 313
    archive_path = temp_dir / "paperspine-update.zip"     try:         with urllib.request.urlopen(url, timeout=60) as response:
  • Network accessline 314
    try:         with urllib.request.urlopen(url, timeout=60) as response:             archive_path.write_bytes(response.read())
  • Network accessline 315
    with urllib.request.urlopen(url, timeout=60) as response:
  • Access to secretsline 440
    [Credential-related source omitted]
  • Access to secretsline 443
    [Credential-related source omitted]
  • Access to secretsline 445
    [Credential-related source omitted]
  • Access to secretsline 446
    [Credential-related source omitted]
  • Access to secretsline 448
    [Credential-related source omitted]
  • Access to secretsline 451
    [Credential-related source omitted]
  • Access to secretsline 601
    [Credential-related source omitted]

dist/openclaw/skills/paper-spine/scripts/preserve_figure_revision.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/progress_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/publication_cycle.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/publication_surface_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 269
    def _docx(path: Path) -> list[_Text]:     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 270
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main",
  • Network accessline 271
    "r": "http://schemas.openxmlformats.org/officeDocument/2006/relationships"}

dist/openclaw/skills/paper-spine/scripts/reference_inventory.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/respond_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/results_validation_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/reviewer_audit_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/revision_audit.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/scientific_evidence_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/section_economy_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/skill_discovery_migration.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/structured_review.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/style_metrics.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/submission_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 65
    A4_HEIGHT_TWIPS = "16838" DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 66
    DEFAULT_MARGIN_TWIPS = "1440" W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" W = f"{{{W_NS}}}"
  • Network accessline 67
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

dist/openclaw/skills/paper-spine/scripts/supplement_evidence_index.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/translate_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 514
    except (zipfile.BadZipFile, ElementTree.ParseError, OSError):         return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 515
    return ""     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 516
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}

dist/openclaw/skills/paper-spine/scripts/usage_ledger.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/visual_readiness_check.py

  • Executable scriptline 1
    #!/usr/bin/env python3

dist/openclaw/skills/paper-spine/scripts/word_guard.py

  • Executable scriptline 1
    #!/usr/bin/env python3
  • Network accessline 172
    W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
  • Network accessline 173
    A_NS = "http://schemas.openxmlformats.org/drawingml/2006/main"
  • Network accessline 174
    WP_NS = "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing"
  • Network accessline 175
    PIC_NS = "http://schemas.openxmlformats.org/drawingml/2006/picture"
  • Network accessline 176
    R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"
  • Network accessline 177
    PACKAGE_NS = "http://schemas.openxmlformats.org/package/2006/relationships"
  • Network accessline 481
    def extract_text(document_xml: bytes) -> tuple[str, int]:     root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 482
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}     paragraphs: list[str] = []
  • Network accessline 483
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 506
    root = ElementTree.fromstring(document_xml)     ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 507
    ns = {"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"}
  • Network accessline 968
    if root.getroottree().docinfo.doctype:         raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 969
    raise ValueError("Word font repair does not accept DTD-bearing XML")     mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"     qname_lists = {f"{{{mc}}}{name}" for name in (
  • Network accessline 970
    mc = "http://schemas.openxmlformats.org/markup-compatibility/2006"
  • Network accessline 1118
    if anchor and not node.get("{http://schemas.openxmlformats.org/officeDocument/2006/relationships}id") and anchor.lower() != "_top" and anchor not in bookmarks:

dist/openclaw/skills/paper-spine/scripts/word_surface_repair.py

  • Executable scriptline 1
    #!/usr/bin/env python3

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/author-voice-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

paperspine5/core/01_PaperSpine4/src/skill/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
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    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

paperspine5/core/01_PaperSpine4/src/skill/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

paperspine5/core/01_PaperSpine4/src/skill/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

paperspine5/core/01_PaperSpine4/src/skill/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

paperspine5/core/02_PaperFigure/02_paperFig_skill/assets/comparison_atlas_builder.py

  • Executable scriptline 1
    #!/usr/bin/env python3

paperspine5/core/02_PaperFigure/02_paperFig_skill/scripts/inspect_figure_project.py

  • Executable scriptline 1
    #!/usr/bin/env python3

paperspine5/core/02_PaperFigure/02_paperFig_skill/scripts/validate_research_figures.py

  • Executable scriptline 1
    #!/usr/bin/env python3

src/skill/references/contracts/adaptive-shadow-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/adaptive-shadow-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/asset-selection-request.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$id": "https://paperspine.local/contracts/asset-selection-request.schema.json",

src/skill/references/contracts/author-voice-profile.schema.json

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    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$id": "https://paperspine.local/contracts/author-voice-profile.schema.json",

src/skill/references/contracts/author-voice-receipt.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
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    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-receipt.schema.json",

src/skill/references/contracts/author-voice-restoration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/author-voice-restoration.schema.json",

src/skill/references/contracts/evidence-review.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/evidence-review.schema.json",

src/skill/references/contracts/open-release-agent-ticket.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-confirmation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-manifest.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-platform-receipts.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/open-release-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/publication-cycle-invocation.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/publication-cycle-result.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/publication-target-profile.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/publication-target-profile.schema.json",

src/skill/references/contracts/review-calibration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/review-calibration.schema.json",

src/skill/references/contracts/skill-discovery-migration-preview.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/skill-discovery-migration-preview.schema.json",

src/skill/references/contracts/skill-discovery-migration.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",

src/skill/references/contracts/submission-package-plan.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/submission-package-plan.schema.json",

src/skill/references/contracts/supplement-evidence-index.schema.json

  • Network accessline 1
    {   "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 2
    "$schema": "https://json-schema.org/draft/2020-12/schema",
  • Network accessline 3
    "$id": "https://paperspine.local/contracts/supplement-evidence-index.schema.json",

src/skill/references/open-release-platforms.json

  • Network accessline 30
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://github.com/",
  • Network accessline 31
    "official_urls": {         "home": "https://github.com/",         "submit": "https://github.com/new",
  • Network accessline 32
    "home": "https://github.com/",
  • Network accessline 33
    "submit": "https://github.com/new",
  • Network accessline 34
    "requirements": "https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-new-repository",
  • Network accessline 35
    "authentication": "https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/about-authentication-to-github"
  • Network accessline 59
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://zenodo.org/",
  • Network accessline 60
    "official_urls": {         "home": "https://zenodo.org/",         "submit": "https://zenodo.org/uploads/new",
  • Network accessline 61
    "home": "https://zenodo.org/",
  • Network accessline 62
    "submit": "https://zenodo.org/uploads/new",
  • Network accessline 63
    "requirements": "https://help.zenodo.org/docs/get-started/quickstart/",
  • Network accessline 64
    "api": "https://developers.zenodo.org/"
  • Network accessline 87
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://arxiv.org/",
  • Network accessline 88
    "official_urls": {         "home": "https://arxiv.org/",         "submit": "https://arxiv.org/submit",
  • Network accessline 89
    "home": "https://arxiv.org/",
  • Network accessline 90
    "submit": "https://arxiv.org/submit",
  • Network accessline 91
    "requirements": "https://info.arxiv.org/help/submit/index.html",
  • Network accessline 92
    "endorsement": "https://info.arxiv.org/help/endorsement.html"
  • Network accessline 116
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://figshare.com/",
  • Network accessline 117
    "official_urls": {         "home": "https://figshare.com/",         "submit": "https://figshare.com/account/home",
  • Network accessline 118
    "home": "https://figshare.com/",
  • Network accessline 119
    "submit": "https://figshare.com/account/home",
  • Network accessline 120
    "requirements": "https://help.figshare.com/article/how-to-upload-and-publish-your-research",
  • Network accessline 121
    "api": "https://info.figshare.com/user-guide/how-to-use-the-figshare-api/"
  • Network accessline 145
    "sensitive_data_policy": "private_workspace_supported_but_public_release_requires_clearance",       "official_urls": {         "home": "https://osf.io/",
  • Network accessline 146
    "official_urls": {         "home": "https://osf.io/",         "submit": "https://osf.io/",
  • Network accessline 147
    "home": "https://osf.io/",
  • Network accessline 148
    "submit": "https://osf.io/",
  • Network accessline 149
    "requirements": "https://help.osf.io/article/387-files",
  • Network accessline 150
    "api": "https://developer.osf.io/"
  • Network accessline 173
    "sensitive_data_policy": "public_only_strict_human_deidentification",       "official_urls": {         "home": "https://datadryad.org/",
  • Network accessline 174
    "official_urls": {         "home": "https://datadryad.org/",         "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 175
    "home": "https://datadryad.org/",
  • Network accessline 176
    "submit": "https://datadryad.org/stash/submissions/new",
  • Network accessline 177
    "requirements": "https://datadryad.org/help/submission_steps/description",
  • Network accessline 178
    "human_data": "https://datadryad.org/docs/HumanSubjectsData.pdf"
  • Network accessline 202
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://huggingface.co/",
  • Network accessline 203
    "official_urls": {         "home": "https://huggingface.co/",         "submit": "https://huggingface.co/new",
  • Network accessline 204
    "home": "https://huggingface.co/",
  • Network accessline 205
    "submit": "https://huggingface.co/new",
  • Network accessline 206
    "requirements": "https://huggingface.co/docs/hub/repositories-getting-started"
  • Network accessline 230
    "sensitive_data_policy": "public_only_no_sensitive",       "official_urls": {         "home": "https://www.protocols.io/",
  • Network accessline 231
    "official_urls": {         "home": "https://www.protocols.io/",         "submit": "https://www.protocols.io/",
  • Network accessline 232
    "home": "https://www.protocols.io/",
  • Network accessline 233
    "submit": "https://www.protocols.io/",
  • Network accessline 234
    "requirements": "https://apidoc.protocols.io/"
  • Network accessline 257
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://www.medrxiv.org/",
  • Network accessline 258
    "official_urls": {         "home": "https://www.medrxiv.org/",         "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 259
    "home": "https://www.medrxiv.org/",
  • Network accessline 260
    "submit": "https://www.medrxiv.org/submit-a-manuscript",
  • Network accessline 261
    "requirements": "https://www.medrxiv.org/submit-a-manuscript"
  • Network accessline 284
    "sensitive_data_policy": "registry_summary_only_no_participant_level_data",       "official_urls": {         "home": "https://clinicaltrials.gov/",
  • Network accessline 285
    "official_urls": {         "home": "https://clinicaltrials.gov/",         "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 286
    "home": "https://clinicaltrials.gov/",
  • Network accessline 287
    "submit": "https://register.clinicaltrials.gov/",
  • Network accessline 288
    "requirements": "https://clinicaltrials.gov/submit-studies/prs-help/user-guide",
  • Network accessline 289
    "accounts": "https://clinicaltrials.gov/submit-studies/prs-accounts"
  • Network accessline 312
    "sensitive_data_policy": "public_manuscript_no_sensitive_attachments",       "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 313
    "official_urls": {         "home": "https://pmc.ncbi.nlm.nih.gov/",         "submit": "https://www.nihms.nih.gov/",
  • Network accessline 314
    "home": "https://pmc.ncbi.nlm.nih.gov/",
  • Network accessline 315
    "submit": "https://www.nihms.nih.gov/",
  • Network accessline 316
    "requirements": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/"
  • Network accessline 339
    "sensitive_data_policy": "public_functional_genomics_no_controlled_human_data",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 340
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/geo/",         "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 341
    "home": "https://www.ncbi.nlm.nih.gov/geo/",
  • Network accessline 342
    "submit": "https://www.ncbi.nlm.nih.gov/geo/info/submission.html",
  • Network accessline 343
    "requirements": "https://www.ncbi.nlm.nih.gov/geo/info/seq.html"
  • Network accessline 366
    "sensitive_data_policy": "public_only_with_explicit_consent_otherwise_route_dbgap",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 367
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/sra/",         "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 368
    "home": "https://www.ncbi.nlm.nih.gov/sra/",
  • Network accessline 369
    "submit": "https://submit.ncbi.nlm.nih.gov/subs/sra/",
  • Network accessline 370
    "requirements": "https://www.ncbi.nlm.nih.gov/sra/docs/submit/"
  • Network accessline 393
    "sensitive_data_policy": "controlled_access_supported",       "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 394
    "official_urls": {         "home": "https://www.ncbi.nlm.nih.gov/gap/",         "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 395
    "home": "https://www.ncbi.nlm.nih.gov/gap/",
  • Network accessline 396
    "submit": "https://submit.ncbi.nlm.nih.gov/dbgap/",
  • Network accessline 397
    "requirements": "https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/",
  • Network accessline 398
    "sequence": "https://www.ncbi.nlm.nih.gov/sra/docs/submitdbgap/"
  • Network accessline 421
    "sensitive_data_policy": "open_restricted_or_credentialed_after_phi_removal",       "official_urls": {         "home": "https://physionet.org/",
  • Network accessline 422
    "official_urls": {         "home": "https://physionet.org/",         "submit": "https://physionet.org/projects/",
  • Network accessline 423
    "home": "https://physionet.org/",
  • Network accessline 424
    "submit": "https://physionet.org/projects/",
  • Network accessline 425
    "requirements": "https://physionet.org/about/publish/"
  • Network accessline 449
    "sensitive_data_policy": "public_only_no_identifiable_health_information",       "official_urls": {         "home": "https://openneuro.org/",
  • Network accessline 450
    "official_urls": {         "home": "https://openneuro.org/",         "submit": "https://openneuro.org/",
  • Network accessline 451
    "home": "https://openneuro.org/",
  • Network accessline 452
    "submit": "https://openneuro.org/",
  • Network accessline 453
    "requirements": "https://docs.openneuro.org/user_guide.html"
  • Network accessline 476
    "sensitive_data_policy": "public_release_requires_clearance",       "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 477
    "official_urls": {         "home": "https://www.ebi.ac.uk/pride/",         "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 478
    "home": "https://www.ebi.ac.uk/pride/",
  • Network accessline 479
    "submit": "https://www.ebi.ac.uk/pride/login",
  • Network accessline 480
    "requirements": "https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/"
  • Network accessline 503
    "sensitive_data_policy": "not_for_patient_level_data",       "official_urls": {         "home": "https://www.wwpdb.org/",
  • Network accessline 504
    "official_urls": {         "home": "https://www.wwpdb.org/",         "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 505
    "home": "https://www.wwpdb.org/",
  • Network accessline 506
    "submit": "https://deposit.wwpdb.org/deposition/",
  • Network accessline 507
    "requirements": "https://www.wwpdb.org/documentation/policy"
  • Network accessline 531
    "sensitive_data_policy": "instance_policy_dependent",       "official_urls": {         "home": "https://dataverse.org/",
  • Network accessline 532
    "official_urls": {         "home": "https://dataverse.org/",         "submit": "https://dataverse.harvard.edu/",
  • Network accessline 533
    "home": "https://dataverse.org/",
  • Network accessline 534
    "submit": "https://dataverse.harvard.edu/",
  • Network accessline 535
    "requirements": "https://guides.dataverse.org/en/latest/user/dataset-management.html"
  • Network accessline 558
    "sensitive_data_policy": "public_release_requires_location_clearance",       "official_urls": {         "home": "https://www.pangaea.de/",
  • Network accessline 559
    "official_urls": {         "home": "https://www.pangaea.de/",         "submit": "https://www.pangaea.de/submit/",
  • Network accessline 560
    "home": "https://www.pangaea.de/",
  • Network accessline 561
    "submit": "https://www.pangaea.de/submit/",
  • Network accessline 562
    "requirements": "https://www.pangaea.de/submit/"
  • Network accessline 583
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://fairsharing.org/",
  • Network accessline 584
    "official_urls": {         "home": "https://fairsharing.org/",         "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 585
    "home": "https://fairsharing.org/",
  • Network accessline 586
    "requirements": "https://fairsharing.gitbook.io/fairsharing/how-to/searching-and-browsing/database-discovery"
  • Network accessline 607
    "sensitive_data_policy": "not_applicable",       "official_urls": {         "home": "https://www.re3data.org/",
  • Network accessline 608
    "official_urls": {         "home": "https://www.re3data.org/",         "requirements": "https://www.re3data.org/faq"
  • Network accessline 609
    "home": "https://www.re3data.org/",
  • Network accessline 610
    "requirements": "https://www.re3data.org/faq"

src/skill/references/publication-cycle-contracts.md

  • Network accessline 25
    "id": "official-guide",       "authority": "official",       "url": "https://journal.example/guide-for-authors",
  • Network accessline 26
    "authority": "official",       "url": "https://journal.example/guide-for-authors",       "checked_at": "2026-08-23"
  • Network accessline 27
    "url": "https://journal.example/guide-for-authors",
  • Network accessline 31
    "id": "recent-corpus",       "authority": "published_corpus",       "url": "https://journal.example/recent-articles",
  • Network accessline 32
    "authority": "published_corpus",       "url": "https://journal.example/recent-articles",       "checked_at": "2026-08-23"
  • Network accessline 33
    "url": "https://journal.example/recent-articles",

src/skill/references/update.md

  • Network accessline 22
    https://raw.githubusercontent.com/WUBING2023/PaperSpine/main/website/downloads/update-channel.json

src/skill/references/upstream-review-protocols.md

  • Network accessline 17
    - <https://github.com/ngstcf/agentic-paper-review>
  • Network accessline 18
    - <https://github.com/amirkiarafiei/open-scholar-peer>
  • Network accessline 19
    - <https://github.com/ResearAI/DeepReviewer-v2>
  • Network accessline 20
    - <https://github.com/UnaryLab/ai-paper-review>

How the signals fit together

Facts from a static read of the files at the pinned commit. They describe what the code does, not why.

Some files could not be read; the facts below still hold.

Declared and executed: 26 facts
Signal confidence: 474 facts

and 424 more

Only the first 500 facts are listed.

Works with

Agent compatibility, from the files in this repository
AgentStatusEvidenceInstall to
Claude CodeNativeManifest .claude-plugin/marketplace.json.claude/skills/<skill-name>/
CodexCompatibleStandard SKILL.md dist/claude/skills/paper-spine/SKILL.md.agents/skills/<skill-name>/
CursorCompatibleStandard SKILL.md dist/claude/skills/paper-spine/SKILL.md.cursor/skills/<skill-name>/
Gemini CLICompatibleStandard SKILL.md dist/claude/skills/paper-spine/SKILL.md.gemini/skills/<skill-name>/
GitHub CopilotCompatibleStandard SKILL.md dist/claude/skills/paper-spine/SKILL.md.github/skills/<skill-name>/
OpenCodeCompatibleStandard SKILL.md dist/claude/skills/paper-spine/SKILL.md.opencode/skills/<skill-name>/
  • Native The repository ships a manifest, folder or frontmatter field for this agent.
  • Compatible A standard SKILL.md that this agent can read.
  • Unknown No evidence either way.

Derived automatically from paths, manifests and frontmatter. Not tested on each agent.

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