6 changed files with 8 additions and 851 deletions
--- a/README.md
+++ b/README.md
@ -1,275 +1,10 @@
 # PyOrgPatcher
-**PyOrgPatcher** is a lightweight command-line utility and Python library for **programmatically editing, extracting, and synchronizing parts of Org-mode documents** — all without Emacs.
+PyOrgPatcher is a Python command-line utility that aid in workflows involving Emacs Org-Mode documents, as used in the PolyPaper project. 
-It provides a simple way to patch Org files from scripts, CI/CD jobs, or AI agents, making it ideal for:
+Functions:
- Collaborators who work with Org files but don’t use Emacs.
+ - List Org-Mode elements in an Org-Mode file that can be modified or extracted.
- Reproducible research pipelines using literate programming.
+ - Replace the content of an Org-Mode element with text from STDIN or from a file.
- AI systems (e.g., LangChain, LangGraph, or MCP agents) that maintain structured text and code artifacts.
+ - With a JSON configuration, either extract multiple Org-Mode elements to associated files (without noweb substitution) or update an Org-Mode document's specified elements with the contents of files.
-
+ - Dry-run capability.
 All components are under:
 ```
 ./code/
 ├── orgpatch.py          # main tool
 ├── example.org          # demonstration Org file
 └── test_orgpatch.py     # pytest unit tests
 ````
 ---
 ## 🔧 Installation & Setup
 ### 1. Requirements
 - **Python 3.8+**
 - **pytest** (for testing)
 Install dependencies:
 ```bash
 python3 -m venv venv
 source venv/bin/activate
 pip install pytest
 ````
 ### 2. Clone or Copy the Tool
 ```bash
 git clone https://git,cns.fyi/welsberr/PyOrgPatcher.git
 cd PyOrgPatcher/code
 ```
 You can also copy just `orgpatch.py` to any project — it’s self-contained and requires no external libraries.
 ---
 ## 🧩 Example Org File
 [`example.org`](./example.org) demonstrates the types of elements PyOrgPatcher understands:
 ```org
 * Main Title
 ** Introduction
 Some intro text.
 #+NAME: intro-para
 This is a named paragraph that will be replaced.
 ** Data
 #+NAME: mytable
 | Item | Value |
 |------+-------|
 | A    | 1     |
 | B    | 2     |
 ** Code
 #+NAME: code-snippet
 #+BEGIN_SRC python
 print("hello world")
 #+END_SRC
 ** My Section
 This section body will be replaced.
 ```
 ---
 ## 🚀 Basic Command-Line Usage
 List available patch targets:
 ```bash
 ./orgpatch.py list example.org
 ```
 Replace a section body:
 ```bash
 ./orgpatch.py replace example.org --section "** My Section" --from section.txt
 ```
 Replace a named block or table:
 ```bash
 ./orgpatch.py replace example.org --name code-snippet --from code.py
 ```
 Or from standard input:
 ```bash
 printf "| X | 42 |\n" | ./orgpatch.py replace example.org --name mytable --stdin
 ```
 Use `--backup` to create `example.org.bak`.
 ---
 ## 🔄 JSON Sync Mode
 Batch operations for multiple elements are defined via JSON mappings.
 ### Example: `mapping.json`
 ```json
 [
  {"name": "code-snippet", "file": "code.py"},
  {"name": "mytable", "file": "table.org"},
  {"section": "** My Section", "file": "section.txt"}
 ]
 ```
 ### Apply Updates *into* the Org File (files → Org)
 ```bash
 ./orgpatch.py sync example.org --map mapping.json --direction in --backup
 ```
 ### Export Org Elements *to* Files (Org → files)
 ```bash
 ./orgpatch.py sync example.org --map mapping.json --direction out --mkdirs
 ```
 Options:
 * `--dry-run` — preview only
 * `--backup` — create a backup before modifying
 * `--mkdirs` — create destination folders automatically
 * `--no-overwrite` — skip existing files on export
 ---
 ## 🧪 Running Unit Tests
 A complete [pytest](https://docs.pytest.org) test suite is included:
 ```bash
 pytest -q
 ```
 This validates:
 * Parsing of headings and `#+NAME:` blocks
 * Section replacement
 * Named block/table/paragraph replacement
 * JSON mapping synchronization (`sync in` and `sync out`)
 ---
 ## 🧠 Integrating with AI Agent Tooling
 ### Why It Matters
 Org-mode provides a **hierarchical, semantic structure** perfect for literate programming, documentation, and multi-language code notebooks — but until now, most AI systems couldn’t safely manipulate it without Emacs or brittle regex hacks.
 **PyOrgPatcher** changes that:
 It gives AI agents and LLM-based systems a structured interface to read, patch, and synchronize `.org` files, **treating them as composable data artifacts**.
 ### Example: Agent Workflow
 Imagine an **AI documentation agent** that:
 1. Reads `mapping.json` to identify relevant files and blocks.
 2. Rebuilds code snippets or analyses (e.g., retraining results, data summaries).
 3. Calls `orgpatch.py` (or its Python API) to update the corresponding Org blocks.
 This lets an AI system manage “literate” files safely without needing to regenerate the entire Org document.
 ### In LangChain / LangGraph
 Within a LangChain or LangGraph workflow, you can use `PyOrgPatcher` as a tool node:
 ```python
 from langchain.tools import tool
 import subprocess, json
@tool("update_org_block")
 def update_org_block(name: str, content: str):
    """Update a named Org-mode block in example.org."""
    cmd = [
        "python3", "orgpatch.py", "replace", "example.org",
        "--name", name, "--stdin"
    ]
    subprocess.run(cmd, input=content.encode("utf-8"), check=True)
    return f"Updated block '{name}' successfully."
 ```
 Agents can then call this tool directly:
 ```python
 update_org_block("analysis-results", "Mean=42\nStd=7.5\n")
 ```
 Similarly, a chain could:
 * Use `sync in` to load generated files into an Org document.
 * Use `sync out` to extract tables or code for downstream tasks (e.g., testing, publishing, or compiling).
 ### Multi-Component Patch (MCP) Integration
 In MCP-style systems — where AI agents patch **specific parts of multi-file projects** —
 PyOrgPatcher acts as the **Org-layer patcher**:
 * `sync in` = inject AI-generated code, results, or summaries.
 * `sync out` = extract training data, code snippets, or narrative text.
 * `replace` = fine-grained control of a single element in context.
 This makes it ideal for **AI-assisted research notebooks**, **literate AI model reports**, and **collaborative documentation systems**.
 ---
 ## 🧰 Python Library Usage
 PyOrgPatcher can also be used as a Python module:
 ```python
 import orgpatch as op
 lines = op.read_lines("example.org")
 new_lines = op.replace_named(lines, "code-snippet", "print('updated via API')\n")
 op.write_lines("example.org", new_lines)
 ```
 This makes it easy to integrate into scripts or notebooks.
 ---
 ## 🧬 Example Use Case: Non-Emacs Collaboration
 Researchers, engineers, or students who use VS Code, Sublime, or other editors can:
 * Edit external files (`.py`, `.csv`, `.txt`) directly.
 * Let an automated process update `main.org` via `sync in`.
 * Keep the literate record synchronized without ever opening Emacs.
 This lowers the barrier for collaboration in mixed-editor teams.
 ---
 ## 🏁 Summary
 | Feature                    | Description                                          |
 | -------------------------- | ---------------------------------------------------- |
 | **CLI + Library**          | Command-line and Python module usage                 |
 | **Emacs-Free Editing**     | Safely patch `.org` files without Emacs              |
 | **JSON Batch Mode**        | Bulk updates and exports                             |
 | **AI/Automation Ready**    | Ideal for LangChain, LangGraph, or MCP agents        |
 | **Fully Tested**           | Comprehensive pytest suite included                  |
 | **Collaboration-Friendly** | Perfect for teams mixing Org-mode with other editors |
 ---
 **Author:** Wesley R. Elsberry
 **Project:** PyOrgPatcher
 **License:** MIT
 **Location:** `./code/`
 > “PyOrgPatcher bridges human-readable structure and machine-editable precision — empowering both collaborators and intelligent agents to work fluently with Org-mode documents.”
 ```
 ---
--- a/code/example.org
+++ b/code/example.org
@ -1,27 +0,0 @@
 * Main Title
 ** Introduction
 Some intro text.
 #+NAME: intro-para
 This is a named paragraph that will be replaced.
 It continues until the first blank line.
 ** Data
 #+NAME: mytable
 | Item | Value |
 |------+-------|
 | A    | 1     |
 | B    | 2     |
 ** Code
 #+NAME: code-snippet
 #+BEGIN_SRC python
 print("hello world")
 #+END_SRC
 ** My Section
 This section body will be replaced.
 It ends at the next heading of level ** or *.
 ** Another Section
 Content of another section.
--- a/code/mapping.json
+++ b/code/mapping.json
@ -1,18 +0,0 @@
 [
  {
    "name": "code-snippet",
    "file": "/mnt/data/orgpatch/code.py"
  },
  {
    "name": "mytable",
    "file": "/mnt/data/orgpatch/tbl.org"
  },
  {
    "section": "** My Section",
    "file": "/mnt/data/orgpatch/my_section.txt"
  },
  {
    "name": "intro-para",
    "file": "/mnt/data/orgpatch/intro.txt"
  }
 ]
--- a/code/mapping_out.json
+++ b/code/mapping_out.json
@ -1,18 +0,0 @@
 [
  {
    "name": "code-snippet",
    "file": "/mnt/data/orgpatch/exported/code.py"
  },
  {
    "name": "mytable",
    "file": "/mnt/data/orgpatch/exported/table.org"
  },
  {
    "section": "** My Section",
    "file": "/mnt/data/orgpatch/exported/section.txt"
  },
  {
    "name": "intro-para",
    "file": "/mnt/data/orgpatch/exported/intro.txt"
  }
 ]
--- a/code/orgpatch.py
+++ b/code/orgpatch.py
@ -1,385 +0,0 @@
 #!/usr/bin/env python3
 # orgpatch.py
 """
 Replace parts of Org-mode files from the command line.
 Supported targets:
  1) Sections by exact heading text (e.g., "** My Section")
  2) '#+NAME:'-labeled elements:
     - Named blocks (#+BEGIN_... / #+END_...)
     - Named tables (consecutive lines beginning with '|')
     - Named paragraphs/lists immediately following '#+NAME:' (until blank line)
 Also supports JSON "sync" to batch update/export:
  - direction=in  : update Org from external files
  - direction=out : export from Org into external files (like tangle, but no noweb)
 Usage:
  List replaceable regions:
    orgpatch.py list FILE.org
  Replace a section body with stdin:
    orgpatch.py replace FILE.org --section "** My Section" --stdin
  Replace a named element with a file:
    orgpatch.py replace FILE.org --name foo --from path.txt
  Sync via JSON mapping (in: files → Org, out: Org → files):
    orgpatch.py sync FILE.org --map mapping.json --direction in  --backup
    orgpatch.py sync FILE.org --map mapping.json --direction out --mkdirs
 Mapping JSON format:
  Either a top-level list:
    [
      {"name": "code-snippet", "file": "code.py"},
      {"name": "mytable", "file": "table.org"},
      {"section": "** My Section", "file": "section.txt"}
    ]
  or an object with "entries": [ ...same as above... ]
 """
 from __future__ import annotations
 import argparse
 import re
 import sys
 import json
 import shutil
 import os
 from typing import List, Tuple, Optional, Dict, Any
 Heading = Dict[str, Any]
 NamedElem = Dict[str, Any]
 HEADING_RE = re.compile(r'^(\*+)\s+(.*)\s*$')
 NAME_RE    = re.compile(r'^\s*#\+NAME:\s*(\S+)\s*$', re.IGNORECASE)
 BEGIN_RE   = re.compile(r'^\s*#\+BEGIN_([A-Z0-9_]+)\b.*$', re.IGNORECASE)
 END_RE_FMT = r'^\s*#\+END_{kind}\b.*$'
 TABLE_RE   = re.compile(r'^\s*\|')
 def read_lines(path: str) -> List[str]:
    with open(path, 'r', encoding='utf-8') as f:
        return f.readlines()
 def write_lines(path: str, lines: List[str]) -> None:
    with open(path, 'w', encoding='utf-8') as f:
        f.writelines(lines)
 def parse_headings(lines: List[str]) -> List[Heading]:
    heads: List[Heading] = []
    for i, line in enumerate(lines):
        m = HEADING_RE.match(line)
        if m:
            level = len(m.group(1))
            title = m.group(2)
            heads.append({'i': i, 'level': level, 'title': title})
    return heads
 def section_bounds(lines: List[str], headings: List[Heading], exact_heading: str) -> Optional[Tuple[int, int]]:
    exact_heading = exact_heading.rstrip('\n')
    start_idx = None
    level = None
    for h in headings:
        heading_line_text = "{} {}".format('*' * h['level'], h['title'])
        if heading_line_text == exact_heading:
            start_idx = h['i']
            level = h['level']
            break
    if start_idx is None:
        return None
    body_start = start_idx + 1
    for h in headings:
        if h['i'] <= start_idx:
            continue
        if h['level'] <= level:
            return (body_start, h['i'])
    return (body_start, len(lines))
 def _scan_named_paragraph(lines: List[str], j: int) -> Optional[Tuple[int, int]]:
    n = len(lines)
    if j >= n:
        return None
    if BEGIN_RE.match(lines[j]) or TABLE_RE.match(lines[j]):
        return None
    if lines[j].strip() == "":
        return None
    k = j + 1
    while k < n and lines[k].strip() != "":
        k += 1
    return (j, k)
 def parse_named_elements(lines: List[str]) -> List[NamedElem]:
    named: List[NamedElem] = []
    i = 0
    n = len(lines)
    while i < n:
        m = NAME_RE.match(lines[i])
        if not m:
            i += 1
            continue
        name = m.group(1)
        j = i + 1
        while j < n and lines[j].strip() == '':
            j += 1
        if j >= n:
            i += 1
            continue
        mbeg = BEGIN_RE.match(lines[j])
        if mbeg:
            kind = mbeg.group(1).upper()
            end_re = re.compile(END_RE_FMT.format(kind=re.escape(kind)), re.IGNORECASE)
            k = j + 1
            while k < n and not end_re.match(lines[k]):
                k += 1
            if k >= n:
                content_start = j + 1
                content_end = n
                named.append({
                    'type': 'block',
                    'name': name,
                    'kind': kind,
                    'begin_i': j,
                    'end_i': n - 1,
                    'content_start': content_start,
                    'content_end': content_end
                })
                i = n
                continue
            named.append({
                'type': 'block',
                'name': name,
                'kind': kind,
                'begin_i': j,
                'end_i': k,
                'content_start': j + 1,
                'content_end': k
            })
            i = k + 1
            continue
        if TABLE_RE.match(lines[j]):
            k = j
            while k < n and TABLE_RE.match(lines[k]):
                k += 1
            named.append({
                'type': 'table',
                'name': name,
                'start_i': j,
                'end_i': k
            })
            i = k
            continue
        para_bounds = _scan_named_paragraph(lines, j)
        if para_bounds is not None:
            s, e = para_bounds
            named.append({
                'type': 'para',
                'name': name,
                'start_i': s,
                'end_i': e
            })
            i = e
            continue
        i = j
    return named
 def list_targets(lines: List[str]) -> None:
    heads = parse_headings(lines)
    print("== Sections ==")
    for h in heads:
        print(f"  L{h['i']+1:>4} | level {h['level']} | {('*'*h['level'])} {h['title']}")
    print("\n== #+NAME elements ==")
    named = parse_named_elements(lines)
    for e in named:
        if e['type'] == 'block':
            beg = e['begin_i'] + 1
            end = e['end_i'] + 1
            print(f"  name={e['name']} | block {e['kind']} | lines {beg}-{end} (content {e['content_start']+1}-{e['content_end']})")
        elif e['type'] == 'table':
            print(f"  name={e['name']} | table     | lines {e['start_i']+1}-{e['end_i']}")
        else:
            print(f"  name={e['name']} | paragraph | lines {e['start_i']+1}-{e['end_i']}")
 def load_replacement(from_file: Optional[str], use_stdin: bool) -> str:
    if from_file and use_stdin:
        raise SystemExit("Choose either --from FILE or --stdin, not both.")
    if from_file:
        with open(from_file, 'r', encoding='utf-8') as f:
            return f.read()
    if use_stdin:
        return sys.stdin.read()
    raise SystemExit("You must provide replacement text with --from FILE or --stdin.")
 def replace_section(lines: List[str], heading_text: str, new_body: str) -> List[str]:
    heads = parse_headings(lines)
    bounds = section_bounds(lines, heads, heading_text)
    if not bounds:
        raise SystemExit(f"Section not found: {heading_text!r}")
    start, end = bounds
    new_lines = [ln if ln.endswith('\n') else (ln + '\n') for ln in new_body.splitlines()]
    return lines[:start] + new_lines + lines[end:]
 def replace_named(lines: List[str], name: str, new_content: str) -> List[str]:
    elems = parse_named_elements(lines)
    target = next((e for e in elems if e['name'] == name), None)
    if not target:
        raise SystemExit(f"No '#+NAME: {name}' element found (supported: named blocks, tables, and paragraphs).")
    if target['type'] == 'block':
        c0, c1 = target['content_start'], target['content_end']
        new_lines = [ln if ln.endswith('\n') else (ln + '\n') for ln in new_content.splitlines()]
        return lines[:c0] + new_lines + lines[c1:]
    elif target['type'] == 'table':
        s, e = target['start_i'], target['end_i']
        new_lines = [ln if ln.endswith('\n') else (ln + '\n') for ln in new_content.splitlines()]
        for idx, ln in enumerate(new_lines, 1):
            if ln.strip() and not ln.lstrip().startswith('|'):
                print(f"Warning: replacement line {idx} for table '{name}' does not begin with '|'", file=sys.stderr)
        return lines[:s] + new_lines + lines[e:]
    else:
        s, e = target['start_i'], target['end_i']
        new_lines = [ln if ln.endswith('\n') else (ln + '\n') for ln in new_content.splitlines()]
        if not new_lines or new_lines[-1].strip() != "":
            new_lines.append("\n")
        return lines[:s] + new_lines + lines[e:]
 # ===== Sync helpers =====
 def extract_named_content(lines: List[str], name: str) -> str:
    elems = parse_named_elements(lines)
    e = next((x for x in elems if x['name'] == name), None)
    if not e:
        raise SystemExit(f"No '#+NAME: {name}' element found.")
    if e['type'] == 'block':
        c0, c1 = e['content_start'], e['content_end']
        return ''.join(lines[c0:c1])
    elif e['type'] == 'table':
        s, eidx = e['start_i'], e['end_i']
        return ''.join(lines[s:eidx])
    else:
        s, eidx = e['start_i'], e['end_i']
        return ''.join(lines[s:eidx])
 def extract_section_body(lines: List[str], heading_text: str) -> str:
    heads = parse_headings(lines)
    bounds = section_bounds(lines, heads, heading_text)
    if not bounds:
        raise SystemExit(f"Section not found: {heading_text!r}")
    s, e = bounds
    return ''.join(lines[s:e])
 def sync_apply_in(lines: List[str], mapping: list) -> List[str]:
    """Apply updates from files into the Org according to mapping entries."""
    for idx, entry in enumerate(mapping, 1):
        if 'file' not in entry:
            raise SystemExit(f"Mapping entry #{idx} is missing 'file' field.")
        fpath = entry['file']
        try:
            with open(fpath, 'r', encoding='utf-8') as fh:
                content = fh.read()
        except FileNotFoundError:
            raise SystemExit(f"Mapping entry #{idx}: source file not found: {fpath!r}")
        if 'section' in entry:
            lines = replace_section(lines, entry['section'], content)
        elif 'name' in entry:
            lines = replace_named(lines, entry['name'], content)
        else:
            raise SystemExit(f"Mapping entry #{idx} must have either 'name' or 'section'.")
    return lines
 def sync_apply_out(lines: List[str], mapping: list, mkdirs: bool = False, overwrite: bool = True) -> None:
    """Extract content from Org into files according to mapping entries (does not alter Org)."""
    for idx, entry in enumerate(mapping, 1):
        if 'file' not in entry:
            raise SystemExit(f"Mapping entry #{idx} is missing 'file' field.")
        fpath = entry['file']
        if mkdirs:
            pathlib.Path(fpath).parent.mkdir(parents=True, exist_ok=True)
        if (not overwrite) and os.path.exists(fpath):
            print(f"Skipping existing file (overwrite disabled): {fpath}", file=sys.stderr)
            continue
        if 'section' in entry:
            text = extract_section_body(lines, entry['section'])
        elif 'name' in entry:
            text = extract_named_content(lines, entry['name'])
        else:
            raise SystemExit(f"Mapping entry #{idx} must have either 'name' or 'section'.")
        with open(fpath, 'w', encoding='utf-8') as fh:
            fh.write(text)
 def load_mapping(path: str) -> list:
    with open(path, 'r', encoding='utf-8') as fh:
        data = json.load(fh)
    if isinstance(data, dict) and 'entries' in data:
        return data['entries']
    if not isinstance(data, list):
        raise SystemExit("Mapping JSON must be a list of entries or an object with an 'entries' list.")
    return data
 def main(argv: Optional[List[str]] = None) -> None:
    p = argparse.ArgumentParser(description="Replace parts of Org files and sync via JSON map.")
    sub = p.add_subparsers(dest='cmd', required=True)
    p_list = sub.add_parser('list', help="List replaceable sections and #+NAME elements")
    p_list.add_argument('file', help="Org file")
    p_rep = sub.add_parser('replace', help="Replace a section body or a named element's contents")
    p_rep.add_argument('file', help="Org file")
    target = p_rep.add_mutually_exclusive_group(required=True)
    target.add_argument('--section', help='Exact heading text to match (e.g., "** My Section")')
    target.add_argument('--name', help="Name after '#+NAME:' to match")
    src = p_rep.add_mutually_exclusive_group(required=True)
    src.add_argument('--from', dest='from_file', metavar='FILE', help="Take replacement text from FILE")
    src.add_argument('--stdin', action='store_true', help="Read replacement text from stdin")
    p_rep.add_argument('--dry-run', action='store_true', help="Show the result to stdout without writing the file")
    p_rep.add_argument('--backup', action='store_true', help="Write FILE.org.bak before modifying")
    p_sync = sub.add_parser('sync', help="Sync blocks/sections using a JSON mapping (in: files → Org, out: Org → files)")
    p_sync.add_argument('file', help='Org file')
    p_sync.add_argument('--map', required=True, help='Path to JSON mapping file')
    p_sync.add_argument('--direction', choices=['in','out'], required=True, help="'in' updates Org from files; 'out' exports from Org to files")
    p_sync.add_argument('--dry-run', action='store_true', help='Preview Org result (direction=in) without writing file')
    p_sync.add_argument('--backup', action='store_true', help='Write FILE.org.bak before modifying (direction=in only)')
    p_sync.add_argument('--mkdirs', action='store_true', help='Create parent directories when exporting (direction=out)')
    p_sync.add_argument('--no-overwrite', action='store_true', help='When exporting, do not overwrite existing files')
    args = p.parse_args(argv)
    lines = read_lines(args.file)
    if args.cmd == 'list':
        list_targets(lines)
        return
    if args.cmd == 'sync':
        mapping = load_mapping(args.map)
        if args.direction == 'in':
            new_lines = sync_apply_in(lines, mapping)
            if args.dry_run:
                sys.stdout.write(''.join(new_lines))
                return
            if args.backup:
                shutil.copyfile(args.file, args.file + '.bak')
            write_lines(args.file, new_lines)
            print(f"Updated {args.file} from {args.map}.")
        else:
            sync_apply_out(lines, mapping, mkdirs=args.mkdirs, overwrite=not args.no_overwrite)
            print(f"Exported content from {args.file} to files per {args.map}.")
        return
    # replace
    replacement = load_replacement(getattr(args, 'from_file', None), getattr(args, 'stdin', False))
    if args.section:
        new_lines = replace_section(lines, args.section, replacement)
    else:
        new_lines = replace_named(lines, args.name, replacement)
    if args.dry_run:
        sys.stdout.write(''.join(new_lines))
    else:
        if args.backup:
            shutil.copyfile(args.file, args.file + ".bak")
        write_lines(args.file, new_lines)
        if args.section:
            print(f"Replaced body of section {args.section!r} in {args.file}")
        else:
            print(f"Replaced contents of '#+NAME: {args.name}' in {args.file}")
 if __name__ == '__main__':
    main()
--- a/code/test_orgpatch.py
+++ b/code/test_orgpatch.py
@ -1,130 +0,0 @@
 import sys
 from pathlib import Path
 # Import module from same folder
 sys.path.insert(0, str(Path(__file__).parent))
 import orgpatch as op
 EXAMPLE_ORG = """* Main Title
 ** Introduction
 Some intro text.
 #+NAME: intro-para
 This is a named paragraph that will be replaced.
 It continues until the first blank line.
 ** Data
 #+NAME: mytable
 | Item | Value |
 |------+-------|
 | A    | 1     |
 | B    | 2     |
 ** Code
 #+NAME: code-snippet
 #+BEGIN_SRC python
 print("hello world")
 #+END_SRC
 ** My Section
 This section body will be replaced.
 It ends at the next heading of level ** or *.
 ** Another Section
 Content of another section.
 """
 def write(p: Path, text: str):
    p.write_text(text, encoding="utf-8")
 def test_parse_headings_and_sections(tmp_path: Path):
    org = tmp_path / "example.org"
    write(org, EXAMPLE_ORG)
    lines = op.read_lines(str(org))
    heads = op.parse_headings(lines)
    titles = [h['title'] for h in heads]
    assert "Introduction" in titles
    assert "My Section" in titles
    b = op.section_bounds(lines, heads, "** My Section")
    assert b is not None
    s, e = b
    body = ''.join(lines[s:e])
    assert "This section body will be replaced." in body
 def test_parse_named_elements(tmp_path: Path):
    org = tmp_path / "example.org"
    write(org, EXAMPLE_ORG)
    lines = op.read_lines(str(org))
    elems = op.parse_named_elements(lines)
    names = {e['name']: e for e in elems}
    assert names['intro-para']['type'] == 'para'
    assert names['mytable']['type'] == 'table'
    assert names['code-snippet']['type'] == 'block'
 def test_replace_section(tmp_path: Path):
    org = tmp_path / "example.org"
    write(org, EXAMPLE_ORG)
    lines = op.read_lines(str(org))
    out = op.replace_section(lines, "** My Section", "New body\nMore\n")
    joined = ''.join(out)
    assert "New body" in joined
    assert "This section body will be replaced." not in joined
 def test_replace_named_block_table_para(tmp_path: Path):
    org = tmp_path / "example.org"
    write(org, EXAMPLE_ORG)
    lines = op.read_lines(str(org))
    out = op.replace_named(lines, "code-snippet", "print('updated')\n")
    assert "print('updated')" in ''.join(out)
    out2 = op.replace_named(out, "mytable", "| X | 9 |\n")
    assert "| X | 9 |" in ''.join(out2)
    out3 = op.replace_named(out2, "intro-para", "New intro\nSecond\n")
    j3 = ''.join(out3)
    assert "New intro" in j3
    assert "named paragraph that will be replaced" not in j3
 def test_sync_in_and_out(tmp_path: Path):
    org = tmp_path / "example.org"
    write(org, EXAMPLE_ORG)
    code_src = tmp_path / "code.py"
    tbl_src = tmp_path / "tbl.org"
    sec_src = tmp_path / "section.txt"
    para_src = tmp_path / "intro.txt"
    write(code_src, "print('via in')\n")
    write(tbl_src, "| Col | Val |\n|-----+-----|\n| A   |  1  |\n")
    write(sec_src, "Replaced via sync in.\nSecond line.\n")
    write(para_src, "Intro via sync in.\n\n")
    mapping = [
        {"name": "code-snippet", "file": str(code_src)},
        {"name": "mytable", "file": str(tbl_src)},
        {"section": "** My Section", "file": str(sec_src)},
        {"name": "intro-para", "file": str(para_src)},
    ]
    lines = op.read_lines(str(org))
    new_lines = op.sync_apply_in(lines, mapping)
    out = ''.join(new_lines)
    assert "print('via in')" in out
    assert "| Col | Val |" in out
    assert "Replaced via sync in." in out
    assert "Intro via sync in." in out
    export_dir = tmp_path / "exported"
    export_dir.mkdir()
    m_out = [
        {"name": "code-snippet", "file": str(export_dir / "code.py")},
        {"name": "mytable", "file": str(export_dir / "table.org")},
        {"section": "** My Section", "file": str(export_dir / "section.txt")},
        {"name": "intro-para", "file": str(export_dir / "intro.txt")},
    ]
    op.sync_apply_out(new_lines, m_out, mkdirs=True, overwrite=True)
    assert (export_dir / "code.py").read_text(encoding="utf-8").strip() == "print('via in')"
    assert "| Col | Val |" in (export_dir / "table.org").read_text(encoding="utf-8")
    assert "Replaced via sync in." in (export_dir / "section.txt").read_text(encoding="utf-8")
    assert "Intro via sync in." in (export_dir / "intro.txt").read_text(encoding="utf-8")