repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
graphrag | unified-search-app/app/knowledge_loader/data_sources/__init__.py | .py | # Copyright (c) 2024 Microsoft Corporation.
# Licensed under the MIT License
"""Data sources module."""
| 5 | 105 |
graphrag | unified-search-app/app/knowledge_loader/data_sources/typing.py | .py | # Copyright (c) 2024 Microsoft Corporation.
# Licensed under the MIT License
"""Data sources typing module."""
from abc import ABC, abstractmethod
from dataclasses import dataclass
from enum import Enum
import pandas as pd
from graphrag.config.models.graph_rag_config import GraphRagConfig
class WriteMode(Enum):
... | 75 | 1,927 |
graphrag | unified-search-app/app/knowledge_loader/data_sources/blob_source.py | .py | # Copyright (c) 2024 Microsoft Corporation.
# Licensed under the MIT License
"""Blob source module."""
import io
import logging
import os
from io import BytesIO
import pandas as pd
import streamlit as st
import yaml
from azure.identity import DefaultAzureCredential
from azure.storage.blob import BlobServiceClient, C... | 126 | 4,107 |
graphrag | unified-search-app/app/knowledge_loader/data_sources/loader.py | .py | # Copyright (c) 2024 Microsoft Corporation.
# Licensed under the MIT License
"""Loader module."""
import json
import logging
import os
from knowledge_loader.data_sources.blob_source import (
BlobDatasource,
load_blob_file,
load_blob_prompt_config,
)
from knowledge_loader.data_sources.default import (
... | 79 | 2,588 |
graphrag | unified-search-app/app/knowledge_loader/data_sources/local_source.py | .py | # Copyright (c) 2024 Microsoft Corporation.
# Licensed under the MIT License
"""Local source module."""
import logging
import os
from pathlib import Path
import pandas as pd
from graphrag.config.load_config import load_config
from graphrag.config.models.graph_rag_config import GraphRagConfig
from knowledge_loader.da... | 72 | 2,215 |
nature-skills | scripts/validate-readme-mirror.py | .py | #!/usr/bin/env python3
"""Validate Chinese/English README mirror consistency for Nature skills.
Checks every skill README pair for:
- required README.md / README_EN.md files
- matching heading counts
- mirrored language-switch links
- matching top-level skill names / titles
- a shared "nature-shared" note that is cons... | 90 | 2,968 |
nature-skills | scripts/update-reference-tocs.py | .py | #!/usr/bin/env python3
"""Insert compact H2 navigation lists into long skill reference files."""
from __future__ import annotations
import re
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
REFERENCES = ROOT / "skills"
MIN_LINES = 100
CONTENTS_RE = re.compile(r"^##\s+(?:Table of Contents|Content... | 73 | 2,238 |
nature-skills | scripts/validate-skill-metadata.py | .py | #!/usr/bin/env python3
"""Validate nature-skills metadata consistency.
Checks every top-level directory under skills/ for:
- required SKILL.md / README.md / README_EN.md / manifest.yaml files
- valid SKILL.md YAML frontmatter with only supported keys
- valid agents/openai.yaml interface metadata for every triggerable ... | 288 | 10,773 |
nature-skills | scripts/generate-star-history.py | .py | #!/usr/bin/env python3
"""Generate a static star-history SVG from GitHub stargazer timestamps."""
from __future__ import annotations
import argparse
import collections
import concurrent.futures
import datetime as dt
import html
import json
import math
import os
import pathlib
import re
import subprocess
import sys
im... | 409 | 15,728 |
nature-skills | scripts/validate-readmes.py | .py | #!/usr/bin/env python3
"""Validate repository README and skill README consistency."""
from __future__ import annotations
import re
import sys
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
SKILLS_DIR = ROOT / "skills"
TOP_READMES = (ROOT / "README.md", ROOT / "README_EN.md")
def fail(message: ... | 85 | 2,816 |
nature-skills | scripts/validate-repository.py | .py | #!/usr/bin/env python3
"""Validate repository-level Nature Skills metadata and README consistency.
This lightweight check intentionally avoids optional runtime dependencies. It is
safe to run locally and in CI to catch stale skill counts, broken README index
links, malformed JSON/TOML configs, and missing per-skill me... | 164 | 5,981 |
nature-skills | scripts/validate-workflows.py | .py | #!/usr/bin/env python3
"""Validate workflow path filters and immutable GitHub Action references.
The repository has several focused validators with `paths` filters so routine
skill edits only run the relevant CI jobs. This check keeps those filters honest:
if a workflow runs a local validation script, changes to that ... | 143 | 4,833 |
nature-skills | scripts/validate-skill-index.py | .py | #!/usr/bin/env python3
"""Validate the main README skill index against the skills/ directory.
Checks:
- the number of listed triggerable skills matches the skill index count
- every non-support skill appears in the README and README_EN tables
- every index entry points to an existing skill README
- nature-shared stays... | 97 | 3,081 |
nature-skills | scripts/tests/test_validate_workflows.py | .py | from __future__ import annotations
import importlib.util
import tempfile
import unittest
from pathlib import Path
SCRIPT = Path(__file__).resolve().parents[1] / "validate-workflows.py"
SPEC = importlib.util.spec_from_file_location("validate_workflows", SCRIPT)
assert SPEC and SPEC.loader
MODULE = importlib.util.modu... | 53 | 1,554 |
nature-skills | scripts/tests/test_validate_skill_metadata.py | .py | from __future__ import annotations
import importlib.util
import tempfile
import unittest
from pathlib import Path
SCRIPT = Path(__file__).parents[1] / "validate-skill-metadata.py"
SPEC = importlib.util.spec_from_file_location("validate_skill_metadata", SCRIPT)
assert SPEC and SPEC.loader
VALIDATOR = importlib.util.m... | 182 | 6,066 |
nature-skills | scripts/tests/test_nmi_submission_requirements.py | .py | from __future__ import annotations
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
CONTRACT = "skills/nature-shared/journal-formats/nature-machine-intelligence.md"
def read(relative: str) -> str:
return (ROOT / relative).read_text(encoding="utf-8")
def squash(text: str) ->... | 178 | 6,783 |
nature-skills | scripts/tests/test_generate_star_history.py | .py | from __future__ import annotations
import datetime as dt
import importlib.util
import unittest
from pathlib import Path
SCRIPT = Path(__file__).resolve().parents[1] / "generate-star-history.py"
SPEC = importlib.util.spec_from_file_location("generate_star_history", SCRIPT)
assert SPEC and SPEC.loader
MODULE = importl... | 87 | 2,905 |
nature-skills | scripts/tests/test_nature_submission_requirements.py | .py | from __future__ import annotations
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
def read(relative: str) -> str:
return (ROOT / relative).read_text(encoding="utf-8")
def squash(text: str) -> str:
return " ".join(text.split())
class FlagshipNatureSubmissionRequireme... | 124 | 4,813 |
nature-skills | scripts/tests/test_nature_figure_ai_graphical_abstract.py | .py | from __future__ import annotations
import json
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
REFERENCE = "skills/nature-figure/references/ai-graphical-abstract-workflow.md"
def read(relative: str) -> str:
return (ROOT / relative).read_text(encoding="utf-8")
def squash(te... | 79 | 2,867 |
nature-skills | skills/nature-shared/tests/test_check_consistency.py | .py | from __future__ import annotations
import importlib.util
import sys
import tempfile
import unittest
from pathlib import Path
SCRIPT = Path(__file__).parents[1] / "scripts" / "check_consistency.py"
SPEC = importlib.util.spec_from_file_location("check_consistency", SCRIPT)
assert SPEC and SPEC.loader
CHECKER = importl... | 64 | 2,283 |
nature-skills | skills/nature-shared/scripts/check_consistency.py | .py | #!/usr/bin/env python3
"""Find mechanically detectable consistency risks in manuscript text files."""
from __future__ import annotations
import argparse
import json
import re
from dataclasses import asdict, dataclass
from decimal import Decimal, InvalidOperation
from pathlib import Path
from typing import Iterable, S... | 274 | 8,924 |
nature-skills | skills/nature-reader/scripts/validate_reader_math.py | .py | #!/usr/bin/env python3
"""Validate equation rendering and traceability in a nature-reader bundle."""
from __future__ import annotations
import argparse
import json
import re
import sys
import tempfile
from dataclasses import asdict, dataclass
from pathlib import Path
from typing import Any
EQUATION_ID_RE = re.compi... | 459 | 17,840 |
nature-skills | skills/nature-academic-search/scripts/format-converter.py | .py | # -*- coding: utf-8 -*-
"""
Multi-source citation downloader with format conversion.
Sources: PubMed (NCBI E-utilities), CrossRef (REST API), arXiv (Atom API).
Outputs: .nbib (PubMed only), .ris, .bib, .enw.
Usage:
python format-converter.py --pmid 28344011
python format-converter.py --pmid 28344011,10645439 --for... | 523 | 19,051 |
nature-skills | skills/nature-academic-search/scripts/academic_search.py | .py | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.10"
# ///
"""No-MCP fallback search for nature-academic-search (OpenAlex, stdlib only).
This is the graceful-degradation path for agents/environments that do not mount
the MCP server (plain CLI use, skill auto-discovery, CI). It mirrors what
`nature-citation... | 431 | 20,940 |
nature-skills | skills/nature-academic-search/scripts/preflight.py | .py | # -*- coding: utf-8 -*-
"""
Pre-flight API endpoint connectivity checker.
Verifies that the 3 direct API endpoints used by format-converter.py are
reachable. Uses urllib.request.urlopen (stdlib) for consistency with the
existing codebase.
Usage:
python preflight.py # run check and print report... | 122 | 3,780 |
nature-skills | skills/nature-academic-search/scripts/converters.py | .py | # -*- coding: utf-8 -*-
"""
Format converters for academic citations.
Supports: MEDLINE/.nbib -> RIS/BibTeX/ENW, CrossRef JSON -> RIS/BibTeX/ENW, arXiv XML -> RIS/BibTeX/ENW.
Each converter accepts parsed data and returns a formatted string.
"""
import re
def ris_escape(text):
"""Strip HTML tags and normalize w... | 594 | 18,506 |
nature-skills | skills/nature-academic-search/mcp-server/academic_search_server.py | .py | """Academic search MCP server.
Unified entry point exposing multi-source search and source-specific tools for
CrossRef, PubMed, arXiv, Scopus, and ScienceDirect.
"""
from __future__ import annotations
import asyncio
import json
import re
from typing import Any
from mcp.server import FastMCP
from sources import (
... | 651 | 21,282 |
nature-skills | skills/nature-academic-search/mcp-server/sources/scopus.py | .py | """Scopus data source via pybliometrics."""
from __future__ import annotations
from typing import Any
from pybliometrics.scopus import (
AbstractRetrieval,
AffiliationRetrieval,
AuthorRetrieval,
CitationOverview,
PlumXMetrics,
SerialTitleISSN,
)
from pybliometrics.utils import URLS, get_conte... | 510 | 19,320 |
nature-skills | skills/nature-academic-search/mcp-server/sources/__init__.py | .py | """Data source modules for academic search."""
from .crossref import CrossRefSource
from .pubmed import PubMedSource
from .arxiv import ArxivSource
from .scopus import ScopusSource
from .sciencedirect import ScienceDirectSource
__all__ = [
"CrossRefSource",
"PubMedSource",
"ArxivSource",
"ScopusSource... | 16 | 352 |
nature-skills | skills/nature-academic-search/mcp-server/sources/crossref.py | .py | """CrossRef data source for academic search."""
from urllib.parse import quote
import requests
from utils.config import get_config
from utils.errors import DataSourceError
CROSSREF_API = "https://api.crossref.org"
class CrossRefSource:
"""CrossRef API wrapper with unified result format."""
SOURCE_NAME = ... | 195 | 7,005 |
nature-skills | skills/nature-academic-search/mcp-server/sources/pubmed.py | .py | """PubMed data source via NCBI E-utilities API."""
from __future__ import annotations
import time
import xml.etree.ElementTree as ET
from typing import Any
import requests
from utils.config import get_config
from utils.errors import DataSourceError
from utils.logging import setup_logging
logger = setup_logging()
... | 336 | 11,288 |
nature-skills | skills/nature-academic-search/mcp-server/sources/elsevier_common.py | .py | """Shared helpers for pybliometrics-backed Elsevier sources."""
from __future__ import annotations
from pathlib import Path
from threading import Lock
from typing import Any
from pybliometrics import init as pybliometrics_init
from pybliometrics.utils.constants import CONFIG_FILE
from utils.errors import DataSource... | 83 | 2,498 |
nature-skills | skills/nature-academic-search/mcp-server/sources/arxiv.py | .py | """arXiv data source via REST API (Atom XML feed)."""
import re
import time
import urllib.parse
import urllib.request
import xml.etree.ElementTree as ET
from datetime import datetime
from utils.config import get_config
from utils.errors import DataSourceError
from utils.logging import setup_logging
ARXIV_API_URL = "... | 353 | 11,342 |
nature-skills | skills/nature-academic-search/mcp-server/sources/sciencedirect.py | .py | """ScienceDirect data source via pybliometrics."""
from __future__ import annotations
from typing import Any
from pybliometrics.utils import URLS, get_content
from utils.errors import DataSourceError
from .elsevier_common import ensure_pybliometrics_config, year_from_date
SOURCE_NAME = "sciencedirect"
class Sc... | 217 | 7,057 |
nature-skills | skills/nature-academic-search/mcp-server/tests/test_elsevier_live.py | .py | """Live API tests for Scopus and ScienceDirect.
These tests intentionally call Elsevier APIs through the local pybliometrics
configuration. They are not mocked.
"""
from __future__ import annotations
import asyncio
import json
import os
import pytest
from sources import ScienceDirectSource, ScopusSource
pytestmar... | 89 | 2,639 |
nature-skills | skills/nature-academic-search/mcp-server/tests/test_mcp_tools.py | .py | """MCP dispatch tests for academic_search_server tools."""
from __future__ import annotations
import asyncio
import json
def _call_tool_json(tool_name: str, arguments: dict) -> dict:
from academic_search_server import mcp
content, _metadata = asyncio.run(mcp.call_tool(tool_name, arguments))
return json... | 96 | 2,699 |
nature-skills | skills/nature-academic-search/mcp-server/tests/test_sources.py | .py | """Unit tests for academic search source modules and ID detection.
All external HTTP calls are mocked -- no network access required.
"""
from __future__ import annotations
import json
import re
import xml.etree.ElementTree as ET
from unittest.mock import MagicMock, patch
import pytest
# ---------------------------... | 743 | 26,539 |
nature-skills | skills/nature-academic-search/mcp-server/utils/logging.py | .py | """Structured logging for academic search operations."""
import json
import logging
import sys
from datetime import datetime, timezone
class JSONFormatter(logging.Formatter):
def format(self, record):
log_data = {
"timestamp": datetime.now(timezone.utc).isoformat(),
"level": recor... | 33 | 1,166 |
nature-skills | skills/nature-academic-search/mcp-server/utils/errors.py | .py | """Unified error types for academic search operations."""
class AcademicSearchError(Exception):
"""Base exception for academic search operations."""
class DataSourceError(AcademicSearchError):
"""Error from a specific data source."""
def __init__(self, source: str, message: str, original_error: Excepti... | 23 | 620 |
nature-skills | skills/nature-academic-search/mcp-server/utils/__init__.py | .py | """Utility modules for academic search."""
from .config import Config, get_config
from .errors import AcademicSearchError, ConfigError, DataSourceError, TimeoutError
from .logging import setup_logging
__all__ = [
"AcademicSearchError",
"DataSourceError",
"TimeoutError",
"ConfigError",
"setup_loggi... | 16 | 359 |
nature-skills | skills/nature-academic-search/mcp-server/utils/config.py | .py | """Configuration management for academic search server."""
import os
from pathlib import Path
import toml
class Config:
def __init__(self, config_path: str | Path | None = None):
if config_path is None:
config_path = Path(__file__).parent.parent / "config.toml"
self._config = toml.lo... | 53 | 1,398 |
nature-skills | skills/nature-citation/tests/test_author_exports.py | .py | from __future__ import annotations
import argparse
import importlib.util
import sys
import tempfile
import unittest
from unittest import mock
from pathlib import Path
import xml.etree.ElementTree as ET
SCRIPT = Path(__file__).parents[1] / "scripts" / "nature_citation.py"
SPEC = importlib.util.spec_from_file_location... | 174 | 7,351 |
nature-skills | skills/nature-citation/scripts/nature_citation.py | .py | #!/usr/bin/env python3
"""
Segment manuscript text, search strict Nature/CNS-family citation candidates, and export a
reference-manager file. By default the script writes one inspectable `.ris` file.
Optional review artifacts can still be generated, but they are opt-in.
"""
from __future__ import annotations
import ... | 2,357 | 85,548 |
nature-skills | skills/nature-paper-to-patent/tests/test_validation.py | .py | import importlib.util
import json
import sys
import tempfile
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
SPEC = importlib.util.spec_from_file_location(
"validate_patent_draft", ROOT / "scripts" / "validate_patent_draft.py"
)
VALIDATOR = importlib.util.module_from_spec(SPEC)... | 157 | 6,104 |
nature-skills | skills/nature-paper-to-patent/scripts/extract_pdf_text.py | .py | #!/usr/bin/env python3
"""Extract searchable text from one PDF or a directory of PDFs."""
import argparse
from pathlib import Path
from pypdf import PdfReader
def extract(source: Path, destination: Path) -> tuple[int, int]:
reader = PdfReader(source)
pages = []
for number, page in enumerate(reader.pages... | 79 | 2,362 |
nature-skills | skills/nature-paper-to-patent/scripts/render_flowchart_svg.py | .py | #!/usr/bin/env python3
"""Render patent-style black-and-white flowchart SVGs from draft JSON."""
import argparse
import html
import json
import re
import textwrap
from pathlib import Path
STEP_PATTERN = re.compile(r"\bS\s*(\d+)\b", re.IGNORECASE)
ASCII_ID = re.compile(r"^[A-Za-z][A-Za-z0-9_-]*$")
VAGUE_FINAL_RESULT ... | 379 | 14,626 |
nature-skills | skills/nature-paper-to-patent/scripts/init_patent_project.py | .py | #!/usr/bin/env python3
"""Create an agent-neutral paper-to-patent project workspace."""
import argparse
import json
import shutil
from pathlib import Path
DIRECTORIES = (
"paper",
"supplementary/source-code",
"source-figures",
"existing-patent",
"work",
"outputs",
)
SKILL_FILES = ("SKILL.md",... | 94 | 3,179 |
nature-skills | skills/nature-paper-to-patent/scripts/render_patent_docx.py | .py | #!/usr/bin/env python3
"""Render a structured Chinese patent draft JSON file as DOCX."""
import argparse
import json
from pathlib import Path
from docx import Document
from docx.enum.section import WD_SECTION
from docx.enum.text import WD_ALIGN_PARAGRAPH
from docx.oxml import OxmlElement
from docx.oxml.ns import qn
f... | 293 | 10,589 |
nature-skills | skills/nature-paper-to-patent/scripts/build_patent_package.py | .py | #!/usr/bin/env python3
"""Build the standard split Chinese patent application package."""
import argparse
import importlib.util
import json
import shutil
import subprocess
import sys
from pathlib import Path
def run(command: list[str]) -> None:
subprocess.run(command, check=True)
def validate(data: dict) -> No... | 170 | 6,624 |
nature-skills | skills/nature-paper-to-patent/scripts/math_to_omml.py | .py | #!/usr/bin/env python3
"""Convert a LaTeX equation into editable Word Office Math (OMML)."""
from copy import deepcopy
from xml.etree import ElementTree
from docx.oxml import OxmlElement
from docx.oxml.ns import qn
MATHML_NS = "{http://www.w3.org/1998/Math/MathML}"
def _element(name: str):
return OxmlElement(... | 157 | 4,873 |
nature-skills | skills/nature-paper-to-patent/scripts/validate_patent_draft.py | .py | #!/usr/bin/env python3
"""Validate traceability, completeness, and quality gates in a patent draft."""
import argparse
import json
import re
from dataclasses import dataclass
from pathlib import Path
SOURCE_ID = re.compile(r"^[PEFC]\d{3,}$")
PLACEHOLDER = re.compile(r"\[(?:TO CONFIRM|待确认)[^\]]*\]", re.IGNORECASE)
VA... | 312 | 14,391 |
nature-skills | skills/nature-paper-to-patent/scripts/audit_claims.py | .py | #!/usr/bin/env python3
"""Run deterministic structural checks on Chinese patent claims."""
import argparse
import json
import re
from dataclasses import dataclass
from pathlib import Path
CLAIM_START = re.compile(r"(?m)^\s*(\d+)\s*[.、．]\s*")
REFERENCE = re.compile(
r"权利要求\s*(\d+)(?:\s*[-—~～至]\s*(\d+))?"
r"|权... | 156 | 5,732 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/cnipa_epub_search.py | .py | # -*- coding: utf-8 -*-
"""
国知局公布站「检索 + 解析」一步完成：内存中持有结果页 HTML，**默认不落盘**。
内部调用 ``cnipa_epub_crawler.search_epub_keyword``（等同先 ``fetch_epub_result_html`` 再
``parse_search_result_html``）。
**输出约定**（便于 Agent 抓取且不触发误判降级）：
- **stdout**：**仅一行** ``EPUB_HITS_JSON:`` + JSON 数组（UTF-8，含中文标题与 ``abstract``）。
- **stderr**：``EPUB_ME... | 171 | 5,889 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/math_render.py | .py | #!/usr/bin/env python3
r"""
将 Markdown 中的 LaTeX 公式渲染为 PNG（matplotlib mathtext），**保留 `$...$` / `\(...\)` / `$$...$$` / `\[...\]` 原文**，
图片引用写入 HTML 注释 ``<!--  -->``（预览不显示图，Word 仍嵌入）。
支持（失败时**保留原文**，不中断）：
- **块级**：``$$ ... $$``（可跨行）、单行 ``$$...$$``、``\\[ ... \\]``
- **行内**：``$...$``、``\(...\)``（渲染失败则保留原文）
用法... | 389 | 12,938 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/cnipa_epub_parse.py | .py | # -*- coding: utf-8 -*-
"""
解析 http://epub.cnipa.gov.cn/ 检索结果页 HTML，提取公布公告列表中的标题、公开号、详情链接、摘要（若有）。
与 `cnipa_epub_crawler.py` / **`cnipa_epub_search.py`**（一步检索+解析）配合：爬虫落盘 HTML 后可用本模块单独再解析；也可被其它脚本 import。
"""
from __future__ import annotations
import json
import re
import sys
from dataclasses import asdict, dataclass
fr... | 261 | 8,826 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/pptx_to_md.py | .py | #!/usr/bin/env python3
"""
将 PowerPoint（.pptx）按页导出为 Markdown，并抽取幻灯片中的嵌入图片，便于 Step 2 扫描与 Agent Read。
依赖 python-pptx（见仓库根目录 requirements.txt）。
用法:
python pptx_to_md.py --input review.pptx --output outputs/case/review.md
python pptx_to_md.py -i a.pptx -o b/out.md --media-dir b/slide_images
默认图片目录：与输出 .md 同级的「{md 文件... | 154 | 5,040 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/cnipa_epub_crawler.py | .py | # -*- coding: utf-8 -*-
"""
中国专利公布公告网站点：http://epub.cnipa.gov.cn/ —— **首页「公布公告查询」** 检索（#indexForm / #searchStr）。
须安装 **Playwright + Chromium**。若只需内存中解析、不落盘 HTML，优先用同目录 **`cnipa_epub_search.py`**；
本文件侧重 **写出结果页 HTML** 与可插拔的 ``fetch_epub_result_html`` API。
---------------------------------------------------------------... | 255 | 10,790 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/iteration_dialog_log.py | .py | #!/usr/bin/env python3
"""
在案件目录追加「交底书修订对话记录.md」一条：含记录时间（本地 + UTC）、用户说明摘要、交付文件名、合并/纠正摘要摘录。
"""
from __future__ import annotations
import argparse
import sys
from datetime import datetime, timezone
from pathlib import Path
DEFAULT_LOG = "交底书修订对话记录.md"
FILE_HEADER = """# 交底书修订对话记录
> 由 `iteration_dialog_log.py` 或 Agen... | 111 | 3,245 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/md_to_docx.py | .py | #!/usr/bin/env python3
"""
将 Markdown 转为 Word（.docx），按标题层级映射为 Word 内置「标题 1–9」样式，
便于交底书交付代理人或所内流程。
支持：ATX 标题 (#–######)、段落、**粗体**、行内 `代码`、无序/有序列表、
围栏代码块、简单 GFM 表格、引用块（>）、水平线（---）、行内图片 ````
（在最大宽、最大高约束下**等比缩放**，竖图自动缩小宽度以整图落入版面）。
**连续多行正文**（中间无空行、且非列表/标题等）时，**每一行**输出为 Word 中**独立一段**，
以便「（1）…（2）…」等分条换行；若须在同一... | 1,008 | 32,805 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/docx_to_md.py | .py | #!/usr/bin/env python3
"""
将 Word（.docx）转为 Markdown，并把内嵌图片抽取到磁盘，便于 Step 2 扫描与 Agent Read。
依赖 mammoth（见仓库根目录 requirements.txt）。
用法:
python docx_to_md.py --input design.docx --output outputs/case/design.md
python docx_to_md.py -i a.docx -o b/out.md --media-dir b/my_images
默认图片目录：与输出 .md 同级的「{md 文件名}_media/」，Markdo... | 122 | 3,835 |
nature-skills | skills/nature-paper-to-patent/scripts/disclosure/mermaid_render.py | .py | #!/usr/bin/env python3
"""
将 Markdown 中的 **mermaid** 围栏与（默认）**LaTeX 公式** 转为 PNG，再写定稿 `.md` 并默认生成 Word。
**公式**：默认先调用同目录 **`math_render.py`**（``matplotlib``；``--no-math`` 可跳过）。**Mermaid** 围栏块逐块渲染为 PNG，**保留** `` ```mermaid`` … `` ``` `` 源码，并在其后追加 HTML 注释
``<!--  -->``（预览不显示图），便于 ``md_to_docx.py`` 将图嵌入 Word（Wor... | 475 | 16,240 |
nature-skills | skills/nature-figure/tests/test_figure_safety.py | .py | from __future__ import annotations
import importlib.util
import sys
import unittest
import zlib
from pathlib import Path
SKILL = Path(__file__).parents[1]
def load_module(name: str, path: Path):
spec = importlib.util.spec_from_file_location(name, path)
assert spec and spec.loader
module = importlib.uti... | 146 | 5,130 |
nature-skills | skills/nature-figure/scripts/generate_openrouter_schematic.py | .py | #!/usr/bin/env python3
"""Generate manuscript schematic drafts with OpenRouter's Images API."""
from __future__ import annotations
import argparse
import base64
import json
import mimetypes
import os
import sys
import time
import urllib.error
import urllib.request
from pathlib import Path
from typing import Any
API... | 261 | 9,468 |
nature-skills | skills/nature-figure/scripts/validate_figure.py | .py | #!/usr/bin/env python3
"""Static preflight for publication-figure Python and R source files.
The validator is intentionally dependency-free. It checks portable source-level
requirements before the selected backend renders the figure; it does not claim
to validate statistics or replace visual inspection.
The rule stru... | 753 | 30,072 |
nature-skills | skills/nature-figure/scripts/audit_pdf_text.py | .py | #!/usr/bin/env python3
"""Audit text font sizes used by PDF content-stream ``Tf`` operators.
This dependency-free check catches reduced mathtext superscripts/subscripts and
other glyph runs that can fall below a journal font-size floor even when the
parent matplotlib ``fontsize`` is compliant. It supports plain and Fl... | 153 | 5,545 |
nature-skills | skills/nature-figure/scripts/nature_figure_backend.py | .py | #!/usr/bin/env python3
"""Read or write the user's default nature-figure plotting backend."""
from __future__ import annotations
import argparse
import json
import os
import sys
from pathlib import Path
VALID_BACKENDS = {"python", "r"}
def config_path() -> Path:
override = os.environ.get("NATURE_FIGURE_CONFIG... | 94 | 2,708 |
nature-skills | skills/nature-figure/scripts/plot_templates.py | .py | #!/usr/bin/env python3
"""Validated Python templates for five common manuscript-figure families.
Subcommands: volcano, roc, dotplot, marginal, and paired. Production runs
require a CSV input. Simulated data is available only through the explicit
--demo flag and is marked as such in the generated QA record.
The templa... | 605 | 29,524 |
nature-skills | skills/nature-figure/scripts/figure_safety.py | .py | #!/usr/bin/env python3
"""Small numerical/layout safety helpers for Python publication figures."""
from __future__ import annotations
from typing import Any
import numpy as np
def interp_monotone(target: Any, xp: Any, fp: Any) -> Any:
"""Interpolate on a strictly monotone grid without silent direction errors.
... | 51 | 2,216 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py | .py | import numpy as np
data_comparison_IEDB = {
'methods': [r'Prime-2.1', r'NetMHCpan', r'MHCnuggets', r'MHCflurry', r'DeepNeo',
r'BigMHC-EL', r'BigMHC-IM', r'BigMHC$_\text{retrained}$', r'ImmunoStruct (ours)'],
'colors': ['#CFCECE', '#F4EEAC', '#FBDFE2', '#D9B9D4', '#DAA87C', '#DDF3DE', '#AADCA9'... | 126 | 4,459 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_ImmunoStruct/plot_bars.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from raw_data import data_comparison_IEDB, data_ablation_IEDB, data_comparison_Cancer, data_ablation_Cancer
def decode_ablation(data_dict):
binary_list = data_dict['ablations']
component_str = data_dict['components']
decoded_list = []
f... | 217 | 7,707 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_ablation = {
'methods': [
r'CellSpliceNet',
r'ViT',
r'SpliceFinder',
r'Pangolin',
r'SpliceTransformer',
r'SpliceAI',
r'ESM2',
],
'color... | 110 | 3,909 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison_cross_species.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_comparison = {
'methods': [
r'CellSpliceNet',
r'Pangolin',
r'SpliceTransformer',
r'SpliceAI',
r'SpliceFinder',
r'ViT',
r'AlphaGenome',
... | 183 | 6,532 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_ablation.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_ablation = {
'methods': [
r'CellSpliceNet',
r'No Expression',
r'No Structure',
r'No ROI',
r'No Sequence',
],
'colors': ['#0F4D92', '#B4E6B4', '#AFE6E6'... | 87 | 2,964 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_ophthal_review/plot_composition.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
import seaborn as sns
DATA = {
'clinical_stage': [
'Benchmark\nEvaluation', 'Expert\nEvaluation', 'Retrospective\nClinical Validation',
'Prospective\nPilot Study', 'Full\nClinical Trial',
],
'pub_by_category':
{
... | 81 | 3,032 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_ophthal_review/plot_trend.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from datetime import datetime
from dateutil.relativedelta import relativedelta
DATA = {
'names': ['Methodological Contribution (Text-only)', 'Evaluation / Application (Text-only)',
'Methodological Contribution (Multimodal)', 'Evaluati... | 125 | 5,531 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_brainteaser/plot_correctness_by_subcategory.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_math_by_category = {
'methods': [
r'DeepSeek R1 Distill Qwen 1.5B',
r'DeepSeek R1 Distill Qwen 14B',
r'DeepSeek R1 Distill Llama 70B',
r'deepseek-chat (Deepseek-V3)',
... | 132 | 6,505 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_brainteaser/plot_selfcorrection_math.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_math_correcting_llm = {
'methods': [r'DeepSeek R1 Distill Qwen 1.5B',
r'DeepSeek R1 Distill Qwen 14B',
r'DeepSeek R1 Distill Llama 70B',
r'deepseek-cha... | 100 | 4,015 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_brainteaser/plot_correctness_by_category.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_math_by_category = {
'methods': [
r'DeepSeek R1 Distill Qwen 1.5B',
r'DeepSeek R1 Distill Qwen 14B',
r'DeepSeek R1 Distill Llama 70B',
r'deepseek-chat (Deepseek-V3)',
... | 133 | 6,403 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_brainteaser/plot_brute_force.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
from matplotlib import patheffects as path_effects
data_brute_force_math = {
'methods': [
r'DeepSeek R1 Distill Qwen 1.5B',
r'DeepSeek R1 Distill Qwen 14B',
r'DeepSeek R1 Distill L... | 249 | 10,181 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_brainteaser/plot_rewriting.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_rewriting_math = {
'methods': [r'DeepSeek R1 Distill Llama 70B',
r'deepseek-reasoner (Deepseek-R1)',
r'OpenAI o3'],
'colors': ['#8BCF8B', '#E9A6A1', '#3775BA'],
... | 106 | 3,694 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_VIGIL/plot_concept.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from scipy.stats import gaussian_kde
from scipy.interpolate import CubicSpline
def _gauss(x, mu, sig):
y = np.exp(-0.5 * ((x - mu) / sig) ** 2)
return y / (y.max() + 1e-12)
def _sample_tube(center_curve, t_samples, rng, sigma_u=0.08, sigma_v=... | 237 | 9,205 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_VIGIL/plot_comparison_radar.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
data_comparison = {
'methods': [
r'DPO',
r'DA-DPO',
r'VIGIL (Ours)',
],
'colors': [
"#D88F8A",
"#8BCF8B",
"#0F4D92"
],
'results': {
'Qwen2.5-VL-7B\nPOPE$_{Adv}$': np.array([82.... | 174 | 7,397 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_VIGIL/plot_posttraining.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
from matplotlib.collections import LineCollection
from matplotlib.colors import to_rgba
from matplotlib.lines import Line2D
data_posttraining = {
'methods': [
'DPO',
'DA-DPO',
'VIG... | 83 | 2,948 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_VIGIL/plot_ablation.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gridspec
data_ablation = {
'methods': [
'DPO',
'DA-DPO',
'VIGIL (Ours)',
],
'colors': [
"#D88F8A",
"#8BCF8B",
"#0F4D92"
],
'$\beta$': [0.05, 0.1, 0.2... | 149 | 6,038 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_comparison.py | .py | import os
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
summary_label = r'\textit{Improvement}'
options = ['VAE', 'DDPM', 'LDM', 'FM',
'DiffAb', 'IgLM', 'NOS-C', 'NOS-D',
'OAE + gradient ascent',
'OAE + MCMC',
'OAE + hill climbing',
... | 229 | 11,236 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_manifold.py | .py | import os
import numpy as np
import matplotlib.pyplot as plt
def function(x, y):
z = 0.6 * np.exp(-((x - 1)**2 + (y + 1)**2))
z += 0.5 * np.exp(-((x - 1)**2 + (y - 4)**2))
z += 0.3 * np.exp(-((x - 2)**2 + (y - 2)**2))
z += 0.2 * np.exp(-((x + 3)**2 + (y + 1)**2))
z += 0.3 * np.exp(-((x + 1)**2 + (... | 62 | 1,811 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_sweep.py | .py | import os
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
# results_increase = {
# r'Median property change': [0.1125, 0.44046, 0.46006, 0.45625, 0.46510],
# r'Percentage improved $\uparrow$': [55.15, 70.11, 71.02, 71.46, 71.52],
# r'Latent space distance $\dow... | 78 | 2,873 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py | .py | import os
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
def function(x, y):
z = 0.6 * np.exp(-((x - 1)**2 + (y + 1)**2))
z += 0.5 * np.exp(-((x - 1)**2 + (y - 4)**2))
z += 0.3 * np.exp(-((x - 2)**2 + (y - 2)**2))
z += 0.2 * np.exp(-((x + 3)**2 ... | 83 | 2,547 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Trajectory.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
data_comparison_Trajectory = {
'methods': [r'TrajectoryNet', r'OT-CFM', r'SB-CFM', r'BEMIOflow (ours)'],
'colors': ['#DDF3DE', '#AADCA9', '#8BCF8B', '#3775BA'],
'metrics': ['PHATE Space RMSE', 'Gene Space RMSE', 'Interpolation EMD'],
'd... | 75 | 2,941 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Ablation.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
data_comparison_Ablation = {
'methods': [r'OT-CFM', r'SB-CFM', r'SF2M', r'Cflows (w/o growth + energy)', r'Cflows (w/o growth)', r'Cflows'],
'colors': ['#AADCA9', '#8BCF8B', '#E9A6A1', '#B8C9E5', '#7097CA', '#3775BA'],
'metrics': [r'RMSE$\d... | 65 | 2,506 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Cflows/diffusion_swiss_roll.py | .py | import numpy as np
import matplotlib.pyplot as plt
from scipy.spatial.distance import pdist, squareform
# Generate Swiss Roll data
def generate_swiss_roll_2d(n_samples=80, noise=0.1):
t = 1.5 * np.pi * (1 + 2 * np.random.rand(n_samples))
x = t * np.cos(t)
z = t * np.sin(t)
# Add some noise
x += no... | 98 | 3,545 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_GeneRegulatory.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
data_comparison_GeneRegulatory = {
'methods': [r'OCE', r'PC', r'mTE', r'mMI', r'NRI', r'DCRNN', r'GTS', r'NIR', r'GC (ours)'],
'colors': ['#D0A3A3', '#EFE7B1', '#F4C2C2', '#D7C4E2', '#E5C09F', '#A8C6C2', '#B7D3B0', '#F5B5A0', '#3775BA'],
'm... | 75 | 3,022 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_FPGM/plot_freq_prior.py | .py | import os
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.ticker import LinearLocator, FormatStrFormatter
def load_freq_prior_data(data_dir):
datasets = {}
for name in sorted(os.listdir(data_dir)):
if not name.endswith(".npz"):
continue
path = os.path.join(d... | 146 | 6,578 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Dispersion/plot_illustration.py | .py | import os
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d
import matplotlib.cm as cm
EPSILON = 1e-6
def pairwise_sqdist(X: np.ndarray) -> np.ndarray:
X2 = np.sum(X**2, axis=1, keepdims=Tr... | 405 | 15,472 |
nature-skills | skills/nature-figure/assets/figures4papers/figure_Dispersion/plot_idea.py | .py | import os
import numpy as np
import matplotlib.pyplot as plt
EPSILON = 1e-6
def sample_points_in_ball(num_points, theta_range=2*np.pi):
r = np.sqrt(np.random.uniform(0, 0.95, num_points))
theta = np.random.uniform(np.pi/2 - theta_range/2, np.pi/2 + theta_range/2, num_points)
x = r * np.cos(theta)
y =... | 77 | 2,432 |
nature-skills | skills/nature-proposal-writer/scripts/build_proposal_docx.py | .py | #!/usr/bin/env python3
"""Convert researchwrite proposal markdown to properly formatted .docx.
Usage: python3 scripts/build_proposal_docx.py <input.md> [output.docx]
Formatting standard for academic proposals:
- Title: centered, Times New Roman + 宋体, 18pt bold
- Headings: Times New Roman + 宋体, 16/14/12pt bold, black
... | 232 | 6,836 |
nature-skills | skills/nature-reviewer/tests/test_reviewer_instruction_contracts.py | .py | from pathlib import Path
ROOT = Path(__file__).parents[1]
def read(relative: str) -> str:
return (ROOT / relative).read_text(encoding="utf-8")
def test_severity_and_blocking_contract_is_present() -> None:
router = read("SKILL.md")
assert "Major Concerns" in router
assert "Minor Comments" in route... | 43 | 1,229 |
nature-skills | skills/nature-paper2ppt/scripts/audit_pptx_quality.py | .py | #!/usr/bin/env python3
"""Lightweight PPTX QA for nature-paper2ppt outputs.
The script intentionally uses only the Python standard library so it can run in
minimal environments. It inspects PPTX XML for common delivery defects; it does
not replace rendered-slide visual review.
"""
from __future__ import annotations
... | 371 | 13,114 |
nature-skills | skills/nature-downloader/tests/python/test_config_wizard.py | .py | import importlib
import json
import os
import subprocess
import sys
import tempfile
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
SRC = ROOT / "src"
SCRIPT = ROOT / "scripts" / "configure_school.py"
class ConfigWizardTest(unittest.TestCase):
def test_start_asks_for_library_... | 186 | 7,390 |
nature-skills | skills/nature-downloader/tests/python/test_config_credentials.py | .py | import json
import os
import stat
import subprocess
import sys
import tempfile
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
SCRIPT = ROOT / "scripts" / "configure_credentials.py"
class ConfigureCredentialsTest(unittest.TestCase):
def test_cli_stdin_saves_key_without_echoin... | 42 | 1,285 |
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