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ShZhao27208/Aut_Sci_Write

Academic research skills suite for AI Agent — literature search/download (WoS+Elsevier+Springer), PDF extraction, figure cropping, review writing, Zotero sync, and PPT/Html generation.

Claude Code Research Writing

History

Review weekly changes to SKILL.md before updating. Dates mark the weeks in which we observed each version; checks apply to the recorded commits.

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`skills/sci-download/SKILL.md`

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`skills/sci-extract/SKILL.md`

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`skills/sci-review/SKILL.md`

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`skills/sci-zotero/SKILL.md`

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View on GitHub Add to my skills

Verified commit 357766f90bd42f4f982d054be55c687c27202f22

Version-pinned installation · Claude Code

git clone --filter=blob:none --no-checkout https://github.com/ShZhao27208/Aut_Sci_Write.git .hotskills/shzhao27208-aut_sci_write && git -C .hotskills/shzhao27208-aut_sci_write checkout --detach 357766f90bd42f4f982d054be55c687c27202f22
# Copy each selected skill directory from .hotskills/shzhao27208-aut_sci_write into .claude/skills/<skill-name>/

216GitHub stars

3stars in 7 days

9skills in this repository

0commits in 30 days

Heat

2.9

Star growth, last 7 daysNot available
Star growth, last 24 hoursNot available
Rank movement, last 7 daysNot available
Commits, last 30 daysNot available
Accounts asking about it through MCP, last 7 daysNot available
Hot votes this weekNot available

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

Stars over time

30-day change not yet available: not enough history.

Individual skills in this repository

sci-download skills/sci-download
sci-extract skills/sci-extract
sci-figure skills/sci-figure
sci-html skills/sci-html
sci-polish skills/sci-polish
sci-ppt skills/sci-ppt
sci-review skills/sci-review
sci-search skills/sci-search
sci-zotero skills/sci-zotero

How it works

Choose a skill

sci-download

When your agent uses it

学术论文 PDF 下载。支持 8 个数据源：Elsevier、Springer Nature、IEEE Xplore、 arXiv、Unpaywall、Semantic Scholar、PubMed Central、知网(CNKI)。自动根据 DOI 前缀路由到对应数据源，未知 DOI 自动尝试 Unpaywall → Semantic Scholar。

What it loads into context

Frontmatter

217 tokens

Always available to the agent

SKILL.md

1,216 tokens

When the skill is activated

Reference documents

44,682 tokens

Loaded on request

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

The playbook

Trigger Phrases
Capabilities
Auto-Routing
Usage
Configuration
Dependencies
© License & Copyright

Scripts executed separately

arxiv_download.py
cnki_download.py
config.py
elsevier_download.py
ieee_download.py
pubmed_download.py
sci_download.py
semantic_scholar_download.py
springer_download.py
unpaywall_download.py
webvpn_crypto.py
../sci-extract/extract_core_insights.py
../sci-extract/harvest_paper.py
../sci-extract/harvester/__init__.py
../sci-extract/harvester/env.py
../sci-extract/harvester/figures.py
../sci-extract/harvester/fulltext.py
../sci-extract/harvester/http.py
../sci-extract/harvester/identify.py
../sci-extract/harvester/jats.py
../sci-extract/harvester/metadata.py
../sci-extract/harvester/oa_package.py
../sci-extract/harvester/render.py
../sci-figure/sci_figure/__init__.py
../sci-figure/sci_figure/annotator.py
../sci-figure/sci_figure/caption_detector.py
../sci-figure/sci_figure/cli.py
../sci-figure/sci_figure/column_detector.py
../sci-figure/sci_figure/exceptions.py
../sci-figure/sci_figure/figure_extractor.py
../sci-figure/sci_figure/image_processor.py
../sci-figure/sci_figure/native_extractor.py
../sci-figure/sci_figure/pdf_parser.py
../sci-figure/sci_figure/region_detector.py
../sci-figure/sci_figure/subfigure_splitter.py
../sci-figure/sci_figure/utils.py
../sci-figure/scripts/extract_figure.py
../sci-figure/setup.py
../sci-figure/tests/__init__.py
../sci-figure/tests/test_caption_dedup.py
../sci-html/conftest.py
../sci-html/scripts/generate_html_deck.py
../sci-html/src/sci_html/__init__.py
../sci-html/src/sci_html/cli.py
../sci-html/src/sci_html/integrations/__init__.py
../sci-html/src/sci_html/integrations/extract/__init__.py
../sci-html/src/sci_html/integrations/extract/core_insights.py
../sci-html/src/sci_html/models.py
../sci-html/src/sci_html/paper_pipeline.py
../sci-html/src/sci_html/parser.py
../sci-html/src/sci_html/renderer.py
../sci-html/templates/deck.js
../sci-html/tests/_path.py
../sci-html/tests/test_paper_pipeline.py
../sci-html/tests/test_parser.py
../sci-html/tests/test_renderer.py
../sci-polish/scripts/ai_score_estimator.py
../sci-polish/scripts/tier1_words.py
../sci-polish/scripts/validate_polish_output.py
../sci-ppt/src/aut_sci_ppt/__init__.py
../sci-ppt/src/aut_sci_ppt/academic_parser.py
../sci-ppt/src/aut_sci_ppt/agent.py
../sci-ppt/src/aut_sci_ppt/config.py
../sci-ppt/src/aut_sci_ppt/enhanced_agent.py
../sci-ppt/src/aut_sci_ppt/generator/__init__.py
../sci-ppt/src/aut_sci_ppt/generator/formula_renderer.py
../sci-ppt/src/aut_sci_ppt/generator/pptx_generator.py
../sci-ppt/src/aut_sci_ppt/image/__init__.py
../sci-ppt/src/aut_sci_ppt/interactive.py
../sci-ppt/src/aut_sci_ppt/layout_engine.py
../sci-ppt/src/aut_sci_ppt/main.py
../sci-ppt/src/aut_sci_ppt/models.py
../sci-ppt/src/aut_sci_ppt/paginator/__init__.py
../sci-ppt/src/aut_sci_ppt/paginator/smart_paginator.py
../sci-ppt/src/aut_sci_ppt/paper_workflow.py
../sci-ppt/src/aut_sci_ppt/parser/__init__.py
../sci-ppt/src/aut_sci_ppt/parser/text_parser.py
../sci-ppt/src/aut_sci_ppt/pdf_extractor.py
../sci-ppt/src/aut_sci_ppt/run.py
../sci-ppt/src/aut_sci_ppt/templates/__init__.py
../sci-ppt/src/aut_sci_ppt/templates/base.py
../sci-ppt/src/aut_sci_ppt/templates/content_detail.py
../sci-ppt/src/aut_sci_ppt/templates/content_figure.py
../sci-ppt/src/aut_sci_ppt/templates/content_list.py
../sci-ppt/src/aut_sci_ppt/templates/cover.py
../sci-ppt/src/aut_sci_ppt/templates/ending.py
../sci-ppt/src/aut_sci_ppt/templates/section.py
../sci-ppt/src/aut_sci_ppt/templates/timeline.py
../sci-ppt/src/aut_sci_ppt/templates/toc.py
../sci-ppt/src/aut_sci_ppt/tests/__init__.py
../sci-ppt/src/aut_sci_ppt/tests/test_agent.py
../sci-review/scripts/validate_review_output.py
../sci-search/sci_search.py
../sci-zotero/zotero.py

Files

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SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
SKILL.mdcore4,316 bytes
arxiv_download.pyruns6,936 bytes
cnki_download.pyruns22,372 bytes
config.pyruns6,337 bytes
elsevier_download.pyruns6,474 bytes
ieee_download.pyruns8,625 bytes
pubmed_download.pyruns9,717 bytes
schools.jsonasset5,277 bytes
sci_download.pyruns9,182 bytes
semantic_scholar_download.pyruns7,503 bytes
springer_download.pyruns7,068 bytes
unpaywall_download.pyruns5,560 bytes
webvpn_crypto.pyruns1,574 bytes
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../sci-zotero/zotero.pyruns27,957 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

sci-extract

When your agent uses it

Read an academic paper end to end and extract professional research insights, figures, metadata, and critique. Use this skill whenever the user shares a scientific paper, review paper, survey paper, systematic review, meta-analysis, scoping review, arXiv link, DOI, PDF, or pasted paper text and asks to read, summarize, analyze, extract, digest, review, critique, or explain it. For original research papers, produce a modified Heilmeier analysis. For review literature, produce a field-map extraction covering scope, taxonomy, evidence quality, consensus, controversies, gaps, and future directions. Do NOT use this skill for non-academic articles, blog posts, or news.

What it loads into context

Frontmatter

337 tokens

Always available to the agent

SKILL.md

4,887 tokens

When the skill is activated

Reference documents

1,264 tokens

Loaded on request

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

The playbook

Features
Steps：
Attribution rules (apply across all questions)
Citation rules (apply across all questions)
Length and pacing
Format and formatting compliance
What not to do
Usage
Configuration
© License & Copyright

Scripts executed separately

extract_core_insights.py
harvest_paper.py
harvester/__init__.py
harvester/env.py
harvester/figures.py
harvester/fulltext.py
harvester/http.py
harvester/identify.py
harvester/jats.py
harvester/metadata.py
harvester/oa_package.py
harvester/render.py

Files

README.mddoc5,271 bytes
SKILL.mdcore23,235 bytes
SKILL.mdcore23,235 bytes
SKILL.mdcore23,235 bytes
SKILL.mdcore23,235 bytes
SKILL.mdcore23,235 bytes
SKILL.mdcore23,235 bytes
_meta.jsonasset395 bytes
extract_core_insights.pyruns37,230 bytes
harvest_paper.pyruns14,071 bytes
harvester/__init__.pyruns477 bytes
harvester/env.pyruns3,124 bytes
harvester/figures.pyruns9,466 bytes
harvester/fulltext.pyruns8,287 bytes
harvester/http.pyruns5,464 bytes
harvester/identify.pyruns4,436 bytes
harvester/jats.pyruns19,397 bytes
harvester/metadata.pyruns41,649 bytes
harvester/oa_package.pyruns6,431 bytes
harvester/render.pyruns31,648 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

sci-figure

When your agent uses it

Extracts figures and sub-figures from academic PDF papers. Supports Fig/Figure, Scheme, Chart, Supplementary Figure, Extended Data Figure (Nature), and Chinese equivalents (图/方案/示意图/附图/补充图). Sub-figure label recognition supports (a)/(A)/a)/(i)/(1)/a. formats. High-quality PNG output at configurable DPI. Use when user asks to "extract figure", "截取文献图片", "提取子图", "get figure from paper", "Scheme", "方案图", "补充图", "Supplementary Figure", or "Extended Data".

What it loads into context

Frontmatter

264 tokens

Always available to the agent

SKILL.md

1,833 tokens

When the skill is activated

Reference documents

2,766 tokens

Loaded on request

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

The playbook

Installation
Preferences (EXTEND.md)
Usage
Options
Examples
Error Handling
Tech Stack
Extraction Engines (v2)
Detected Figure Fields
Extension Support
© License & Copyright

Scripts executed separately

sci_figure/__init__.py
sci_figure/annotator.py
sci_figure/caption_detector.py
sci_figure/cli.py
sci_figure/column_detector.py
sci_figure/exceptions.py
sci_figure/figure_extractor.py
sci_figure/image_processor.py
sci_figure/native_extractor.py
sci_figure/pdf_parser.py
sci_figure/region_detector.py
sci_figure/subfigure_splitter.py
sci_figure/utils.py
scripts/extract_figure.py
setup.py
tests/__init__.py
tests/test_caption_dedup.py

Files

CHANGELOG.mddoc529 bytes
LICENSEasset965 bytes
README.mddoc4,247 bytes
README_CN.mddoc4,790 bytes
SKILL.mdcore6,628 bytes
SKILL.mdcore6,628 bytes
SKILL.mdcore6,628 bytes
SKILL.mdcore6,628 bytes
SKILL.mdcore6,628 bytes
_meta.jsonasset203 bytes
requirements.txtdoc105 bytes
sci_figure.egg-info/PKG-INFOasset5,546 bytes
sci_figure.egg-info/SOURCES.txtdoc601 bytes
sci_figure.egg-info/dependency_links.txtdoc1 bytes
sci_figure.egg-info/entry_points.txtdoc51 bytes
sci_figure.egg-info/requires.txtdoc127 bytes
sci_figure.egg-info/top_level.txtdoc17 bytes
sci_figure/__init__.pyruns102 bytes
sci_figure/annotator.pyruns3,954 bytes
sci_figure/caption_detector.pyruns8,257 bytes
sci_figure/cli.pyruns8,259 bytes
sci_figure/column_detector.pyruns3,958 bytes
sci_figure/exceptions.pyruns1,521 bytes
sci_figure/figure_extractor.pyruns15,504 bytes
sci_figure/image_processor.pyruns1,642 bytes
sci_figure/native_extractor.pyruns7,791 bytes
sci_figure/pdf_parser.pyruns4,317 bytes
sci_figure/region_detector.pyruns10,921 bytes
sci_figure/subfigure_splitter.pyruns18,567 bytes
sci_figure/utils.pyruns1,423 bytes
scripts/extract_figure.pyruns276 bytes
setup.pyruns1,408 bytes
tests/__init__.pyruns0 bytes
tests/test_caption_dedup.pyruns4,074 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

sci-html

When your agent uses it

Generate academic presentation-style HTML slide decks and browser reports from PDFs, structured text, Markdown, paper summaries, outlines, or research notes. Use whenever the user wants to convert a scientific paper PDF directly into an interactive HTML report, clickable web presentation, shareable browser deck, or PPT-like HTML output with figures, structured insights, section pages, and offline deck-directory output. In the Aut_Sci_Write suite, choose this skill when the user wants HTML/web output; choose sci-ppt when they explicitly need a .pptx file.

What it loads into context

Frontmatter

235 tokens

Always available to the agent

SKILL.md

1,231 tokens

When the skill is activated

Reference documents

6,237 tokens

Loaded on request

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

The playbook

When To Use
Output
Workflow
PDF Paper Workflow
Presentation Markup
Navigation Controls
Design Rules
Aut_Sci_Write Integration

Scripts executed separately

conftest.py
scripts/generate_html_deck.py
src/sci_html/__init__.py
src/sci_html/cli.py
src/sci_html/integrations/__init__.py
src/sci_html/integrations/extract/__init__.py
src/sci_html/integrations/extract/core_insights.py
src/sci_html/models.py
src/sci_html/paper_pipeline.py
src/sci_html/parser.py
src/sci_html/renderer.py
templates/deck.js
tests/_path.py
tests/test_paper_pipeline.py
tests/test_parser.py
tests/test_renderer.py

Files

.gitignoreasset80 bytes
LICENSEasset1,530 bytes
README.mddoc3,453 bytes
SKILL.mdcore5,669 bytes
SKILL.mdcore5,669 bytes
SKILL.mdcore5,669 bytes
SKILL.mdcore5,669 bytes
SKILL.mdcore5,669 bytes
THIRD_PARTY_NOTICES.mddoc1,150 bytes
_meta.jsonasset267 bytes
archives/.keepasset0 bytes
conftest.pyruns488 bytes
examples/sample_outline.mddoc929 bytes
examples/sample_slides.mddoc578 bytes
examples/uconversion_review.mddoc4,034 bytes
pyproject.tomlasset522 bytes
requirements.txtdoc333 bytes
scripts/generate_html_deck.pyruns322 bytes
src/sci_html/__init__.pyruns230 bytes
src/sci_html/cli.pyruns4,434 bytes
src/sci_html/integrations/__init__.pyruns4 bytes
src/sci_html/integrations/extract/SKILL.sci-extract.mddoc19,406 bytes
src/sci_html/integrations/extract/__init__.pyruns4 bytes
src/sci_html/integrations/extract/core_insights.pyruns23,267 bytes
src/sci_html/models.pyruns2,190 bytes
src/sci_html/paper_pipeline.pyruns15,503 bytes
src/sci_html/parser.pyruns10,901 bytes
src/sci_html/renderer.pyruns10,369 bytes
templates/deck.jsruns2,506 bytes
templates/index.html.j2asset958 bytes
tests/_path.pyruns708 bytes
tests/test_paper_pipeline.pyruns3,902 bytes
tests/test_parser.pyruns1,992 bytes
tests/test_renderer.pyruns3,587 bytes
themes/academic-blue.cssasset15,492 bytes
themes/journal-dark.cssasset5,859 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

sci-ppt

When your agent uses it

Generate professional academic PowerPoint (PPTX) presentations from paper PDFs, structured outlines, or plain text. Use for thesis defense, seminar reports, literature presentations, and graduate school applications. Supports automatic figure extraction, LaTeX formula rendering, and bilingual (Chinese/English) layouts.

What it loads into context

Frontmatter

192 tokens

Always available to the agent

SKILL.md

798 tokens

When the skill is activated

Reference documents

4,827 tokens

Loaded on request

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

The playbook

Core Behavioral Rules (The 12 Laws)
Usage
API keys
© License & Copyright

Scripts executed separately

src/aut_sci_ppt/__init__.py
src/aut_sci_ppt/academic_parser.py
src/aut_sci_ppt/agent.py
src/aut_sci_ppt/config.py
src/aut_sci_ppt/enhanced_agent.py
src/aut_sci_ppt/generator/__init__.py
src/aut_sci_ppt/generator/formula_renderer.py
src/aut_sci_ppt/generator/pptx_generator.py
src/aut_sci_ppt/image/__init__.py
src/aut_sci_ppt/interactive.py
src/aut_sci_ppt/layout_engine.py
src/aut_sci_ppt/main.py
src/aut_sci_ppt/models.py
src/aut_sci_ppt/paginator/__init__.py
src/aut_sci_ppt/paginator/smart_paginator.py
src/aut_sci_ppt/paper_workflow.py
src/aut_sci_ppt/parser/__init__.py
src/aut_sci_ppt/parser/text_parser.py
src/aut_sci_ppt/pdf_extractor.py
src/aut_sci_ppt/run.py
src/aut_sci_ppt/templates/__init__.py
src/aut_sci_ppt/templates/base.py
src/aut_sci_ppt/templates/content_detail.py
src/aut_sci_ppt/templates/content_figure.py
src/aut_sci_ppt/templates/content_list.py
src/aut_sci_ppt/templates/cover.py
src/aut_sci_ppt/templates/ending.py
src/aut_sci_ppt/templates/section.py
src/aut_sci_ppt/templates/timeline.py
src/aut_sci_ppt/templates/toc.py
src/aut_sci_ppt/tests/__init__.py
src/aut_sci_ppt/tests/test_agent.py

Files

.gitignoreasset366 bytes
LICENSEasset1,081 bytes
README.mddoc1,628 bytes
SKILL.mdcore3,129 bytes
SKILL.mdcore3,129 bytes
SKILL.mdcore3,129 bytes
_meta.jsonasset168 bytes
pyproject.tomlasset656 bytes
references/rules.mddoc1,596 bytes
references/style-spec.mddoc1,355 bytes
requirements.txtdoc110 bytes
src/aut_sci_ppt/USER_GUIDE.mddoc12,097 bytes
src/aut_sci_ppt/__init__.pyruns825 bytes
src/aut_sci_ppt/academic_parser.pyruns4,129 bytes
src/aut_sci_ppt/agent.pyruns6,223 bytes
src/aut_sci_ppt/config.pyruns6,706 bytes
src/aut_sci_ppt/enhanced_agent.pyruns4,640 bytes
src/aut_sci_ppt/generator/__init__.pyruns20 bytes
src/aut_sci_ppt/generator/formula_renderer.pyruns4,954 bytes
src/aut_sci_ppt/generator/pptx_generator.pyruns5,966 bytes
src/aut_sci_ppt/image/__init__.pyruns16 bytes
src/aut_sci_ppt/interactive.pyruns3,030 bytes
src/aut_sci_ppt/layout_engine.pyruns3,258 bytes
src/aut_sci_ppt/main.pyruns4,700 bytes
src/aut_sci_ppt/models.pyruns3,495 bytes
src/aut_sci_ppt/paginator/__init__.pyruns20 bytes
src/aut_sci_ppt/paginator/smart_paginator.pyruns7,049 bytes
src/aut_sci_ppt/paper_workflow.pyruns19,460 bytes
src/aut_sci_ppt/parser/__init__.pyruns17 bytes
src/aut_sci_ppt/parser/text_parser.pyruns9,968 bytes
src/aut_sci_ppt/pdf_extractor.pyruns9,442 bytes
src/aut_sci_ppt/run.pyruns174 bytes
src/aut_sci_ppt/templates/__init__.pyruns1,508 bytes
src/aut_sci_ppt/templates/base.pyruns10,868 bytes
src/aut_sci_ppt/templates/content_detail.pyruns4,186 bytes
src/aut_sci_ppt/templates/content_figure.pyruns12,665 bytes
src/aut_sci_ppt/templates/content_list.pyruns3,514 bytes
src/aut_sci_ppt/templates/cover.pyruns3,884 bytes
src/aut_sci_ppt/templates/ending.pyruns1,545 bytes
src/aut_sci_ppt/templates/section.pyruns2,069 bytes
src/aut_sci_ppt/templates/timeline.pyruns4,483 bytes
src/aut_sci_ppt/templates/toc.pyruns3,215 bytes
src/aut_sci_ppt/tests/__init__.pyruns20 bytes
src/aut_sci_ppt/tests/test_agent.pyruns4,405 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

Skills included

sci-download
sci-extract
sci-figure
sci-html
sci-polish
sci-ppt
sci-review
sci-search
sci-zotero

Repository facts

License: No license detected
Created: Apr 6, 2026
Last pushed: Aug 13, 2026
Forks: 28
Open issues: 2
Project activity: Slowing

Before you install

Network or broad shell

Automated signals, not a guarantee

Checked Nov 6, 2026

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

Show 54 notes

skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-download/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-html/pyproject.toml:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-ppt/pyproject.toml:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-search/_meta.json:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-extract/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-extract/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-extract/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-extract/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-extract/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-figure/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-figure/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
skills/sci-figure/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed

No broad tool permissions
No dangerous shell commands
687 network referencesin 33 files: skills/sci-search/sci_search.py:271 skills/sci-extract/harvester/metadata.py:18 skills/sci-zotero/zotero.py:42 and 30 more
3 obfuscation signalsin 2 files: skills/sci-extract/harvester/jats.py:103 sci-download/cnki_download.py:477
No instruction overrides
177 executable scriptsin 94 files: skills/sci-extract/extract_core_insights.py:1 skills/sci-extract/harvest_paper.py:1 skills/sci-extract/harvester/__init__.py:1 and 91 more
429 references to secretsin 26 files: skills/sci-zotero/zotero.py:4 skills/sci-search/sci_search.py:41 skills/sci-extract/harvester/metadata.py:438 and 23 more
No requests to vote in Hot

Show all 1,296 signals by file

`.claude-plugin/marketplace.json`

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{   "$schema": "https://anthropic.com/claude-code/marketplace.schema.json",

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"$schema": "https://anthropic.com/claude-code/marketplace.schema.json",

`skills/sci-download/SKILL.md`

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| Service | URL | Notes | |---------|-----|-------| | Elsevier | https://dev.elsevier.com/ | Free, Article Retrieval API |

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|---------|-----|-------| | Elsevier | https://dev.elsevier.com/ | Free, Article Retrieval API | | Springer | https://dev.springernature.com/ | Free, OA only |

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| Elsevier | https://dev.elsevier.com/ | Free, Article Retrieval API |

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| Springer | https://dev.springernature.com/ | Free, OA only |

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| IEEE | https://developer.ieee.org/ | Free tier |

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python skills/sci-download/cnki_download.py set-mode fsso python skills/sci-download/cnki_download.py status # Login at https://fsso.cnki.net → export cookies → save to ~/.aut_sci_write/webvpn_cookies.json

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# Login at https://fsso.cnki.net → export cookies → save to ~/.aut_sci_write/webvpn_cookies.json

`skills/sci-download/arxiv_download.py`

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```
Executable file
```

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MIN_PDF_SIZE = 10_000 ARXIV_API = "https://export.arxiv.org/api/query"

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ARXIV_API = "https://export.arxiv.org/api/query"

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ARXIV_PDF_BASE = "https://arxiv.org/pdf"

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def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

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```
s = requests.Session()
```

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def _extract_arxiv_id(identifier: str) -> str | None:     identifier = identifier.strip()     for prefix in ("https://arxiv.org/abs/", "https://arxiv.org/pdf/", "http://arxiv.org/abs/", "arXiv:"):

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identifier = identifier.strip()     for prefix in ("https://arxiv.org/abs/", "https://arxiv.org/pdf/", "http://arxiv.org/abs/", "arXiv:"):         if identifier.startswith(prefix):

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for prefix in ("https://arxiv.org/abs/", "https://arxiv.org/pdf/", "http://arxiv.org/abs/", "arXiv:"):

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def _parse_atom_feed(xml_text: str) -> list[dict[str, str]]:     ns = {"atom": "http://www.w3.org/2005/Atom"}

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ns = {"atom": "http://www.w3.org/2005/Atom"}

`skills/sci-download/cnki_download.py`

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Access modes:     - fsso (default): Direct access to kns.cnki.net via CARSI/FSSO session cookie.       Login at https://fsso.cnki.net → select school → CAS login → export cookie.

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- fsso (default): Direct access to kns.cnki.net via CARSI/FSSO session cookie.       Login at https://fsso.cnki.net → select school → CAS login → export cookie.     - webvpn: Access via university WebVPN proxy (AES-encrypted URLs).

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Login at https://fsso.cnki.net → select school → CAS login → export cookie.

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```
CNKI_BASE = "https://kns.cnki.net"
```

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def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

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```
s = requests.Session()
```

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if not cookie_file.exists():         login_hint = "https://fsso.cnki.net" if mode == "fsso" else config.get("webvpn_host", "WebVPN portal")

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login_hint = "https://fsso.cnki.net" if mode == "fsso" else config.get("webvpn_host", "WebVPN portal")

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session = _get_session(config)     test_url = _resolve_url("https://kns.cnki.net/kns8/defaultresult/index", config)

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test_url = _resolve_url("https://kns.cnki.net/kns8/defaultresult/index", config)

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is_caj = content[:4] in (b"CAJ-", b"\xc8\xaf\xc8\xaf")

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if mode == "fsso":         info["login_url"] = "https://fsso.cnki.net"

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info["login_url"] = "https://fsso.cnki.net"

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info["instructions"] = (             "1. Open https://fsso.cnki.net in browser\n"             "2. Select your institution and login via CAS/Shibboleth\n"

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"1. Open https://fsso.cnki.net in browser\n"

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`skills/sci-download/config.py`

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# Aut_Sci_Download API Keys # Elsevier: https://dev.elsevier.com/ (free)

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# Elsevier: https://dev.elsevier.com/ (free)

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# Springer Nature: https://dev.springernature.com/ (free, OA only)

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# IEEE Xplore: https://developer.ieee.org/ (free tier)

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# NCBI/PubMed: https://www.ncbi.nlm.nih.gov/account/settings/ (free)

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# Semantic Scholar (optional, for higher rate limits): https://www.semanticscholar.org/product/api#api-key

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entry = schools[school_name]             return {                 "host": f"https://{entry['host']}",

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return {                 "host": f"https://{entry['host']}",                 "crypto_key": entry.get("crypto_key", WEBVPN_DEFAULT_KEY),

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```
"host": f"https://{entry['host']}",
```

`skills/sci-download/elsevier_download.py`

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Endpoint: https://api.elsevier.com/content/article/doi/{doi}

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def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

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s = requests.Session()
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url = f"https://api.elsevier.com/content/article/doi/{doi}"

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try:         resp = session.get(             "https://api.elsevier.com/content/serial/title",

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"https://api.elsevier.com/content/serial/title",

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identifier = identifier.strip()     identifier = identifier.replace("–", "-").replace("—", "-")     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

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identifier = identifier.replace("–", "-").replace("—", "-")     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):         if identifier.lower().startswith(prefix.lower()):

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for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

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`skills/sci-download/ieee_download.py`

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Endpoint: https://ieeexploreapi.ieee.org/api/v1/search/articles

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MIN_PDF_SIZE = 10_000 API_BASE = "https://ieeexploreapi.ieee.org/api/v1/search/articles"

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API_BASE = "https://ieeexploreapi.ieee.org/api/v1/search/articles"

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def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

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s = requests.Session()
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def _normalize_doi(identifier: str) -> str:     identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

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identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):         if identifier.lower().startswith(prefix.lower()):

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for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

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```

`skills/sci-download/pubmed_download.py`

Executable scriptline 1
```
Executable file
```

Network accessline 27

MIN_PDF_SIZE = 10_000 NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

Network accessline 28

NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

Network accessline 29

EUROPEPMC_BASE = "https://www.ebi.ac.uk/europepmc/webservices/rest"

Network accessline 32

def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

Network accessline 33
```
s = requests.Session()
```
Access to secretsline 43
```
[Credential-related source omitted]
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```
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```
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```
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```
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```

Network accessline 137

europepmc_url = f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={pmcid}&blobtype=pdf"

Network accessline 144

ncbi_url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{pmcid}/pdf/"

Network accessline 208

for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

`skills/sci-download/sci_download.py`

Executable scriptline 1
```
Executable file
```

Network accessline 39

def route_identifier(identifier: str) -> str | None:     identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Network accessline 40

identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):         if identifier.lower().startswith(prefix.lower()):

Network accessline 41

for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Network accessline 46

if ARXIV_PATTERN.match(identifier) or identifier.startswith("arXiv:"):         return "arxiv"     if identifier.startswith("https://arxiv.org/"):

Network accessline 47

return "arxiv"     if identifier.startswith("https://arxiv.org/"):         return "arxiv"

Network accessline 48

if identifier.startswith("https://arxiv.org/"):

Access to secretsline 168
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
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```
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```
Access to secretsline 173
```
[Credential-related source omitted]
```

`skills/sci-download/semantic_scholar_download.py`

Executable scriptline 1
```
Executable file
```

Network accessline 7

No API key required (rate-limited to 100 req/5min without key). Endpoint: https://api.semanticscholar.org/graph/v1/paper/

Network accessline 8

Endpoint: https://api.semanticscholar.org/graph/v1/paper/

Network accessline 28

MIN_PDF_SIZE = 10_000 API_BASE = "https://api.semanticscholar.org/graph/v1"

Network accessline 29

API_BASE = "https://api.semanticscholar.org/graph/v1"

Network accessline 32

def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

Network accessline 33
```
s = requests.Session()
```
Access to secretsline 36
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```

Network accessline 168

identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Network accessline 169

for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

`skills/sci-download/springer_download.py`

Executable scriptline 1
```
Executable file
```
Network accessline 7
```
[Credential-related source omitted]
```
Access to secretsline 7
```
[Credential-related source omitted]
```

Network accessline 8

Endpoint: https://api.springernature.com/openaccess/json

Network accessline 29

MIN_PDF_SIZE = 10_000 API_BASE = "https://api.springernature.com"

Network accessline 30

API_BASE = "https://api.springernature.com"

Network accessline 33

def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

Network accessline 34
```
s = requests.Session()
```
Access to secretsline 57
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
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```
Access to secretsline 78
```
[Credential-related source omitted]
```

Network accessline 134

doi = record.get("doi", "")     if doi:         return f"https://link.springer.com/content/pdf/{doi}.pdf"

Network accessline 136

return f"https://link.springer.com/content/pdf/{doi}.pdf"

Access to secretsline 141
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```

Network accessline 163

def _normalize_doi(identifier: str) -> str:     identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Network accessline 164

identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):         if identifier.lower().startswith(prefix.lower()):

Network accessline 165

for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Access to secretsline 185
```
[Credential-related source omitted]
```

`skills/sci-download/unpaywall_download.py`

Executable scriptline 1
```
Executable file
```
Network accessline 6
```
[Credential-related source omitted]
```
Access to secretsline 6
```
[Credential-related source omitted]
```

Network accessline 7

Endpoint: https://api.unpaywall.org/v2/{doi}?email=xxx

Network accessline 27

MIN_PDF_SIZE = 10_000 API_BASE = "https://api.unpaywall.org/v2"

Network accessline 28

API_BASE = "https://api.unpaywall.org/v2"

Network accessline 31

def _get_session(config: dict[str, Any]) -> requests.Session:     s = requests.Session()

Network accessline 32
```
s = requests.Session()
```
Access to secretsline 65
```
[Credential-related source omitted]
```

Network accessline 138

def _normalize_doi(identifier: str) -> str:     identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

Network accessline 139

identifier = identifier.strip()     for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):         if identifier.lower().startswith(prefix.lower()):

Network accessline 140

for prefix in ("https://doi.org/", "http://doi.org/", "doi:"):

`skills/sci-download/webvpn_crypto.py`

Executable scriptline 1
```
Executable file
```

Network accessline 22

Args:         url: Original URL (e.g. https://kns.cnki.net/kns8/...)

Network accessline 23

url: Original URL (e.g. https://kns.cnki.net/kns8/...)

Network accessline 24

webvpn_base: WebVPN base (e.g. https://webvpn.tsinghua.edu.cn)

`skills/sci-extract/README.md`

Access to secretsline 126
```
[Credential-related source omitted]
```
Access to secretsline 126
```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
[Credential-related source omitted]
```
Access to secretsline 141
```
[Credential-related source omitted]
```
Access to secretsline 141
```
[Credential-related source omitted]
```

`skills/sci-extract/extract_core_insights.py`

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

`skills/sci-extract/harvest_paper.py`

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

`skills/sci-extract/harvester/init.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

`skills/sci-extract/harvester/env.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```
Access to secretsline 3
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
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```
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```
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```
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```
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```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
Access to secretsline 68
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
Access to secretsline 69
```
[Credential-related source omitted]
```
Access to secretsline 89
```
[Credential-related source omitted]
```
Access to secretsline 89
```
[Credential-related source omitted]
```

`skills/sci-extract/harvester/figures.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 123

package = oa_package.fetch(meta.pmcid, verbose=verbose)

Network accessline 123

package = oa_package.fetch(meta.pmcid, verbose=verbose)

`skills/sci-extract/harvester/fulltext.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 16

PMC_EFETCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"

Network accessline 16

PMC_EFETCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"

Network accessline 17

EUROPEPMC_FULLTEXT = "https://www.ebi.ac.uk/europepmc/webservices/rest"

Network accessline 17

EUROPEPMC_FULLTEXT = "https://www.ebi.ac.uk/europepmc/webservices/rest"

Network accessline 18

ELSEVIER_FULLTEXT = "https://api.elsevier.com/content/article/doi"

Network accessline 18

ELSEVIER_FULLTEXT = "https://api.elsevier.com/content/article/doi"

Network accessline 19

SPRINGER_OA_API = "https://api.springernature.com/openaccess/json"

Network accessline 19

SPRINGER_OA_API = "https://api.springernature.com/openaccess/json"

Access to secretsline 77
```
[Credential-related source omitted]
```
Access to secretsline 77
```
[Credential-related source omitted]
```
Access to secretsline 78
```
[Credential-related source omitted]
```
Access to secretsline 78
```
[Credential-related source omitted]
```
Access to secretsline 145
```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
[Credential-related source omitted]
```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
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```
Access to secretsline 179
```
[Credential-related source omitted]
```
Access to secretsline 179
```
[Credential-related source omitted]
```
Network accessline 223
```
package = oa_package.fetch(meta.pmcid)
```
Network accessline 223
```
package = oa_package.fetch(meta.pmcid)
```

Network accessline 225

urls.append(package.pdf_url)         urls.append(             f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"

Network accessline 225

urls.append(package.pdf_url)         urls.append(             f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"

Network accessline 226

urls.append(             f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"         )

Network accessline 226

urls.append(             f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"         )

Network accessline 227

f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"

Network accessline 227

f"https://europepmc.org/backend/ptpmcrender.fcgi?accid={meta.pmcid}&blobtype=pdf"

Network accessline 228

)     if meta.arxiv_id:         urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")

Network accessline 228

)     if meta.arxiv_id:         urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")

Network accessline 229

if meta.arxiv_id:         urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")     seen: set = set()

Network accessline 229

if meta.arxiv_id:         urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")     seen: set = set()

Network accessline 230

urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")

Network accessline 230

urls.append(f"https://arxiv.org/pdf/{meta.arxiv_id}")

`skills/sci-extract/harvester/http.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 68

def _session() -> requests.Session:     session = requests.Session()

Network accessline 68

def _session() -> requests.Session:     session = requests.Session()

Network accessline 69
```
session = requests.Session()
```
Network accessline 69
```
session = requests.Session()
```

`skills/sci-extract/harvester/identify.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 24

_DOI_URL_PREFIXES = (     "https://doi.org/",

Network accessline 24

_DOI_URL_PREFIXES = (     "https://doi.org/",

Network accessline 25
```
"https://doi.org/",
```
Network accessline 25
```
"https://doi.org/",
```
Network accessline 26
```
"http://doi.org/",
```
Network accessline 26
```
"http://doi.org/",
```
Network accessline 27
```
"https://dx.doi.org/",
```
Network accessline 27
```
"https://dx.doi.org/",
```
Network accessline 28
```
"http://dx.doi.org/",
```
Network accessline 28
```
"http://dx.doi.org/",
```

`skills/sci-extract/harvester/jats.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 15

NS = {     "ce": "http://www.elsevier.com/xml/common/dtd",

Network accessline 15

NS = {     "ce": "http://www.elsevier.com/xml/common/dtd",

Network accessline 16

"ce": "http://www.elsevier.com/xml/common/dtd",

Network accessline 16

"ce": "http://www.elsevier.com/xml/common/dtd",

Network accessline 17

"xocs": "http://www.elsevier.com/xml/xocs/dtd",

Network accessline 17

"xocs": "http://www.elsevier.com/xml/xocs/dtd",

Network accessline 18

"ja": "http://www.elsevier.com/xml/ja/dtd",

Network accessline 18

"ja": "http://www.elsevier.com/xml/ja/dtd",

Network accessline 19

"xlink": "http://www.w3.org/1999/xlink",

Network accessline 19

"xlink": "http://www.w3.org/1999/xlink",

Network accessline 20

"mml": "http://www.w3.org/1998/Math/MathML",

Network accessline 20

"mml": "http://www.w3.org/1998/Math/MathML",

Possible obfuscationline 103

return cleaned.lstrip("<U+FEFF> \n\r\t")

Possible obfuscationline 103

return cleaned.lstrip("<U+FEFF> \n\r\t")

Network accessline 179

return node.get("{http://www.w3.org/1999/xlink}href") or node.get("href") or ""

Network accessline 179

return node.get("{http://www.w3.org/1999/xlink}href") or node.get("href") or ""

Network accessline 518

label=_text_of(_find_any(figure, "label")),                 caption=_text_of(_find_any(figure, "caption")),                 graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")

Network accessline 518

label=_text_of(_find_any(figure, "label")),                 caption=_text_of(_find_any(figure, "caption")),                 graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")

Network accessline 519

caption=_text_of(_find_any(figure, "caption")),                 graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")                 if link is not None

Network accessline 519

caption=_text_of(_find_any(figure, "caption")),                 graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")                 if link is not None

Network accessline 520

graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")

Network accessline 520

graphic_href=(link.get("{http://www.w3.org/1999/xlink}href") or link.get("locator") or "")

`skills/sci-extract/harvester/metadata.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 18

CROSSREF_API = "https://api.crossref.org/works"

Network accessline 18

CROSSREF_API = "https://api.crossref.org/works"

Network accessline 19

OPENALEX_API = "https://api.openalex.org/works"

Network accessline 19

OPENALEX_API = "https://api.openalex.org/works"

Network accessline 20

S2_API = "https://api.semanticscholar.org/graph/v1/paper"

Network accessline 20

S2_API = "https://api.semanticscholar.org/graph/v1/paper"

Network accessline 21

NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

Network accessline 21

NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

Network accessline 22

UNPAYWALL_API = "https://api.unpaywall.org/v2"

Network accessline 22

UNPAYWALL_API = "https://api.unpaywall.org/v2"

Network accessline 23

ARXIV_API = "https://export.arxiv.org/api/query"

Network accessline 23

ARXIV_API = "https://export.arxiv.org/api/query"

Network accessline 24

WOS_API = "https://api.clarivate.com/apis/wos-starter/v1/documents"

Network accessline 24

WOS_API = "https://api.clarivate.com/apis/wos-starter/v1/documents"

Network accessline 25

SCOPUS_API = "https://api.elsevier.com/content/abstract/doi"

Network accessline 25

SCOPUS_API = "https://api.elsevier.com/content/abstract/doi"

Network accessline 26

SPRINGER_META_API = "https://api.springernature.com/meta/v2/json"

Network accessline 26

SPRINGER_META_API = "https://api.springernature.com/meta/v2/json"

Network accessline 27

ELSEVIER_API = "https://api.elsevier.com/content/article/doi"

Network accessline 27

ELSEVIER_API = "https://api.elsevier.com/content/article/doi"

Network accessline 283

family=entry.get("family", ""),         name=entry.get("name", ""),         orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(

Network accessline 283

family=entry.get("family", ""),         name=entry.get("name", ""),         orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(

Network accessline 284

name=entry.get("name", ""),         orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(             "https://orcid.org/", ""

Network accessline 284

name=entry.get("name", ""),         orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(             "https://orcid.org/", ""

Network accessline 285

orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(

Network accessline 285

orcid=(entry.get("ORCID") or "").replace("http://orcid.org/", "").replace(

Network accessline 286
```
"https://orcid.org/", ""
```
Network accessline 286
```
"https://orcid.org/", ""
```

Network accessline 314

email = env.key("OPENALEX_EMAIL") or env.contact_email()     params = {"mailto": email} if email else {}     work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)

Network accessline 314

email = env.key("OPENALEX_EMAIL") or env.contact_email()     params = {"mailto": email} if email else {}     work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)

Network accessline 315

params = {"mailto": email} if email else {}     work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)     if not work or work.get("id") is None:

Network accessline 315

params = {"mailto": email} if email else {}     work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)     if not work or work.get("id") is None:

Network accessline 316

work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)

Network accessline 316

work = http.get_json(f"{OPENALEX_API}/https://doi.org/{doi}", params=params)

Network accessline 418

given=" ".join(parts[:-1]) if len(parts) > 1 else "",         family=parts[-1] if parts else "",         orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),

Network accessline 418

given=" ".join(parts[:-1]) if len(parts) > 1 else "",         family=parts[-1] if parts else "",         orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),

Network accessline 419

family=parts[-1] if parts else "",         orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),         affiliations=[i.get("display_name", "") for i in entry.get("institutions") or []],

Network accessline 419

family=parts[-1] if parts else "",         orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),         affiliations=[i.get("display_name", "") for i in entry.get("institutions") or []],

Network accessline 420

orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),

Network accessline 420

orcid=(author.get("orcid") or "").replace("https://orcid.org/", ""),

Access to secretsline 438
```
[Credential-related source omitted]
```
Access to secretsline 438
```
[Credential-related source omitted]
```
Access to secretsline 439
```
[Credential-related source omitted]
```
Access to secretsline 439
```
[Credential-related source omitted]
```
Access to secretsline 440
```
[Credential-related source omitted]
```
Access to secretsline 440
```
[Credential-related source omitted]
```
Access to secretsline 496
```
[Credential-related source omitted]
```
Access to secretsline 496
```
[Credential-related source omitted]
```
Access to secretsline 497
```
[Credential-related source omitted]
```
Access to secretsline 497
```
[Credential-related source omitted]
```

Network accessline 510

return     payload = http.get_json(         "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",

Network accessline 510

return     payload = http.get_json(         "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",

Network accessline 511

payload = http.get_json(         "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",         params={"ids": probe, "format": "json", "tool": "sci-extract"},

Network accessline 511

payload = http.get_json(         "https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",         params={"ids": probe, "format": "json", "tool": "sci-extract"},

Network accessline 512

"https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",

Network accessline 512

"https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/",

Network accessline 645

ns = {"atom": "http://www.w3.org/2005/Atom", "arxiv": "http://arxiv.org/schemas/atom"}

Network accessline 645

ns = {"atom": "http://www.w3.org/2005/Atom", "arxiv": "http://arxiv.org/schemas/atom"}

Network accessline 687

)             )     meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")

Network accessline 687

)             )     meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")

Network accessline 688

)     meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")     meta.oa_pdf_url = _first_nonempty(meta.oa_pdf_url, f"https://arxiv.org/pdf/{arxiv_id}")

Network accessline 688

)     meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")     meta.oa_pdf_url = _first_nonempty(meta.oa_pdf_url, f"https://arxiv.org/pdf/{arxiv_id}")

Network accessline 689

meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")

Network accessline 689

meta.urls.setdefault("arxiv_abs", f"https://arxiv.org/abs/{arxiv_id}")

Network accessline 690

meta.oa_pdf_url = _first_nonempty(meta.oa_pdf_url, f"https://arxiv.org/pdf/{arxiv_id}")

Network accessline 690

meta.oa_pdf_url = _first_nonempty(meta.oa_pdf_url, f"https://arxiv.org/pdf/{arxiv_id}")

Access to secretsline 699
```
[Credential-related source omitted]
```
Access to secretsline 699
```
[Credential-related source omitted]
```
Access to secretsline 700
```
[Credential-related source omitted]
```
Access to secretsline 700
```
[Credential-related source omitted]
```
Access to secretsline 705
```
[Credential-related source omitted]
```
Access to secretsline 705
```
[Credential-related source omitted]
```

Network accessline 729

if meta.wos_uid:         meta.urls.setdefault(             "wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"

Network accessline 729

if meta.wos_uid:         meta.urls.setdefault(             "wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"

Network accessline 730

meta.urls.setdefault(             "wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"         )

Network accessline 730

meta.urls.setdefault(             "wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"         )

Network accessline 731

"wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"

Network accessline 731

"wos", f"https://www.webofscience.com/wos/woscc/full-record/{meta.wos_uid}"

Access to secretsline 739
```
[Credential-related source omitted]
```
Access to secretsline 739
```
[Credential-related source omitted]
```
Access to secretsline 740
```
[Credential-related source omitted]
```
Access to secretsline 740
```
[Credential-related source omitted]
```
Access to secretsline 742
```
[Credential-related source omitted]
```
Access to secretsline 742
```
[Credential-related source omitted]
```
Access to secretsline 779
```
[Credential-related source omitted]
```
Access to secretsline 779
```
[Credential-related source omitted]
```
Access to secretsline 780
```
[Credential-related source omitted]
```
Access to secretsline 780
```
[Credential-related source omitted]
```
Access to secretsline 783
```
[Credential-related source omitted]
```
Access to secretsline 783
```
[Credential-related source omitted]
```
Access to secretsline 820
```
[Credential-related source omitted]
```
Access to secretsline 820
```
[Credential-related source omitted]
```
Access to secretsline 821
```
[Credential-related source omitted]
```
Access to secretsline 821
```
[Credential-related source omitted]
```
Access to secretsline 823
```
[Credential-related source omitted]
```
Access to secretsline 823
```
[Credential-related source omitted]
```

Network accessline 911

meta.year = meta.published_date[:4]     if meta.doi:         meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")

Network accessline 911

meta.year = meta.published_date[:4]     if meta.doi:         meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")

Network accessline 912

if meta.doi:         meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")     if meta.pmcid:

Network accessline 912

if meta.doi:         meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")     if meta.pmcid:

Network accessline 913

meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")

Network accessline 913

meta.urls.setdefault("doi", f"https://doi.org/{meta.doi}")

Network accessline 914

if meta.pmcid:         meta.urls.setdefault(             "pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"

Network accessline 914

if meta.pmcid:         meta.urls.setdefault(             "pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"

Network accessline 915

meta.urls.setdefault(             "pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"         )

Network accessline 915

meta.urls.setdefault(             "pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"         )

Network accessline 916

"pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"

Network accessline 916

"pmc", f"https://www.ncbi.nlm.nih.gov/pmc/articles/{meta.pmcid}/"

Network accessline 917

)     if meta.pmid:         meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")

Network accessline 917

)     if meta.pmid:         meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")

Network accessline 918

if meta.pmid:         meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")     if meta.title:

Network accessline 918

if meta.pmid:         meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")     if meta.title:

Network accessline 919

meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")

Network accessline 919

meta.urls.setdefault("pubmed", f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/")

`skills/sci-extract/harvester/oa_package.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 17

Docs: https://pmc.ncbi.nlm.nih.gov/tools/pmcaws/

Network accessline 17

Docs: https://pmc.ncbi.nlm.nih.gov/tools/pmcaws/

Network accessline 27

BUCKET = "https://pmc-oa-opendata.s3.amazonaws.com"

Network accessline 27

BUCKET = "https://pmc-oa-opendata.s3.amazonaws.com"

Network accessline 94

def fetch(pmcid: str, *, verbose: bool = False) -> OAPackage:

Network accessline 94

def fetch(pmcid: str, *, verbose: bool = False) -> OAPackage:

`skills/sci-extract/harvester/render.py`

Executable scriptline 1
```
Executable file
```
Executable scriptline 1
```
Executable file
```

Network accessline 259

def _raw_identifiers(out, meta: PaperMetadata) -> None:     ids = [         ("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),

Network accessline 259

def _raw_identifiers(out, meta: PaperMetadata) -> None:     ids = [         ("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),

Network accessline 260

ids = [         ("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),         ("PMID", meta.pmid, f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/" if meta.pmid else ""),

Network accessline 260

ids = [         ("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),         ("PMID", meta.pmid, f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/" if meta.pmid else ""),

Network accessline 261

("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),

Network accessline 261

("DOI", meta.doi, f"https://doi.org/{meta.doi}" if meta.doi else ""),

Network accessline 262

("PMID", meta.pmid, f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/" if meta.pmid else ""),

Network accessline 262

("PMID", meta.pmid, f"https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/" if meta.pmid else ""),

Network accessline 264

"PMCID",             meta.pmcid,             f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",

Network accessline 264

"PMCID",             meta.pmcid,             f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",

Network accessline 265

meta.pmcid,             f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",         ),

Network accessline 265

meta.pmcid,             f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",         ),

Network accessline 266

f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",

Network accessline 266

f"https://pmc.ncbi.nlm.nih.gov/articles/{meta.pmcid}/" if meta.pmcid else "",

Network accessline 267

),         ("arXiv", meta.arxiv_id, f"https://arxiv.org/abs/{meta.arxiv_id}" if meta.arxiv_id else ""),         ("Scopus", meta.scopus_id, ""),

Network accessline 267

),         ("arXiv", meta.arxiv_id, f"https://arxiv.org/abs/{meta.arxiv_id}" if meta.arxiv_id else ""),         ("Scopus", meta.scopus_id, ""),

Network accessline 268

("arXiv", meta.arxiv_id, f"https://arxiv.org/abs/{meta.arxiv_id}" if meta.arxiv_id else ""),

Network accessline 268

("arXiv", meta.arxiv_id, f"https://arxiv.org/abs/{meta.arxiv_id}" if meta.arxiv_id else ""),

Network accessline 499

doi = ref.get("doi")             if doi and doi not in text:                 text = f"{text} https://doi.org/{doi}".strip()

Network accessline 499

doi = ref.get("doi")             if doi and doi not in text:                 text = f"{text} https://doi.org/{doi}".strip()

Network accessline 500

if doi and doi not in text:                 text = f"{text} https://doi.org/{doi}".strip()             if text:

Network accessline 500

if doi and doi not in text:                 text = f"{text} https://doi.org/{doi}".strip()             if text:

Network accessline 501

text = f"{text} https://doi.org/{doi}".strip()

Network accessline 501

text = f"{text} https://doi.org/{doi}".strip()

Network accessline 606

routes: list[str] = []     landing = meta.urls.get("doi") or (         f"https://doi.org/{meta.doi}" if meta.doi else ""

Network accessline 606

routes: list[str] = []     landing = meta.urls.get("doi") or (         f"https://doi.org/{meta.doi}" if meta.doi else ""

Network accessline 607

landing = meta.urls.get("doi") or (         f"https://doi.org/{meta.doi}" if meta.doi else ""     )

Network accessline 607

landing = meta.urls.get("doi") or (         f"https://doi.org/{meta.doi}" if meta.doi else ""     )

Network accessline 608

f"https://doi.org/{meta.doi}" if meta.doi else ""

Network accessline 608

f"https://doi.org/{meta.doi}" if meta.doi else ""

Network accessline 612

if meta.pmid:         routes.append(             f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"

Network accessline 612

if meta.pmid:         routes.append(             f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"

Network accessline 613

routes.append(             f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"         )

Network accessline 613

routes.append(             f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"         )

Network accessline 614

f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"

Network accessline 614

f"- PubMed record: https://pubmed.ncbi.nlm.nih.gov/{meta.pmid}/"

Access to secretsline 624
```
[Credential-related source omitted]
```
Access to secretsline 624
```
[Credential-related source omitted]
```

`skills/sci-figure/LICENSE`

Network accessline 16

You should have received a copy of the GNU Affero General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.

Network accessline 16

You should have received a copy of the GNU Affero General Public License along with this program.  If not, see <https://www.gnu.org/licenses/>.

Network accessline 17

along with this program.  If not, see <https://www.gnu.org/licenses/>.

Network accessline 17

along with this program.  If not, see <https://www.gnu.org/licenses/>.

Network accessline 26

For the full AGPL v3 license text, see: https://www.gnu.org/licenses/agpl-3.0.html

Network accessline 26

For the full AGPL v3 license text, see: https://www.gnu.org/licenses/agpl-3.0.html

Network accessline 27

https://www.gnu.org/licenses/agpl-3.0.html

Network accessline 27

https://www.gnu.org/licenses/agpl-3.0.html

`skills/sci-figure/README.md`

Network accessline 16

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 16

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 17

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 17

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 25

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 25

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 107

| Library | Role | |---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 107

| Library | Role | |---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 108

|---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction | | [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 108

|---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction | | [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 109

| [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 109

| [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 110

| [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 110

| [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 111

| [opencv-python](https://opencv.org/) | Image processing |

Network accessline 111

| [opencv-python](https://opencv.org/) | Image processing |

Network accessline 112

| [Pillow](https://pillow.readthedocs.io/) | Image format conversion |

Network accessline 112

| [Pillow](https://pillow.readthedocs.io/) | Image format conversion |

Network accessline 113

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR for sub-figure labels |

Network accessline 113

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR for sub-figure labels |

Network accessline 114

| [NumPy](https://numpy.org/) | Array operations |

Network accessline 114

| [NumPy](https://numpy.org/) | Array operations |

Network accessline 130

**Note**: This project uses [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is licensed under AGPL v3. Therefore, this entire project is also licensed under AGPL v3 or later.

Network accessline 130

**Note**: This project uses [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is licensed under AGPL v3. Therefore, this entire project is also licensed under AGPL v3 or later.

`skills/sci-figure/README_CN.md`

Network accessline 18

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 18

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 19

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 19

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 26

`<U+0008>ash git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 26

`<U+0008>ash git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 27

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 27

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 158

| 库 | 用途 | |----|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 |

Network accessline 158

| 库 | 用途 | |----|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 |

Network accessline 159

|----|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 | | [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/) | PDF → 高质量图像渲染 |

Network accessline 159

|----|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 | | [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/) | PDF → 高质量图像渲染 |

Network accessline 160

| [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 |

Network accessline 160

| [pdfplumber](https://github.com/jsvine/pdfplumber) | 文本 + 坐标提取 |

Network accessline 161

| [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/) | PDF → 高质量图像渲染 |

Network accessline 161

| [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/) | PDF → 高质量图像渲染 |

Network accessline 162

| [opencv-python](https://opencv.org/) | 边界检测、轮廓分析 |

Network accessline 162

| [opencv-python](https://opencv.org/) | 边界检测、轮廓分析 |

Network accessline 163

| [Pillow](https://pillow.readthedocs.io/) | 图像格式转换 |

Network accessline 163

| [Pillow](https://pillow.readthedocs.io/) | 图像格式转换 |

Network accessline 164

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR 子图标签识别 |

Network accessline 164

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR 子图标签识别 |

Network accessline 165

| [NumPy](https://numpy.org/) | 数组操作 |

Network accessline 165

| [NumPy](https://numpy.org/) | 数组操作 |

Network accessline 179

如有问题或建议，请在 [GitHub Issues](https://github.com/xssjqx/Sh_Sci_Fig/issues) 中提出。

Network accessline 179

如有问题或建议，请在 [GitHub Issues](https://github.com/xssjqx/Sh_Sci_Fig/issues) 中提出。

`skills/sci-figure/SKILL.md`

Network accessline 29

> **License note**: sci-figure is licensed under **AGPL-3.0-or-later** because it links [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is AGPL-licensed.

Network accessline 29

> **License note**: sci-figure is licensed under **AGPL-3.0-or-later** because it links [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is AGPL-licensed.

`skills/sci-figure/sci_figure.egg-info/PKG-INFO`

Network accessline 3

Version: 2.0.0 Summary: Scientific figure extractor for academic PDF papers — three-engine fusion Home-page: https://github.com/xssjqx/Sh_Sci_Fig

Network accessline 3

Version: 2.0.0 Summary: Scientific figure extractor for academic PDF papers — three-engine fusion Home-page: https://github.com/xssjqx/Sh_Sci_Fig

Network accessline 4

Summary: Scientific figure extractor for academic PDF papers — three-engine fusion Home-page: https://github.com/xssjqx/Sh_Sci_Fig Author: ShClaw

Network accessline 4

Summary: Scientific figure extractor for academic PDF papers — three-engine fusion Home-page: https://github.com/xssjqx/Sh_Sci_Fig Author: ShClaw

Network accessline 5

Home-page: https://github.com/xssjqx/Sh_Sci_Fig

Network accessline 5

Home-page: https://github.com/xssjqx/Sh_Sci_Fig

Network accessline 55

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 55

- Python 3.9+ - [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 56

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 56

- [Tesseract OCR](https://github.com/tesseract-ocr/tesseract)

Network accessline 63

```bash git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 63

```bash git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 64

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 64

git clone https://github.com/xssjqx/Sh_Sci_Fig.git

Network accessline 146

| Library | Role | |---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 146

| Library | Role | |---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 147

|---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction | | [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 147

|---------|------| | [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction | | [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 148

| [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 148

| [pdfplumber](https://github.com/jsvine/pdfplumber) | Text + coordinate extraction |

Network accessline 149

| [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 149

| [PyMuPDF](https://pymupdf.readthedocs.io/) | PDF → image rendering |

Network accessline 150

| [opencv-python](https://opencv.org/) | Image processing |

Network accessline 150

| [opencv-python](https://opencv.org/) | Image processing |

Network accessline 151

| [Pillow](https://pillow.readthedocs.io/) | Image format conversion |

Network accessline 151

| [Pillow](https://pillow.readthedocs.io/) | Image format conversion |

Network accessline 152

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR for sub-figure labels |

Network accessline 152

| [pytesseract](https://github.com/madmaze/pytesseract) | OCR for sub-figure labels |

Network accessline 153

| [NumPy](https://numpy.org/) | Array operations |

Network accessline 153

| [NumPy](https://numpy.org/) | Array operations |

Network accessline 169

**Note**: This project uses [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is licensed under AGPL v3. Therefore, this entire project is also licensed under AGPL v3 or later.

Network accessline 169

**Note**: This project uses [PyMuPDF (fitz)](https://pymupdf.readthedocs.io/), which is licensed under AGPL v3. Therefore, this entire project is also licensed under AGPL v3 or later.

`skills/sci-figure/sci_figure/init.py`

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`skills/sci-figure/sci_figure/annotator.py`

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`skills/sci-figure/sci_figure/caption_detector.py`

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`skills/sci-figure/sci_figure/cli.py`

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`skills/sci-figure/sci_figure/column_detector.py`

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`skills/sci-figure/sci_figure/exceptions.py`

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`skills/sci-figure/sci_figure/region_detector.py`

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`skills/sci-figure/sci_figure/subfigure_splitter.py`

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for nr in range(1, n_expected + 1):             if n_expected % nr == 0:                 nc = n_expected // nr

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for nr in range(1, n_expected + 1):             if n_expected % nr == 0:                 nc = n_expected // nr

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if n_expected % nr == 0:                 nc = n_expected // nr                 factorizations.append((nr, nc))

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if n_expected % nr == 0:                 nc = n_expected // nr                 factorizations.append((nr, nc))

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```
nc = n_expected // nr
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nc = n_expected // nr
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for nr, nc in factorizations:
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for nr, nc in factorizations:
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h_score = self._check_grid_gaps(gray, axis="horizontal", n_splits=nr - 1)             v_score = self._check_grid_gaps(gray, axis="vertical", n_splits=nc - 1)

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h_score = self._check_grid_gaps(gray, axis="horizontal", n_splits=nr - 1)             v_score = self._check_grid_gaps(gray, axis="vertical", n_splits=nc - 1)

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v_score = self._check_grid_gaps(gray, axis="vertical", n_splits=nc - 1)

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v_score = self._check_grid_gaps(gray, axis="vertical", n_splits=nc - 1)

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# Generate cells for this grid.                 # Guard against tiny images where h // nr or w // nc == 0.

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# Generate cells for this grid.                 # Guard against tiny images where h // nr or w // nc == 0.

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# Guard against tiny images where h // nr or w // nc == 0.

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# Guard against tiny images where h // nr or w // nc == 0.

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`skills/sci-figure/sci_figure/utils.py`

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`skills/sci-figure/scripts/extract_figure.py`

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`skills/sci-figure/setup.py`

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long_description_content_type='text/markdown',     author='ShClaw',     url='https://github.com/xssjqx/Sh_Sci_Fig',

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long_description_content_type='text/markdown',     author='ShClaw',     url='https://github.com/xssjqx/Sh_Sci_Fig',

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author='ShClaw',     url='https://github.com/xssjqx/Sh_Sci_Fig',     license='AGPL-3.0-or-later',

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author='ShClaw',     url='https://github.com/xssjqx/Sh_Sci_Fig',     license='AGPL-3.0-or-later',

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url='https://github.com/xssjqx/Sh_Sci_Fig',

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url='https://github.com/xssjqx/Sh_Sci_Fig',

`skills/sci-figure/tests/init.py`

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`skills/sci-figure/tests/test_caption_dedup.py`

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`skills/sci-html/conftest.py`

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`skills/sci-html/scripts/generate_html_deck.py`

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`skills/sci-html/src/sci_html/init.py`

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`skills/sci-html/src/sci_html/paper_pipeline.py`

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`skills/sci-html/src/sci_html/parser.py`

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`skills/sci-html/src/sci_html/renderer.py`

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`skills/sci-html/templates/deck.js`

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`skills/sci-html/tests/_path.py`

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`skills/sci-polish/scripts/ai_score_estimator.py`

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`skills/sci-polish/scripts/tier1_words.py`

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`skills/sci-polish/scripts/validate_polish_output.py`

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`skills/sci-ppt/.gitignore`

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`skills/sci-ppt/README.md`

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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

`skills/sci-ppt/src/aut_sci_ppt/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/academic_parser.py`

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`skills/sci-ppt/src/aut_sci_ppt/agent.py`

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`skills/sci-ppt/src/aut_sci_ppt/config.py`

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`skills/sci-ppt/src/aut_sci_ppt/enhanced_agent.py`

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`skills/sci-ppt/src/aut_sci_ppt/generator/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/generator/formula_renderer.py`

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url = (                 f"https://latex.codecogs.com/png.image?"

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url = (                 f"https://latex.codecogs.com/png.image?"

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f"https://latex.codecogs.com/png.image?"

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f"https://latex.codecogs.com/png.image?"

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f"\\dpi{{{self.dpi}}}\\bg{{transparent}}\\fg{{{color}}}\\inline {encoded}"             )             response = requests.get(url, timeout=10)

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f"\\dpi{{{self.dpi}}}\\bg{{transparent}}\\fg{{{color}}}\\inline {encoded}"             )             response = requests.get(url, timeout=10)

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)             response = requests.get(url, timeout=10)             if response.status_code == 200:

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)             response = requests.get(url, timeout=10)             if response.status_code == 200:

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response = requests.get(url, timeout=10)

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response = requests.get(url, timeout=10)

`skills/sci-ppt/src/aut_sci_ppt/generator/pptx_generator.py`

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`skills/sci-ppt/src/aut_sci_ppt/image/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/interactive.py`

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`skills/sci-ppt/src/aut_sci_ppt/layout_engine.py`

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`skills/sci-ppt/src/aut_sci_ppt/main.py`

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`skills/sci-ppt/src/aut_sci_ppt/models.py`

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`skills/sci-ppt/src/aut_sci_ppt/paginator/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/paginator/smart_paginator.py`

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`skills/sci-ppt/src/aut_sci_ppt/paper_workflow.py`

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`skills/sci-ppt/src/aut_sci_ppt/parser/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/parser/text_parser.py`

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`skills/sci-ppt/src/aut_sci_ppt/pdf_extractor.py`

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`skills/sci-ppt/src/aut_sci_ppt/run.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/init.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/content_figure.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/content_list.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/cover.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/ending.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/timeline.py`

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`skills/sci-ppt/src/aut_sci_ppt/templates/toc.py`

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`skills/sci-ppt/src/aut_sci_ppt/tests/init.py`

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`skills/sci-review/scripts/validate_review_output.py`

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#!/usr/bin/env python3
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#!/usr/bin/env python3
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`skills/sci-search/.gitignore`

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`skills/sci-search/SKILL.md`

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Apply for a free API key at: https://developer.clarivate.com/apis/wos-starter

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Apply for a free API key at: https://developer.clarivate.com/apis/wos-starter

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Apply for free API keys at: https://dev.springernature.com/

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Apply for free API keys at: https://dev.springernature.com/

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Apply for a free API key at: https://dev.elsevier.com/

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Apply for a free API key at: https://dev.elsevier.com/

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Request a key at: https://www.semanticscholar.org/product/api#api-key

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Request a key at: https://www.semanticscholar.org/product/api#api-key

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`skills/sci-search/sci_search.py`

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#!/usr/bin/env python3
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#!/usr/bin/env python3
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class ArxivFetcher:     API_URL = "https://export.arxiv.org/api/query"

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class ArxivFetcher:     API_URL = "https://export.arxiv.org/api/query"

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API_URL = "https://export.arxiv.org/api/query"

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API_URL = "https://export.arxiv.org/api/query"

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NS = {'atom': 'http://www.w3.org/2005/Atom'}

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NS = {'atom': 'http://www.w3.org/2005/Atom'}

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url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         try:             with urllib.request.urlopen(url, timeout=15) as resp:

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url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         try:             with urllib.request.urlopen(url, timeout=15) as resp:

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try:             with urllib.request.urlopen(url, timeout=15) as resp:                 content = resp.read().decode('utf-8')

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try:             with urllib.request.urlopen(url, timeout=15) as resp:                 content = resp.read().decode('utf-8')

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with urllib.request.urlopen(url, timeout=15) as resp:

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with urllib.request.urlopen(url, timeout=15) as resp:

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Apply for a free API key at: https://developer.clarivate.com/apis/wos-starter

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Apply for a free API key at: https://developer.clarivate.com/apis/wos-starter

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API_URL = "https://api.clarivate.com/apis/wos-starter/v1/documents"

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API_URL = "https://api.clarivate.com/apis/wos-starter/v1/documents"

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}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

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}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

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req = urllib.request.Request(url, headers={

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req = urllib.request.Request(url, headers={

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```

Network accessline 327

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 327

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 328

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 328

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 329

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 329

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 355

uid = hit.get("uid", "")                 url_link = f"https://www.webofscience.com/wos/woscc/full-record/{uid}" if uid else ""

Network accessline 355

uid = hit.get("uid", "")                 url_link = f"https://www.webofscience.com/wos/woscc/full-record/{uid}" if uid else ""

Network accessline 356

url_link = f"https://www.webofscience.com/wos/woscc/full-record/{uid}" if uid else ""

Network accessline 356

url_link = f"https://www.webofscience.com/wos/woscc/full-record/{uid}" if uid else ""

Network accessline 378
```
[Credential-related source omitted]
```
Network accessline 378
```
[Credential-related source omitted]
```
Access to secretsline 378
```
[Credential-related source omitted]
```
Access to secretsline 378
```
[Credential-related source omitted]
```

Network accessline 379

Apply for a free API key at: https://dev.springernature.com/

Network accessline 379

Apply for a free API key at: https://dev.springernature.com/

Network accessline 382

API_URL = "https://api.springernature.com/meta/v2/json"

Network accessline 382

API_URL = "https://api.springernature.com/meta/v2/json"

Access to secretsline 385
```
[Credential-related source omitted]
```
Access to secretsline 385
```
[Credential-related source omitted]
```
Access to secretsline 388
```
[Credential-related source omitted]
```
Access to secretsline 388
```
[Credential-related source omitted]
```
Access to secretsline 391
```
[Credential-related source omitted]
```
Access to secretsline 391
```
[Credential-related source omitted]
```
Access to secretsline 396
```
[Credential-related source omitted]
```
Access to secretsline 396
```
[Credential-related source omitted]
```

Network accessline 399

}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 399

}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 400

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={             "Accept": "application/json",

Network accessline 400

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={             "Accept": "application/json",

Network accessline 401

req = urllib.request.Request(url, headers={

Network accessline 401

req = urllib.request.Request(url, headers={

Network accessline 403

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 403

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 404

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 404

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 405

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 405

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 416

doi = record.get("doi", "")                 doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 416

doi = record.get("doi", "")                 doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 417

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 417

doi_url = f"https://doi.org/{doi}" if doi else ""

Access to secretsline 446
```
[Credential-related source omitted]
```
Access to secretsline 446
```
[Credential-related source omitted]
```
Network accessline 452
```
[Credential-related source omitted]
```
Network accessline 452
```
[Credential-related source omitted]
```
Access to secretsline 452
```
[Credential-related source omitted]
```
Access to secretsline 452
```
[Credential-related source omitted]
```
Network accessline 453
```
[Credential-related source omitted]
```
Network accessline 453
```
[Credential-related source omitted]
```
Access to secretsline 453
```
[Credential-related source omitted]
```
Access to secretsline 453
```
[Credential-related source omitted]
```

Network accessline 454

Apply for access at: https://dev.springernature.com/

Network accessline 454

Apply for access at: https://dev.springernature.com/

Network accessline 457

API_URL = "https://api.springernature.com/openaccess/json"

Network accessline 457

API_URL = "https://api.springernature.com/openaccess/json"

Access to secretsline 460
```
[Credential-related source omitted]
```
Access to secretsline 460
```
[Credential-related source omitted]
```
Access to secretsline 463
```
[Credential-related source omitted]
```
Access to secretsline 463
```
[Credential-related source omitted]
```
Access to secretsline 466
```
[Credential-related source omitted]
```
Access to secretsline 466
```
[Credential-related source omitted]
```
Access to secretsline 471
```
[Credential-related source omitted]
```
Access to secretsline 471
```
[Credential-related source omitted]
```

Network accessline 474

}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 474

}         url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 475

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={             "Accept": "application/json",

Network accessline 475

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={             "Accept": "application/json",

Network accessline 476

req = urllib.request.Request(url, headers={

Network accessline 476

req = urllib.request.Request(url, headers={

Network accessline 478

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 478

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 479

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 479

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 480

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 480

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 491

doi = record.get("doi", "")                 doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 491

doi = record.get("doi", "")                 doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 492

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 492

doi_url = f"https://doi.org/{doi}" if doi else ""

Access to secretsline 538
```
[Credential-related source omitted]
```
Access to secretsline 538
```
[Credential-related source omitted]
```
Network accessline 544
```
[Credential-related source omitted]
```
Network accessline 544
```
[Credential-related source omitted]
```
Access to secretsline 544
```
[Credential-related source omitted]
```
Access to secretsline 544
```
[Credential-related source omitted]
```

Network accessline 545

Apply for a free API key at: https://dev.elsevier.com/

Network accessline 545

Apply for a free API key at: https://dev.elsevier.com/

Network accessline 547

API_URL = "https://api.elsevier.com/content/search/scopus"

Network accessline 547

API_URL = "https://api.elsevier.com/content/search/scopus"

Access to secretsline 550
```
[Credential-related source omitted]
```
Access to secretsline 550
```
[Credential-related source omitted]
```
Access to secretsline 554
```
[Credential-related source omitted]
```
Access to secretsline 554
```
[Credential-related source omitted]
```
Access to secretsline 557
```
[Credential-related source omitted]
```
Access to secretsline 557
```
[Credential-related source omitted]
```
Access to secretsline 568
```
[Credential-related source omitted]
```
Access to secretsline 568
```
[Credential-related source omitted]
```

Network accessline 572

if self.insttoken:             headers["X-ELS-Insttoken"] = self.insttoken         req = urllib.request.Request(url, headers=headers)

Network accessline 572

if self.insttoken:             headers["X-ELS-Insttoken"] = self.insttoken         req = urllib.request.Request(url, headers=headers)

Network accessline 573

headers["X-ELS-Insttoken"] = self.insttoken         req = urllib.request.Request(url, headers=headers)         try:

Network accessline 573

headers["X-ELS-Insttoken"] = self.insttoken         req = urllib.request.Request(url, headers=headers)         try:

Network accessline 574

req = urllib.request.Request(url, headers=headers)

Network accessline 574

req = urllib.request.Request(url, headers=headers)

Network accessline 575

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 575

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 576

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 576

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 590

doi = entry.get("prism:doi", "")                     doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 590

doi = entry.get("prism:doi", "")                     doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 591

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 591

doi_url = f"https://doi.org/{doi}" if doi else ""

Access to secretsline 621
```
[Credential-related source omitted]
```
Access to secretsline 621
```
[Credential-related source omitted]
```

Network accessline 627

No API key required for basic use (rate-limited).     Optional SEMANTIC_SCHOLAR_API_KEY for higher rate limits.     Request key at: https://www.semanticscholar.org/product/api#api-key

Network accessline 627

No API key required for basic use (rate-limited).     Optional SEMANTIC_SCHOLAR_API_KEY for higher rate limits.     Request key at: https://www.semanticscholar.org/product/api#api-key

Network accessline 628
```
[Credential-related source omitted]
```
Network accessline 628
```
[Credential-related source omitted]
```
Access to secretsline 628
```
[Credential-related source omitted]
```
Access to secretsline 628
```
[Credential-related source omitted]
```

Network accessline 629

Request key at: https://www.semanticscholar.org/product/api#api-key

Network accessline 629

Request key at: https://www.semanticscholar.org/product/api#api-key

Network accessline 631

API_URL = "https://api.semanticscholar.org/graph/v1/paper/search"

Network accessline 631

API_URL = "https://api.semanticscholar.org/graph/v1/paper/search"

Access to secretsline 634
```
[Credential-related source omitted]
```
Access to secretsline 634
```
[Credential-related source omitted]
```
Access to secretsline 647
```
[Credential-related source omitted]
```
Access to secretsline 647
```
[Credential-related source omitted]
```
Access to secretsline 648
```
[Credential-related source omitted]
```
Access to secretsline 648
```
[Credential-related source omitted]
```

Network accessline 650

req = urllib.request.Request(url, headers=headers)

Network accessline 650

req = urllib.request.Request(url, headers=headers)

Network accessline 652

for attempt in range(2):             try:                 with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 652

for attempt in range(2):             try:                 with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 653

try:                 with urllib.request.urlopen(req, timeout=15) as resp:                     data = json.loads(resp.read().decode("utf-8"))

Network accessline 653

try:                 with urllib.request.urlopen(req, timeout=15) as resp:                     data = json.loads(resp.read().decode("utf-8"))

Network accessline 654

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 654

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 674

ext_ids = item.get("externalIds") or {}             doi = ext_ids.get("DOI", "")             doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 674

ext_ids = item.get("externalIds") or {}             doi = ext_ids.get("DOI", "")             doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 675

doi = ext_ids.get("DOI", "")             doi_url = f"https://doi.org/{doi}" if doi else ""             s2_url = item.get("url", "")

Network accessline 675

doi = ext_ids.get("DOI", "")             doi_url = f"https://doi.org/{doi}" if doi else ""             s2_url = item.get("url", "")

Network accessline 676

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 676

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 697

Completely free, no API key needed.     Optional OPENALEX_EMAIL for polite pool (higher rate limits).     Docs: https://docs.openalex.org/

Network accessline 697

Completely free, no API key needed.     Optional OPENALEX_EMAIL for polite pool (higher rate limits).     Docs: https://docs.openalex.org/

Network accessline 698

Optional OPENALEX_EMAIL for polite pool (higher rate limits).     Docs: https://docs.openalex.org/     """

Network accessline 698

Optional OPENALEX_EMAIL for polite pool (higher rate limits).     Docs: https://docs.openalex.org/     """

Network accessline 699
```
Docs: https://docs.openalex.org/
```
Network accessline 699
```
Docs: https://docs.openalex.org/
```

Network accessline 701

API_URL = "https://api.openalex.org/works"

Network accessline 701

API_URL = "https://api.openalex.org/works"

Network accessline 718

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 718

url = f"{self.API_URL}?{urllib.parse.urlencode(params)}"         req = urllib.request.Request(url, headers={

Network accessline 719

req = urllib.request.Request(url, headers={

Network accessline 719

req = urllib.request.Request(url, headers={

Network accessline 722

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 722

})         try:             with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 723

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 723

try:             with urllib.request.urlopen(req, timeout=15) as resp:                 data = json.loads(resp.read().decode("utf-8"))

Network accessline 724

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 724

with urllib.request.urlopen(req, timeout=15) as resp:

Network accessline 737

year = str(work.get("publication_year", "")) if work.get("publication_year") else ""                 doi = (work.get("doi") or "").replace("https://doi.org/", "")

Network accessline 737

year = str(work.get("publication_year", "")) if work.get("publication_year") else ""                 doi = (work.get("doi") or "").replace("https://doi.org/", "")

Network accessline 738

doi = (work.get("doi") or "").replace("https://doi.org/", "")

Network accessline 738

doi = (work.get("doi") or "").replace("https://doi.org/", "")

Network accessline 739

doi_url = f"https://doi.org/{doi}" if doi else ""

Network accessline 739

doi_url = f"https://doi.org/{doi}" if doi else ""

Access to secretsline 768
```
[Credential-related source omitted]
```
Access to secretsline 768
```
[Credential-related source omitted]
```
Access to secretsline 769
```
[Credential-related source omitted]
```
Access to secretsline 769
```
[Credential-related source omitted]
```

Network accessline 773

ESEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"

Network accessline 773

ESEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"

Network accessline 774

EFETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"

Network accessline 774

EFETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"

Access to secretsline 777
```
[Credential-related source omitted]
```
Access to secretsline 777
```
[Credential-related source omitted]
```
Access to secretsline 786
```
[Credential-related source omitted]
```
Access to secretsline 786
```
[Credential-related source omitted]
```
Access to secretsline 787
```
[Credential-related source omitted]
```
Access to secretsline 787
```
[Credential-related source omitted]
```
Network accessline 789
```
req = urllib.request.Request(
```
Network accessline 789
```
req = urllib.request.Request(
```

Network accessline 791

headers={"User-Agent": f"{self.tool}/1.0"},         )         with urllib.request.urlopen(req, timeout=timeout) as resp:

Network accessline 791

headers={"User-Agent": f"{self.tool}/1.0"},         )         with urllib.request.urlopen(req, timeout=timeout) as resp:

Network accessline 792

)         with urllib.request.urlopen(req, timeout=timeout) as resp:             return resp.read()

Network accessline 792

)         with urllib.request.urlopen(req, timeout=timeout) as resp:             return resp.read()

Network accessline 793

with urllib.request.urlopen(req, timeout=timeout) as resp:

Network accessline 793

with urllib.request.urlopen(req, timeout=timeout) as resp:

Network accessline 874

"year": year,             "journal": journal,             "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",

Network accessline 874

"year": year,             "journal": journal,             "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",

Network accessline 875

"journal": journal,             "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",             "doi": doi,

Network accessline 875

"journal": journal,             "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",             "doi": doi,

Network accessline 876

"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",

Network accessline 876

"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/",

Access to secretsline 885
```
[Credential-related source omitted]
```
Access to secretsline 885
```
[Credential-related source omitted]
```
Access to secretsline 886
```
[Credential-related source omitted]
```
Access to secretsline 886
```
[Credential-related source omitted]
```

Network accessline 1016

results.extend(wos.search(args.query, args.limit))         elif args.source == 'wos':             print("  WOS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://developer.clarivate.com/apis/wos-starter")

Network accessline 1016

results.extend(wos.search(args.query, args.limit))         elif args.source == 'wos':             print("  WOS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://developer.clarivate.com/apis/wos-starter")

Network accessline 1017

elif args.source == 'wos':             print("  WOS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://developer.clarivate.com/apis/wos-starter")             return

Network accessline 1017

elif args.source == 'wos':             print("  WOS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://developer.clarivate.com/apis/wos-starter")             return

Network accessline 1018
```
[Credential-related source omitted]
```
Network accessline 1018
```
[Credential-related source omitted]
```
Access to secretsline 1018
```
[Credential-related source omitted]
```
Access to secretsline 1018
```
[Credential-related source omitted]
```
Access to secretsline 1021
```
[Credential-related source omitted]
```
Access to secretsline 1021
```
[Credential-related source omitted]
```

Network accessline 1028

time.sleep(RATE_LIMIT_DELAY)         elif args.source in ('springer', 'springer_meta'):             print("  SPRINGER_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.springernature.com/")

Network accessline 1028

time.sleep(RATE_LIMIT_DELAY)         elif args.source in ('springer', 'springer_meta'):             print("  SPRINGER_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.springernature.com/")

Network accessline 1029

elif args.source in ('springer', 'springer_meta'):             print("  SPRINGER_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.springernature.com/")             return

Network accessline 1029

elif args.source in ('springer', 'springer_meta'):             print("  SPRINGER_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.springernature.com/")             return

Network accessline 1030
```
[Credential-related source omitted]
```
Network accessline 1030
```
[Credential-related source omitted]
```
Access to secretsline 1030
```
[Credential-related source omitted]
```
Access to secretsline 1030
```
[Credential-related source omitted]
```
Access to secretsline 1033
```
[Credential-related source omitted]
```
Access to secretsline 1033
```
[Credential-related source omitted]
```

Network accessline 1040

time.sleep(RATE_LIMIT_DELAY)         elif args.source == 'springer_oa':             print("  SPRINGER_OA_API_KEY / SPRINGER_API_KEY is not configured. Get a free key at: https://dev.springernature.com/")

Network accessline 1040

time.sleep(RATE_LIMIT_DELAY)         elif args.source == 'springer_oa':             print("  SPRINGER_OA_API_KEY / SPRINGER_API_KEY is not configured. Get a free key at: https://dev.springernature.com/")

Network accessline 1041

elif args.source == 'springer_oa':             print("  SPRINGER_OA_API_KEY / SPRINGER_API_KEY is not configured. Get a free key at: https://dev.springernature.com/")             return

Network accessline 1041

elif args.source == 'springer_oa':             print("  SPRINGER_OA_API_KEY / SPRINGER_API_KEY is not configured. Get a free key at: https://dev.springernature.com/")             return

Network accessline 1042
```
[Credential-related source omitted]
```
Network accessline 1042
```
[Credential-related source omitted]
```
Access to secretsline 1042
```
[Credential-related source omitted]
```
Access to secretsline 1042
```
[Credential-related source omitted]
```

Network accessline 1052

time.sleep(RATE_LIMIT_DELAY)         elif args.source == 'scopus':             print("  SCOPUS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.elsevier.com/")

Network accessline 1052

time.sleep(RATE_LIMIT_DELAY)         elif args.source == 'scopus':             print("  SCOPUS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.elsevier.com/")

Network accessline 1053

elif args.source == 'scopus':             print("  SCOPUS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.elsevier.com/")             return

Network accessline 1053

elif args.source == 'scopus':             print("  SCOPUS_API_KEY is not configured in ~/.aut_sci_write/.env. Get a free key at: https://dev.elsevier.com/")             return

Network accessline 1054
```
[Credential-related source omitted]
```
Network accessline 1054
```
[Credential-related source omitted]
```
Access to secretsline 1054
```
[Credential-related source omitted]
```
Access to secretsline 1054
```
[Credential-related source omitted]
```
Access to secretsline 1057
```
[Credential-related source omitted]
```
Access to secretsline 1057
```
[Credential-related source omitted]
```

`skills/sci-zotero/.gitignore`

Access to secretsline 1
```
[Credential-related source omitted]
```
Access to secretsline 1
```
[Credential-related source omitted]
```

`skills/sci-zotero/SKILL.md`

Access to secretsline 31
```
[Credential-related source omitted]
```
Access to secretsline 31
```
[Credential-related source omitted]
```

`skills/sci-zotero/zotero.py`

Executable scriptline 1
```
#!/usr/bin/env python3
```
Executable scriptline 1
```
#!/usr/bin/env python3
```
Access to secretsline 4
```
[Credential-related source omitted]
```
Access to secretsline 4
```
[Credential-related source omitted]
```
Access to secretsline 5
```
[Credential-related source omitted]
```
Access to secretsline 5
```
[Credential-related source omitted]
```
Network accessline 42
```
API_BASE = "https://api.zotero.org"
```
Network accessline 42
```
API_BASE = "https://api.zotero.org"
```
Access to secretsline 77
```
[Credential-related source omitted]
```
Access to secretsline 77
```
[Credential-related source omitted]
```
Access to secretsline 97
```
[Credential-related source omitted]
```
Access to secretsline 97
```
[Credential-related source omitted]
```
Access to secretsline 101
```
[Credential-related source omitted]
```
Access to secretsline 101
```
[Credential-related source omitted]
```
Access to secretsline 105
```
[Credential-related source omitted]
```
Access to secretsline 105
```
[Credential-related source omitted]
```
Access to secretsline 106
```
[Credential-related source omitted]
```
Access to secretsline 106
```
[Credential-related source omitted]
```

Network accessline 107

raise ZoteroError(             "ZOTERO_API_KEY is not configured in ~/.aut_sci_write/.env\n"             "Create a key at https://www.zotero.org/settings/keys/new"

Network accessline 107

raise ZoteroError(             "ZOTERO_API_KEY is not configured in ~/.aut_sci_write/.env\n"             "Create a key at https://www.zotero.org/settings/keys/new"

Network accessline 108
```
[Credential-related source omitted]
```
Network accessline 108
```
[Credential-related source omitted]
```
Access to secretsline 108
```
[Credential-related source omitted]
```
Access to secretsline 108
```
[Credential-related source omitted]
```

Network accessline 109

"Create a key at https://www.zotero.org/settings/keys/new"

Network accessline 109

"Create a key at https://www.zotero.org/settings/keys/new"

Access to secretsline 118
```
[Credential-related source omitted]
```
Access to secretsline 118
```
[Credential-related source omitted]
```
Access to secretsline 127
```
[Credential-related source omitted]
```
Access to secretsline 127
```
[Credential-related source omitted]
```
Access to secretsline 139
```
[Credential-related source omitted]
```
Access to secretsline 139
```
[Credential-related source omitted]
```

Network accessline 156

for attempt in range(_MAX_RETRIES + 1):         req = urllib.request.Request(url, data=body, headers=headers, method=method)

Network accessline 156

for attempt in range(_MAX_RETRIES + 1):         req = urllib.request.Request(url, data=body, headers=headers, method=method)

Network accessline 157

req = urllib.request.Request(url, data=body, headers=headers, method=method)

Network accessline 157

req = urllib.request.Request(url, data=body, headers=headers, method=method)

Network accessline 158

try:             with urllib.request.urlopen(req, timeout=30) as resp:                 resp_body = resp.read().decode("utf-8")

Network accessline 158

try:             with urllib.request.urlopen(req, timeout=30) as resp:                 resp_body = resp.read().decode("utf-8")

Network accessline 159

with urllib.request.urlopen(req, timeout=30) as resp:

Network accessline 159

with urllib.request.urlopen(req, timeout=30) as resp:

Access to secretsline 179
```
[Credential-related source omitted]
```
Access to secretsline 179
```
[Credential-related source omitted]
```
Access to secretsline 181
```
[Credential-related source omitted]
```
Access to secretsline 181
```
[Credential-related source omitted]
```
Access to secretsline 185
```
[Credential-related source omitted]
```
Access to secretsline 185
```
[Credential-related source omitted]
```
Access to secretsline 193
```
[Credential-related source omitted]
```
Access to secretsline 193
```
[Credential-related source omitted]
```
Access to secretsline 227
```
[Credential-related source omitted]
```
Access to secretsline 227
```
[Credential-related source omitted]
```
Access to secretsline 230
```
[Credential-related source omitted]
```
Access to secretsline 230
```
[Credential-related source omitted]
```
Access to secretsline 238
```
[Credential-related source omitted]
```
Access to secretsline 238
```
[Credential-related source omitted]
```
Access to secretsline 240
```
[Credential-related source omitted]
```
Access to secretsline 240
```
[Credential-related source omitted]
```
Access to secretsline 249
```
[Credential-related source omitted]
```
Access to secretsline 249
```
[Credential-related source omitted]
```
Access to secretsline 250
```
[Credential-related source omitted]
```
Access to secretsline 250
```
[Credential-related source omitted]
```
Access to secretsline 255
```
[Credential-related source omitted]
```
Access to secretsline 255
```
[Credential-related source omitted]
```
Access to secretsline 257
```
[Credential-related source omitted]
```
Access to secretsline 257
```
[Credential-related source omitted]
```
Access to secretsline 269
```
[Credential-related source omitted]
```
Access to secretsline 269
```
[Credential-related source omitted]
```
Access to secretsline 270
```
[Credential-related source omitted]
```
Access to secretsline 270
```
[Credential-related source omitted]
```
Access to secretsline 279
```
[Credential-related source omitted]
```
Access to secretsline 279
```
[Credential-related source omitted]
```
Access to secretsline 280
```
[Credential-related source omitted]
```
Access to secretsline 280
```
[Credential-related source omitted]
```

Network accessline 294

req = urllib.request.Request(url, headers={"User-Agent": "zotero-cli/1.0"})

Network accessline 294

req = urllib.request.Request(url, headers={"User-Agent": "zotero-cli/1.0"})

Network accessline 295

try:         with urllib.request.urlopen(req, timeout=30) as resp:             return json.loads(resp.read().decode("utf-8"))

Network accessline 295

try:         with urllib.request.urlopen(req, timeout=30) as resp:             return json.loads(resp.read().decode("utf-8"))

Network accessline 296

with urllib.request.urlopen(req, timeout=30) as resp:

Network accessline 296

with urllib.request.urlopen(req, timeout=30) as resp:

Access to secretsline 304
```
[Credential-related source omitted]
```
Access to secretsline 304
```
[Credential-related source omitted]
```
Access to secretsline 306
```
[Credential-related source omitted]
```
Access to secretsline 306
```
[Credential-related source omitted]
```
Network accessline 311
```
[Credential-related source omitted]
```
Network accessline 311
```
[Credential-related source omitted]
```
Access to secretsline 311
```
[Credential-related source omitted]
```
Access to secretsline 311
```
[Credential-related source omitted]
```

Network accessline 312

doi = args.identifier.strip()     crossref_url = f"https://api.crossref.org/works/{urllib.parse.quote(doi, safe='')}"     data = _external_get_json(crossref_url)

Network accessline 312

doi = args.identifier.strip()     crossref_url = f"https://api.crossref.org/works/{urllib.parse.quote(doi, safe='')}"     data = _external_get_json(crossref_url)

Network accessline 313

crossref_url = f"https://api.crossref.org/works/{urllib.parse.quote(doi, safe='')}"

Network accessline 313

crossref_url = f"https://api.crossref.org/works/{urllib.parse.quote(doi, safe='')}"

Access to secretsline 316
```
[Credential-related source omitted]
```
Access to secretsline 316
```
[Credential-related source omitted]
```
Access to secretsline 334
```
[Credential-related source omitted]
```
Access to secretsline 334
```
[Credential-related source omitted]
```
Access to secretsline 341
```
[Credential-related source omitted]
```
Access to secretsline 341
```
[Credential-related source omitted]
```

Network accessline 342

isbn = re.sub(r"[^0-9X]", "", args.identifier.upper())     ol_url = (         f"https://openlibrary.org/api/books"

Network accessline 342

isbn = re.sub(r"[^0-9X]", "", args.identifier.upper())     ol_url = (         f"https://openlibrary.org/api/books"

Network accessline 343

ol_url = (         f"https://openlibrary.org/api/books"         f"?bibkeys=ISBN:{isbn}&format=json&jscmd=data"

Network accessline 343

ol_url = (         f"https://openlibrary.org/api/books"         f"?bibkeys=ISBN:{isbn}&format=json&jscmd=data"

Network accessline 344
```
f"https://openlibrary.org/api/books"
```
Network accessline 344
```
f"https://openlibrary.org/api/books"
```
Access to secretsline 351
```
[Credential-related source omitted]
```
Access to secretsline 351
```
[Credential-related source omitted]
```
Access to secretsline 367
```
[Credential-related source omitted]
```
Access to secretsline 367
```
[Credential-related source omitted]
```
Access to secretsline 374
```
[Credential-related source omitted]
```
Access to secretsline 374
```
[Credential-related source omitted]
```

Network accessline 375

pmid = args.identifier.strip()     esummary_url = (         f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"

Network accessline 375

pmid = args.identifier.strip()     esummary_url = (         f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"

Network accessline 376

esummary_url = (         f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"         f"?db=pubmed&id={urllib.parse.quote(pmid, safe='')}&retmode=json"

Network accessline 376

esummary_url = (         f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"         f"?db=pubmed&id={urllib.parse.quote(pmid, safe='')}&retmode=json"

Network accessline 377

f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"         f"?db=pubmed&id={urllib.parse.quote(pmid, safe='')}&retmode=json"     )

Network accessline 377

f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"         f"?db=pubmed&id={urllib.parse.quote(pmid, safe='')}&retmode=json"     )

Access to secretsline 384
```
[Credential-related source omitted]
```
Access to secretsline 384
```
[Credential-related source omitted]
```
Access to secretsline 406
```
[Credential-related source omitted]
```
Access to secretsline 406
```
[Credential-related source omitted]
```
Access to secretsline 413
```
[Credential-related source omitted]
```
Access to secretsline 413
```
[Credential-related source omitted]
```
Access to secretsline 415
```
[Credential-related source omitted]
```
Access to secretsline 415
```
[Credential-related source omitted]
```
Access to secretsline 422
```
[Credential-related source omitted]
```
Access to secretsline 422
```
[Credential-related source omitted]
```
Access to secretsline 440
```
[Credential-related source omitted]
```
Access to secretsline 440
```
[Credential-related source omitted]
```
Access to secretsline 447
```
[Credential-related source omitted]
```
Access to secretsline 447
```
[Credential-related source omitted]
```

Network accessline 453

for citation in citations:         query = urllib.parse.quote(citation[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 453

for citation in citations:         query = urllib.parse.quote(citation[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 454

query = urllib.parse.quote(citation[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"         try:

Network accessline 454

query = urllib.parse.quote(citation[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"         try:

Network accessline 455

cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 455

cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Access to secretsline 481
```
[Credential-related source omitted]
```
Access to secretsline 481
```
[Credential-related source omitted]
```
Access to secretsline 483
```
[Credential-related source omitted]
```
Access to secretsline 483
```
[Credential-related source omitted]
```

Network accessline 497

continue         query = urllib.parse.quote(f"{title} {author}"[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 497

continue         query = urllib.parse.quote(f"{title} {author}"[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 498

query = urllib.parse.quote(f"{title} {author}"[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"         try:

Network accessline 498

query = urllib.parse.quote(f"{title} {author}"[:200])         cr_url = f"https://api.crossref.org/works?query={query}&rows=1"         try:

Network accessline 499

cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Network accessline 499

cr_url = f"https://api.crossref.org/works?query={query}&rows=1"

Access to secretsline 513
```
[Credential-related source omitted]
```
Access to secretsline 513
```
[Credential-related source omitted]
```

Network accessline 526

req = urllib.request.Request(url, headers={"User-Agent": "zotero-cli/1.0"})

Network accessline 526

req = urllib.request.Request(url, headers={"User-Agent": "zotero-cli/1.0"})

Network accessline 528

os.close(tmp_fd)     try:         with urllib.request.urlopen(req, timeout=60) as resp:

Network accessline 528

os.close(tmp_fd)     try:         with urllib.request.urlopen(req, timeout=60) as resp:

Network accessline 529

try:         with urllib.request.urlopen(req, timeout=60) as resp:             content_type = (resp.headers.get("Content-Type") or "").lower()

Network accessline 529

try:         with urllib.request.urlopen(req, timeout=60) as resp:             content_type = (resp.headers.get("Content-Type") or "").lower()

Network accessline 530

with urllib.request.urlopen(req, timeout=60) as resp:

Network accessline 530

with urllib.request.urlopen(req, timeout=60) as resp:

Access to secretsline 561
```
[Credential-related source omitted]
```
Access to secretsline 561
```
[Credential-related source omitted]
```
Access to secretsline 568
```
[Credential-related source omitted]
```
Access to secretsline 568
```
[Credential-related source omitted]
```
Access to secretsline 571
```
[Credential-related source omitted]
```
Access to secretsline 571
```
[Credential-related source omitted]
```
Access to secretsline 577
```
[Credential-related source omitted]
```
Access to secretsline 577
```
[Credential-related source omitted]
```

Network accessline 592

doi = d.get("DOI", "")         unpaywall_url = (             f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"

Network accessline 592

doi = d.get("DOI", "")         unpaywall_url = (             f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"

Network accessline 593

unpaywall_url = (             f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"             f"?email={urllib.parse.quote(unpaywall_email, safe='')}"

Network accessline 593

unpaywall_url = (             f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"             f"?email={urllib.parse.quote(unpaywall_email, safe='')}"

Network accessline 594

f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"

Network accessline 594

f"https://api.unpaywall.org/v2/{urllib.parse.quote(doi, safe='')}"

Access to secretsline 615
```
[Credential-related source omitted]
```
Access to secretsline 615
```
[Credential-related source omitted]
```
Access to secretsline 621
```
[Credential-related source omitted]
```
Access to secretsline 621
```
[Credential-related source omitted]
```
Access to secretsline 638
```
[Credential-related source omitted]
```
Access to secretsline 638
```
[Credential-related source omitted]
```

Network accessline 660

suffix_bytes = f"\r\n--{boundary}--\r\n".encode()         upload_body = prefix_bytes + pdf_bytes + suffix_bytes         upload_req = urllib.request.Request(

Network accessline 660

suffix_bytes = f"\r\n--{boundary}--\r\n".encode()         upload_body = prefix_bytes + pdf_bytes + suffix_bytes         upload_req = urllib.request.Request(

Network accessline 661

upload_body = prefix_bytes + pdf_bytes + suffix_bytes         upload_req = urllib.request.Request(             upload_url,

Network accessline 661

upload_body = prefix_bytes + pdf_bytes + suffix_bytes         upload_req = urllib.request.Request(             upload_url,

Network accessline 662
```
upload_req = urllib.request.Request(
```
Network accessline 662
```
upload_req = urllib.request.Request(
```

Network accessline 667

)         try:             with urllib.request.urlopen(upload_req, timeout=120):

Network accessline 667

)         try:             with urllib.request.urlopen(upload_req, timeout=120):

Network accessline 668

try:             with urllib.request.urlopen(upload_req, timeout=120):                 pass

Network accessline 668

try:             with urllib.request.urlopen(upload_req, timeout=120):                 pass

Network accessline 669

with urllib.request.urlopen(upload_req, timeout=120):

Network accessline 669

with urllib.request.urlopen(upload_req, timeout=120):

Access to secretsline 678
```
[Credential-related source omitted]
```
Access to secretsline 678
```
[Credential-related source omitted]
```

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: 37 facts

Contacts export.arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/arxiv_download.py:29High confidence
Contacts arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/arxiv_download.py:30High confidence
Contacts www.w3.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/arxiv_download.py:93High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/elsevier_download.py:143High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/ieee_download.py:208High confidence
Contacts eutils.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-download/pubmed_download.py:28High confidence
Contacts www.ebi.ac.uk, which SKILL.md, the README and the plugin manifest do not mentionsci-download/pubmed_download.py:29High confidence
Contacts europepmc.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/pubmed_download.py:137High confidence
Contacts www.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-download/pubmed_download.py:144High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/pubmed_download.py:208High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/sci_download.py:41High confidence
Contacts arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/sci_download.py:48High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/semantic_scholar_download.py:169High confidence
Contacts link.springer.com, which SKILL.md, the README and the plugin manifest do not mentionsci-download/springer_download.py:136High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/springer_download.py:165High confidence
Contacts api.unpaywall.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/unpaywall_download.py:28High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-download/unpaywall_download.py:140High confidence
Contacts eutils.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/fulltext.py:16High confidence
Contacts www.ebi.ac.uk, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/fulltext.py:17High confidence
Contacts europepmc.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/fulltext.py:227High confidence
Contacts arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/fulltext.py:230High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/identify.py:25High confidence
Contacts dx.doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/identify.py:27High confidence
Contacts www.w3.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/jats.py:19High confidence
Contacts api.crossref.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:18High confidence
Contacts api.openalex.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:19High confidence
Contacts eutils.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:21High confidence
Contacts api.unpaywall.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:22High confidence
Contacts export.arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:23High confidence
Contacts orcid.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:285High confidence
Contacts doi.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:316High confidence
Contacts www.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:512High confidence
Contacts www.w3.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:645High confidence
Contacts arxiv.org, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:645High confidence
Contacts www.webofscience.com, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:731High confidence
Contacts pubmed.ncbi.nlm.nih.gov, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/metadata.py:919High confidence
Contacts pmc-oa-opendata.s3.amazonaws.com, which SKILL.md, the README and the plugin manifest do not mentionsci-extract/harvester/oa_package.py:27High confidence

Signal confidence: 463 facts

Access to secrets in code of the SKILL.md: a variable, placeholder or call, not a stored valuesci-download/SKILL.md:108Low confidence
Access to secrets in code of the SKILL.md: a variable, placeholder or call, not a stored valuesci-download/SKILL.md:109Low confidence
Access to secrets in code of the SKILL.md: a variable, placeholder or call, not a stored valuesci-download/SKILL.md:110Low confidence
Network access in prose of the SKILL.mdsci-download/SKILL.md:116Low confidence
Network access in prose of the SKILL.mdsci-download/SKILL.md:117Low confidence
Network access in prose of the SKILL.mdsci-download/SKILL.md:118Low confidence
Network access in prose of the SKILL.mdsci-download/SKILL.md:119Low confidence
Network access in prose of the SKILL.mdsci-download/SKILL.md:120Low confidence
Network access in code of the SKILL.mdsci-download/SKILL.md:129High confidence
Network access in code of the SKILL.mdsci-download/SKILL.md:131High confidence
Executable script in prose of a file that runssci-download/arxiv_download.py:1Low confidence
Network access in code of a file that runssci-download/arxiv_download.py:28High confidence
Network access in code of a file that runssci-download/arxiv_download.py:29High confidence
Network access in code of a file that runssci-download/arxiv_download.py:30High confidence
Network access in code of a file that runssci-download/arxiv_download.py:38High confidence
Network access in code of a file that runssci-download/arxiv_download.py:39High confidence
Network access in code of a file that runssci-download/arxiv_download.py:48High confidence
Network access in code of a file that runssci-download/arxiv_download.py:49High confidence
Network access in code of a file that runssci-download/arxiv_download.py:50High confidence
Network access in code of a file that runssci-download/arxiv_download.py:92High confidence
Network access in code of a file that runssci-download/arxiv_download.py:93High confidence
Executable script in prose of a file that runssci-download/cnki_download.py:1Low confidence
Network access in prose of a file that runssci-download/cnki_download.py:10Low confidence
Network access in prose of a file that runssci-download/cnki_download.py:11Low confidence
Network access in prose of a file that runssci-download/cnki_download.py:12Low confidence
Access to secrets in prose of a file that runs: a variable, placeholder or call, not a stored valuesci-download/cnki_download.py:17Low confidence
Network access in code of a file that runssci-download/cnki_download.py:40High confidence
Network access in code of a file that runssci-download/cnki_download.py:62High confidence
Network access in code of a file that runssci-download/cnki_download.py:63High confidence
Network access in code of a file that runssci-download/cnki_download.py:119High confidence
Network access in code of a file that runssci-download/cnki_download.py:120High confidence
Network access in code of a file that runssci-download/cnki_download.py:123High confidence
Network access in code of a file that runssci-download/cnki_download.py:124High confidence
Possible obfuscation in code of a file that runssci-download/cnki_download.py:477High confidence
Network access in code of a file that runssci-download/cnki_download.py:535High confidence
Network access in code of a file that runssci-download/cnki_download.py:536High confidence
Network access in code of a file that runssci-download/cnki_download.py:537High confidence
Network access in code of a file that runssci-download/cnki_download.py:538High confidence
Access to secrets in code of a file that runs: a variable, placeholder or call, not a stored valuesci-download/cnki_download.py:540Low confidence
Access to secrets in code of a file that runs: a variable, placeholder or call, not a stored valuesci-download/cnki_download.py:549Low confidence
Executable script in prose of a file that runssci-download/config.py:1Low confidence
Access to secrets in prose of a file that runssci-download/config.py:3Low confidence
Access to secrets in code of a file that runs: a variable, placeholder or call, not a stored valuesci-download/config.py:18Low confidence
Access to secrets in code of a file that runssci-download/config.py:34High confidence
Access to secrets in code of a file that runssci-download/config.py:37High confidence
Access to secrets in code of a file that runssci-download/config.py:39High confidence
Access to secrets in code of a file that runssci-download/config.py:40High confidence
Access to secrets in code of a file that runssci-download/config.py:42High confidence
Access to secrets in code of a file that runssci-download/config.py:43High confidence
Network access in a comment of a file that runssci-download/config.py:47Low confidence

and 413 more

Only the first 500 facts are listed.

Works with

Agent compatibility, from the files in this repository
Agent	Status	Evidence	Install to
Claude Code	Native	Manifest .claude-plugin/marketplace.json	`.claude/skills/<skill-name>/`
Codex	Compatible	Standard SKILL.md skills/sci-download/SKILL.md	`.agents/skills/<skill-name>/`
Cursor	Compatible	Standard SKILL.md skills/sci-download/SKILL.md	`.cursor/skills/<skill-name>/`
Gemini CLI	Compatible	Standard SKILL.md skills/sci-download/SKILL.md	`.gemini/skills/<skill-name>/`
GitHub Copilot	Compatible	Standard SKILL.md skills/sci-download/SKILL.md	`.github/skills/<skill-name>/`
OpenCode	Compatible	Standard SKILL.md skills/sci-download/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.

ShZhao27208/Aut_Sci_Write

History

skills/sci-download/SKILL.md

skills/sci-extract/SKILL.md

skills/sci-figure/SKILL.md

skills/sci-html/SKILL.md

skills/sci-polish/SKILL.md

skills/sci-ppt/SKILL.md

skills/sci-review/SKILL.md

skills/sci-search/SKILL.md

skills/sci-zotero/SKILL.md

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Individual skills in this repository

How it works

sci-download

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-extract

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-figure

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-html

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-polish

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-ppt

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-review

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-search

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

sci-zotero

Frontmatter

SKILL.md

Reference documents

The playbook

Scripts executed separately

Files

Skills included

`skills/sci-download/SKILL.md`

`skills/sci-extract/SKILL.md`

`skills/sci-figure/SKILL.md`

`skills/sci-html/SKILL.md`

`skills/sci-polish/SKILL.md`

`skills/sci-ppt/SKILL.md`

`skills/sci-review/SKILL.md`

`skills/sci-search/SKILL.md`

`skills/sci-zotero/SKILL.md`

`.claude-plugin/marketplace.json`

`skills/sci-download/SKILL.md`

`skills/sci-download/arxiv_download.py`

`skills/sci-download/cnki_download.py`

`skills/sci-download/config.py`

`skills/sci-download/elsevier_download.py`

`skills/sci-download/ieee_download.py`

`skills/sci-download/pubmed_download.py`

`skills/sci-download/sci_download.py`

`skills/sci-download/semantic_scholar_download.py`

`skills/sci-download/springer_download.py`

`skills/sci-download/unpaywall_download.py`

`skills/sci-download/webvpn_crypto.py`

`skills/sci-extract/README.md`

`skills/sci-extract/extract_core_insights.py`

`skills/sci-extract/harvest_paper.py`

`skills/sci-extract/harvester/init.py`

`skills/sci-extract/harvester/env.py`

`skills/sci-extract/harvester/figures.py`

`skills/sci-extract/harvester/fulltext.py`

`skills/sci-extract/harvester/http.py`

`skills/sci-extract/harvester/identify.py`

`skills/sci-extract/harvester/jats.py`

`skills/sci-extract/harvester/metadata.py`

`skills/sci-extract/harvester/oa_package.py`

`skills/sci-extract/harvester/render.py`

`skills/sci-figure/LICENSE`

`skills/sci-figure/README.md`

`skills/sci-figure/README_CN.md`

`skills/sci-figure/SKILL.md`

`skills/sci-figure/sci_figure.egg-info/PKG-INFO`

`skills/sci-figure/sci_figure/init.py`

`skills/sci-figure/sci_figure/annotator.py`

`skills/sci-figure/sci_figure/caption_detector.py`

`skills/sci-figure/sci_figure/cli.py`

`skills/sci-figure/sci_figure/column_detector.py`

`skills/sci-figure/sci_figure/exceptions.py`

`skills/sci-figure/sci_figure/figure_extractor.py`

`skills/sci-figure/sci_figure/image_processor.py`

`skills/sci-figure/sci_figure/native_extractor.py`

`skills/sci-figure/sci_figure/pdf_parser.py`

`skills/sci-figure/sci_figure/region_detector.py`

`skills/sci-figure/sci_figure/subfigure_splitter.py`

`skills/sci-figure/sci_figure/utils.py`

`skills/sci-figure/scripts/extract_figure.py`

`skills/sci-figure/setup.py`

`skills/sci-figure/tests/init.py`

`skills/sci-figure/tests/test_caption_dedup.py`

`skills/sci-html/conftest.py`

`skills/sci-html/scripts/generate_html_deck.py`

`skills/sci-html/src/sci_html/init.py`

`skills/sci-html/src/sci_html/cli.py`

`skills/sci-html/src/sci_html/integrations/init.py`

`skills/sci-html/src/sci_html/integrations/extract/init.py`

`skills/sci-html/src/sci_html/integrations/extract/core_insights.py`

`skills/sci-html/src/sci_html/models.py`

`skills/sci-html/src/sci_html/paper_pipeline.py`

`skills/sci-html/src/sci_html/parser.py`

`skills/sci-html/src/sci_html/renderer.py`

`skills/sci-html/templates/deck.js`

`skills/sci-html/tests/_path.py`

`skills/sci-html/tests/test_paper_pipeline.py`

`skills/sci-html/tests/test_parser.py`

`skills/sci-html/tests/test_renderer.py`

`skills/sci-polish/scripts/ai_score_estimator.py`

`skills/sci-polish/scripts/tier1_words.py`

`skills/sci-polish/scripts/validate_polish_output.py`

`skills/sci-ppt/.gitignore`