mirror of
https://github.com/harvard-edge/cs249r_book.git
synced 2026-07-20 04:45:11 -05:00
Vijay Janapa Reddi
af79ff3edd
Introduce 13 LaTeX-typeset algorithm blocks across 8 chapters (Adam update,
gradient checkpointing, FlashAttention, backpropagation, mini-batch SGD,
reverse-mode AD, PTQ calibration, tiled GEMM, ring all-reduce, 1F1B pipeline,
continuous-batching scheduler, speculative decoding, power-of-two routing),
each integrated into existing prose with a motivating lead-in and a
systems-consequence follow-up.
Extension (book/quarto/_extensions/mlsysbook-ext/pseudocode):
- Vendored under the owned mlsysbook-ext/ namespace (moved from leovan/,
version -mlsysbook-custom) and wired into the html, pdf, and epub filters.
- MIT Press cross-ref casing: @algo- -> 'algorithm N' mid-sentence,
@Algo- -> 'Algorithm N' at sentence start.
- Right-aligned italic triangle comments (CLRS column convention).
- Static EPUB renderer (upstream supports only HTML via pseudocode.js and PDF
via algpseudocodex; EPUB previously emitted raw \begin{algorithm}).
- Uses the algo- prefix: native @alg- collides with Quarto's algorithm theorem
environment and FATALs the build.
Ref tooling (book/cli/commands): teach validate.py, bib.py, and info.py the
algo-/Algo- crossref prefix (LABEL_REF_PATTERN, EXCLUDED_CITATION_PREFIXES,
Algorithm label-def patterns, and a chunk-option label harvest that runs inside
the pseudocode fence) so check refs and check labels resolve @algo-/@Algo-
instead of misreading them as missing citations.
Verified rendering in HTML, PDF, and EPUB; check refs and check labels pass
book-wide.
1129 lines
44 KiB
Python
1129 lines
44 KiB
Python
"""
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``binder info`` — Book statistics and figure extraction.
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Subcommands:
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stats — Count figures, tables, equations, listings, text lines, words
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figures — Extract figure list with labels, captions, and alt-text
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Use --with-pdf to merge LaTeX figure numbers and page numbers
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from a previous PDF build.
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"""
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import argparse
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import re
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import sys
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from collections import defaultdict
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from pathlib import Path
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from typing import Dict, List, Optional, Tuple
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from rich.console import Console
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from rich.panel import Panel
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from rich.table import Table
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console = Console()
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# ---------------------------------------------------------------------------
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# Patterns
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# ---------------------------------------------------------------------------
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_FIGURE_DEF = [
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re.compile(r"\{#(fig-[\w-]+)"),
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re.compile(r"#\|\s*label:\s*(fig-[\w-]+)"),
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]
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_TABLE_DEF = [re.compile(r"\{#(tbl-[\w-]+)")]
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_EQUATION_DEF = [re.compile(r"\{#(eq-[\w-]+)")]
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_LISTING_DEF = [re.compile(r"\{#(lst-[\w-]+)")]
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_SECTION_DEF = [re.compile(r"\{#(sec-[\w-]+)")]
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_CODE_FENCE = re.compile(r"^```")
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_YAML_FENCE = re.compile(r"^---\s*$")
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# Figure extraction patterns — greedy .* anchored to end-of-line so interior
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# braces from LaTeX (e.g. $W_{hh}$, \mathcal{F}) don't truncate the match.
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_DIV_FIG = re.compile(
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r"^:{3,}\s*\{(.*#fig-.*)\}\s*$", re.MULTILINE
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)
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_IMG_FIG = re.compile(
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r"!\[((?:[^\[\]]|\[[^\]]*\])*)\]"
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r"\([^)]+\)"
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r"\{(.*#fig-[^\n]*)\}\s*$",
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re.MULTILINE,
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)
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_ATTR_CAP = re.compile(r'fig-cap\s*=\s*"([^"]*)"')
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_ATTR_ALT = re.compile(r'fig-alt\s*=\s*"([^"]*)"')
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# Code-block figure pattern: ```{python} with #| cell options
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_CODE_BLOCK_FIG = re.compile(
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r"```\{(?:python|r|julia|ojs)\}[^\n]*\n"
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r"((?:#\|[^\n]*\n)+)",
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re.MULTILINE,
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)
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# LaTeX manifest
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_MANIFEST_HEADER = "LATEX FIGURE MANIFEST"
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_LATEX_FIG_PAT = re.compile(r"Figure\s+([A-Z\d]+\.\d+)\s*\|\s*Page\s*(\d+)")
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class InfoCommand:
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"""Native ``binder info`` command group."""
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def __init__(self, config_manager, chapter_discovery):
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self.config_manager = config_manager
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self.chapter_discovery = chapter_discovery
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# ------------------------------------------------------------------
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# Entry point
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# ------------------------------------------------------------------
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def run(self, args: List[str]) -> bool:
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if args == ["help"]:
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self._print_help()
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return True
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parser = argparse.ArgumentParser(
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prog="binder info",
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description="Book statistics and figure extraction",
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)
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parser.add_argument(
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"subcommand",
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nargs="?",
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choices=["stats", "figures", "concepts", "headers", "acronyms"],
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help="Subcommand to run",
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)
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parser.add_argument("--path", default=None, help="File or directory")
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parser.add_argument("--vol1", action="store_true", help="Volume I only")
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parser.add_argument("--vol2", action="store_true", help="Volume II only")
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parser.add_argument(
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"--format",
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choices=["text", "markdown", "csv"],
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default="text",
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help="Output format for figures (default: text)",
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)
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parser.add_argument("--output", default=None, help="Write to file")
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parser.add_argument("--json", action="store_true", help="JSON output (stats)")
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parser.add_argument(
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"--by-chapter",
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action="store_true",
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help="Break down stats per chapter",
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)
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parser.add_argument(
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"--with-pdf",
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action="store_true",
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help="Merge LaTeX figure numbers/pages from a previous PDF build",
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)
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parser.add_argument(
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"--manifest",
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default=None,
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help="Path to LaTeX figure manifest (*_figures.txt). Auto-detected if omitted.",
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)
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try:
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ns = parser.parse_args(args)
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except SystemExit:
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return ("-h" in args) or ("--help" in args)
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if not ns.subcommand:
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self._print_help()
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return True
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root = self._resolve_path(ns.path, ns.vol1, ns.vol2)
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if not root.exists():
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console.print(f"[red]Path not found: {root}[/red]")
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return False
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if ns.subcommand == "stats":
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return self._run_stats(root, ns)
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elif ns.subcommand == "figures":
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return self._run_figures(root, ns)
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elif ns.subcommand == "concepts":
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return self._run_concepts(root, ns)
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elif ns.subcommand == "headers":
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return self._run_headers(root, ns)
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elif ns.subcommand == "acronyms":
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return self._run_acronyms(root, ns)
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return False
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# ------------------------------------------------------------------
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# Help
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# ------------------------------------------------------------------
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def _print_help(self) -> None:
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table = Table(show_header=True, header_style="bold cyan", box=None)
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table.add_column("Subcommand", style="cyan", width=14)
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table.add_column("Description", style="white", width=50)
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table.add_row("stats", "Count figures, tables, equations, listings, words, text lines")
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table.add_row("figures", "Extract figure list with labels, captions, and alt-text")
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table.add_row("concepts", "Extract key concepts (bold terms, definitions, headers)")
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table.add_row("headers", "List all section headers with levels")
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table.add_row("acronyms", "Find acronyms in parentheses (e.g., (CNN))")
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console.print(Panel(table, title="binder info <subcommand>", border_style="cyan"))
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console.print("[dim]Examples:[/dim]")
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console.print(" [cyan]./binder info stats --vol1[/cyan]")
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console.print(" [cyan]./binder info stats --by-chapter[/cyan]")
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console.print(" [cyan]./binder info figures --vol1[/cyan]")
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console.print(" [cyan]./binder info figures --vol1 --with-pdf[/cyan] [dim]# merge LaTeX fig numbers + pages[/dim]")
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console.print(" [cyan]./binder info concepts --vol1[/cyan]")
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console.print(" [cyan]./binder info headers --vol1[/cyan]")
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console.print(" [cyan]./binder info acronyms --vol1[/cyan]")
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console.print()
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# ------------------------------------------------------------------
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# Path resolution
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# ------------------------------------------------------------------
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def _resolve_path(self, path_arg: Optional[str], vol1: bool, vol2: bool) -> Path:
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if path_arg:
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p = Path(path_arg)
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return p if p.is_absolute() else Path.cwd() / p
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base = self.config_manager.book_dir
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if vol1:
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return base / "contents" / "vol1"
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if vol2:
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return base / "contents" / "vol2"
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return base / "contents"
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def _qmd_files(self, root: Path) -> List[Path]:
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if root.is_file():
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return [root] if root.suffix == ".qmd" else []
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return sorted(root.rglob("*.qmd"))
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def _chapter_name(self, path: Path) -> str:
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"""Extract a human-readable chapter name from a QMD file."""
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try:
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content = path.read_text(encoding="utf-8")
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except Exception:
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return path.stem
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# Skip YAML front matter
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if content.startswith("---"):
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end = content.find("---", 3)
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if end != -1:
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content = content[end + 3:]
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m = re.search(r"^#\s+([^{\n]+)", content, re.MULTILINE)
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if m:
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return m.group(1).strip()
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return path.stem.replace("_", " ").title()
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def _relative(self, path: Path) -> str:
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try:
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return str(path.relative_to(self.config_manager.book_dir))
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except ValueError:
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return str(path)
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# ------------------------------------------------------------------
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# Stats
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# ------------------------------------------------------------------
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def _run_stats(self, root: Path, ns: argparse.Namespace) -> bool:
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files = self._qmd_files(root)
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if not files:
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console.print("[yellow]No QMD files found.[/yellow]")
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return False
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# Filter out parts/, frontmatter/ for cleaner stats
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chapter_files = [
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f for f in files
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if "/parts/" not in str(f) and "/frontmatter/" not in str(f)
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]
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all_stats: List[Dict] = []
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for path in chapter_files:
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stats = self._count_file(path)
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stats["file"] = self._relative(path)
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stats["chapter"] = self._chapter_name(path)
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all_stats.append(stats)
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if ns.json:
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import json
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totals = self._aggregate(all_stats)
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payload = {
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"path": str(root),
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"files": len(all_stats),
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"totals": totals,
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}
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if ns.by_chapter:
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payload["chapters"] = all_stats
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print(json.dumps(payload, indent=2))
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return True
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# Rich table output
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totals = self._aggregate(all_stats)
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if ns.by_chapter:
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self._print_chapter_stats(all_stats, totals)
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else:
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self._print_summary_stats(all_stats, totals, root)
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return True
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def _count_file(self, path: Path) -> Dict:
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"""Count elements in a single QMD file."""
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try:
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content = path.read_text(encoding="utf-8")
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except Exception:
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return self._empty_stats()
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lines = content.splitlines()
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in_code = False
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in_yaml = False
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text_lines = 0
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word_count = 0
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code_blocks = 0
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figures = 0
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tables = 0
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equations = 0
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listings = 0
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sections = 0
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footnotes = 0
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citations = 0
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citation_pat = re.compile(r"@[\w-]+")
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footnote_def_pat = re.compile(r"^\[\^[^\]]+\]:")
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for idx, line in enumerate(lines):
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stripped = line.strip()
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# YAML front matter
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if idx == 0 and _YAML_FENCE.match(stripped):
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in_yaml = True
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continue
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if in_yaml:
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if _YAML_FENCE.match(stripped):
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in_yaml = False
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continue
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# Code blocks
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if _CODE_FENCE.match(stripped):
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if not in_code:
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code_blocks += 1
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in_code = not in_code
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continue
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if in_code:
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# Count figure labels inside code blocks
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for pat in _FIGURE_DEF:
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figures += len(pat.findall(line))
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continue
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# Blank lines don't count as text
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if not stripped:
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continue
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# Skip div fences, HTML comments, raw LaTeX for text counting
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if stripped.startswith(":::") or stripped.startswith("<!--"):
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# But still check for labels in div lines
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for pat in _FIGURE_DEF:
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figures += len(pat.findall(line))
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for pat in _TABLE_DEF:
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tables += len(pat.findall(line))
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for pat in _LISTING_DEF:
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listings += len(pat.findall(line))
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continue
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# Count definitions
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for pat in _FIGURE_DEF:
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figures += len(pat.findall(line))
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for pat in _TABLE_DEF:
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tables += len(pat.findall(line))
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for pat in _EQUATION_DEF:
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equations += len(pat.findall(line))
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for pat in _LISTING_DEF:
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listings += len(pat.findall(line))
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for pat in _SECTION_DEF:
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sections += len(pat.findall(line))
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# Footnote definitions
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if footnote_def_pat.match(stripped):
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footnotes += 1
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# Citations (rough count of unique @cite patterns, excluding cross-refs)
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for cm in citation_pat.finditer(line):
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ref = cm.group(0)[1:] # strip @
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if not any(ref.startswith(p) for p in ("fig-", "tbl-", "sec-", "eq-", "lst-", "alg-", "algo-", "Algo-")):
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citations += 1
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# Text lines and words (prose lines only)
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# Skip heading attribute lines, pipe table separators, etc.
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if stripped.startswith("#|") or stripped.startswith("%%|"):
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continue
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if stripped.startswith("|") and set(stripped.replace("|", "").strip()) <= {"-", ":", " "}:
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continue # table separator line
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text_lines += 1
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# Word count: strip markdown formatting, count words
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clean = re.sub(r"`\{python\}[^`]*`", "PYVAL", stripped)
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clean = re.sub(r"\{[^}]+\}", "", clean) # strip attributes
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clean = re.sub(r"[#*_`~\[\](){}|>]", " ", clean)
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words = [w for w in clean.split() if len(w) > 0 and not w.startswith("\\")]
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word_count += len(words)
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return {
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"figures": figures,
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"tables": tables,
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"equations": equations,
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"listings": listings,
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"sections": sections,
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"footnotes": footnotes,
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"citations": citations,
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"code_blocks": code_blocks,
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"text_lines": text_lines,
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"words": word_count,
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}
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@staticmethod
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def _empty_stats() -> Dict:
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return {
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"figures": 0, "tables": 0, "equations": 0, "listings": 0,
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"sections": 0, "footnotes": 0, "citations": 0,
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"code_blocks": 0, "text_lines": 0, "words": 0,
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}
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@staticmethod
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def _aggregate(stats_list: List[Dict]) -> Dict:
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totals: Dict = {}
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for s in stats_list:
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for k, v in s.items():
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if isinstance(v, int):
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totals[k] = totals.get(k, 0) + v
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return totals
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def _print_summary_stats(self, all_stats, totals, root) -> None:
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table = Table(show_header=True, header_style="bold cyan", box=None)
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table.add_column("Metric", style="cyan", width=20)
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table.add_column("Count", style="white", justify="right", width=10)
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table.add_row("Chapters", str(len(all_stats)))
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table.add_row("Sections", f"{totals['sections']:,}")
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table.add_row("Figures", f"{totals['figures']:,}")
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table.add_row("Tables", f"{totals['tables']:,}")
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table.add_row("Equations", f"{totals['equations']:,}")
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table.add_row("Listings", f"{totals['listings']:,}")
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table.add_row("Footnotes", f"{totals['footnotes']:,}")
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table.add_row("Citations", f"{totals['citations']:,}")
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table.add_row("Code blocks", f"{totals['code_blocks']:,}")
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table.add_row("Text lines", f"{totals['text_lines']:,}")
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table.add_row("Words (approx)", f"{totals['words']:,}")
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|
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scope = str(root)
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try:
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scope = str(root.relative_to(self.config_manager.book_dir))
|
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except ValueError:
|
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pass
|
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console.print(Panel(table, title=f"Book Statistics — {scope}", border_style="cyan"))
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|
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def _print_chapter_stats(self, all_stats, totals) -> None:
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table = Table(show_header=True, header_style="bold cyan", box=None)
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table.add_column("Chapter", style="white", width=32, no_wrap=True)
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table.add_column("Fig", justify="right", width=5)
|
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table.add_column("Tbl", justify="right", width=5)
|
|
table.add_column("Eq", justify="right", width=5)
|
|
table.add_column("Lst", justify="right", width=5)
|
|
table.add_column("Sec", justify="right", width=5)
|
|
table.add_column("Fn", justify="right", width=5)
|
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table.add_column("Cite", justify="right", width=6)
|
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table.add_column("Words", justify="right", width=8)
|
|
|
|
for s in all_stats:
|
|
name = s["chapter"]
|
|
if len(name) > 30:
|
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name = name[:28] + "…"
|
|
table.add_row(
|
|
name,
|
|
str(s["figures"]),
|
|
str(s["tables"]),
|
|
str(s["equations"]),
|
|
str(s["listings"]),
|
|
str(s["sections"]),
|
|
str(s["footnotes"]),
|
|
str(s["citations"]),
|
|
f"{s['words']:,}",
|
|
)
|
|
|
|
# Totals row
|
|
table.add_row(
|
|
"[bold]TOTAL[/bold]",
|
|
f"[bold]{totals['figures']}[/bold]",
|
|
f"[bold]{totals['tables']}[/bold]",
|
|
f"[bold]{totals['equations']}[/bold]",
|
|
f"[bold]{totals['listings']}[/bold]",
|
|
f"[bold]{totals['sections']}[/bold]",
|
|
f"[bold]{totals['footnotes']}[/bold]",
|
|
f"[bold]{totals['citations']}[/bold]",
|
|
f"[bold]{totals['words']:,}[/bold]",
|
|
)
|
|
|
|
console.print(Panel(table, title="Book Statistics — By Chapter", border_style="cyan"))
|
|
|
|
# ------------------------------------------------------------------
|
|
# Figures
|
|
# ------------------------------------------------------------------
|
|
|
|
def _run_figures(self, root: Path, ns: argparse.Namespace) -> bool:
|
|
with_pdf = getattr(ns, "with_pdf", False)
|
|
|
|
# Determine chapter file list
|
|
if with_pdf:
|
|
# Use config-ordered list so sequential merge with LaTeX works
|
|
vol = "vol1" if ns.vol1 else ("vol2" if ns.vol2 else None)
|
|
chapter_files = self._config_ordered_chapters(vol)
|
|
if not chapter_files:
|
|
console.print("[yellow]Could not read chapter order from config. Falling back to directory scan.[/yellow]")
|
|
chapter_files = self._chapter_files_from_root(root)
|
|
else:
|
|
chapter_files = self._chapter_files_from_root(root)
|
|
|
|
if not chapter_files:
|
|
console.print("[yellow]No QMD files found.[/yellow]")
|
|
return False
|
|
|
|
# Extract QMD figures
|
|
all_figures: List[Dict] = []
|
|
for path in chapter_files:
|
|
chapter = self._chapter_name(path)
|
|
figs = self._extract_figures(path)
|
|
for i, fig in enumerate(figs, 1):
|
|
fig["chapter"] = chapter
|
|
fig["file"] = self._relative(path)
|
|
fig["seq"] = i # per-chapter sequential number
|
|
all_figures.extend(figs)
|
|
|
|
if not all_figures:
|
|
console.print("[yellow]No figures found.[/yellow]")
|
|
return True
|
|
|
|
# Merge with LaTeX manifest if requested
|
|
if with_pdf:
|
|
vol = "vol1" if ns.vol1 else ("vol2" if ns.vol2 else None)
|
|
manifest_path = self._find_latex_manifest(ns.manifest, vol)
|
|
if manifest_path:
|
|
latex_figs = self._parse_latex_manifest(manifest_path)
|
|
console.print(
|
|
f"[dim]LaTeX manifest: {manifest_path.name} "
|
|
f"({len(latex_figs)} figures)[/dim]"
|
|
)
|
|
if len(latex_figs) != len(all_figures):
|
|
console.print(
|
|
f"[yellow]Warning: LaTeX ({len(latex_figs)}) and QMD "
|
|
f"({len(all_figures)}) figure counts differ. "
|
|
f"Manifest may be stale — rebuild PDF to fix.[/yellow]"
|
|
)
|
|
# Merge by sequential position
|
|
for i, fig in enumerate(all_figures):
|
|
if i < len(latex_figs):
|
|
fig["fig_number"] = latex_figs[i]["number"]
|
|
fig["page"] = latex_figs[i]["page"]
|
|
else:
|
|
fig["fig_number"] = "?"
|
|
fig["page"] = "?"
|
|
else:
|
|
console.print(
|
|
"[yellow]No LaTeX manifest found. Build PDF first, "
|
|
"or pass --manifest PATH.[/yellow]"
|
|
)
|
|
for fig in all_figures:
|
|
fig["fig_number"] = "?"
|
|
fig["page"] = "?"
|
|
else:
|
|
# No PDF data — assign per-chapter sequential numbers
|
|
for fig in all_figures:
|
|
fig["fig_number"] = ""
|
|
fig["page"] = ""
|
|
|
|
output = self._format_figures(all_figures, ns.format, with_pdf)
|
|
|
|
if ns.output:
|
|
Path(ns.output).write_text(output, encoding="utf-8")
|
|
console.print(f"[green]Wrote {len(all_figures)} figures to {ns.output}[/green]")
|
|
else:
|
|
if ns.format == "text":
|
|
self._print_figures_rich(all_figures, with_pdf)
|
|
else:
|
|
print(output)
|
|
|
|
return True
|
|
|
|
def _chapter_files_from_root(self, root: Path) -> List[Path]:
|
|
"""Get chapter QMD files from a directory, filtering out parts/."""
|
|
files = self._qmd_files(root)
|
|
return [f for f in files if "/parts/" not in str(f)]
|
|
|
|
# ------------------------------------------------------------------
|
|
# Config reading
|
|
# ------------------------------------------------------------------
|
|
|
|
def _pdf_config_paths(self, vol: Optional[str] = None) -> List[Path]:
|
|
"""Return candidate PDF config YAML paths in priority order."""
|
|
quarto_dir = self.config_manager.book_dir
|
|
vol_str = vol or "vol1"
|
|
return [
|
|
quarto_dir / "_quarto.yml",
|
|
quarto_dir / f"config/_quarto-pdf-{vol_str}.yml",
|
|
quarto_dir / f"config/_quarto-pdf-{vol_str}-copyedit.yml",
|
|
]
|
|
|
|
def _read_pdf_config(self, vol: Optional[str] = None) -> Tuple[Optional[Path], Optional[dict], str]:
|
|
"""Read the first valid PDF config for *vol*.
|
|
|
|
Returns (config_path, parsed_yaml, raw_text). Any element may
|
|
be ``None`` / empty if no config was found.
|
|
"""
|
|
import yaml
|
|
|
|
for config_path in self._pdf_config_paths(vol):
|
|
if not config_path.exists():
|
|
continue
|
|
resolved = config_path.resolve() if config_path.is_symlink() else config_path
|
|
try:
|
|
raw = resolved.read_text(encoding="utf-8")
|
|
parsed = yaml.safe_load(raw)
|
|
except Exception:
|
|
continue
|
|
if parsed and "book" in parsed:
|
|
return resolved, parsed, raw
|
|
return None, None, ""
|
|
|
|
def _output_dirs_from_configs(self, vol: Optional[str] = None) -> List[Path]:
|
|
"""Return all ``output-dir`` values declared in the PDF configs for *vol*.
|
|
|
|
This is the authoritative way to locate build artifacts — the
|
|
YAML configs define exactly where Quarto writes its output.
|
|
"""
|
|
import yaml
|
|
|
|
quarto_dir = self.config_manager.book_dir
|
|
dirs: List[Path] = []
|
|
|
|
for config_path in self._pdf_config_paths(vol):
|
|
if not config_path.exists():
|
|
continue
|
|
resolved = config_path.resolve() if config_path.is_symlink() else config_path
|
|
try:
|
|
parsed = yaml.safe_load(resolved.read_text(encoding="utf-8"))
|
|
except Exception:
|
|
continue
|
|
if not parsed:
|
|
continue
|
|
output_dir = (parsed.get("project") or {}).get("output-dir")
|
|
if output_dir:
|
|
full = quarto_dir / output_dir
|
|
if full not in dirs:
|
|
dirs.append(full)
|
|
|
|
return dirs
|
|
|
|
def _config_ordered_chapters(self, vol: Optional[str] = None) -> List[Path]:
|
|
"""Read chapter order from Quarto YAML config (same order as PDF build).
|
|
|
|
This is critical for --with-pdf because the LaTeX manifest is
|
|
sequential — Figure N in the manifest corresponds to the Nth
|
|
figure extracted from the QMD files in config order.
|
|
"""
|
|
quarto_dir = self.config_manager.book_dir
|
|
vol_str = vol or "vol1"
|
|
|
|
_, _, raw = self._read_pdf_config(vol)
|
|
if not raw:
|
|
return []
|
|
|
|
qmd_files: List[Path] = []
|
|
|
|
# Read both commented and uncommented chapter entries (full intended order)
|
|
# Pattern: lines like " - contents/vol1/chapter/chapter.qmd"
|
|
# or " # - contents/vol1/chapter/chapter.qmd"
|
|
comment_pat = re.compile(
|
|
rf"^\s*#?\s*-\s*(contents/{vol_str}/[^\s#]+\.qmd)\s*$",
|
|
re.MULTILINE,
|
|
)
|
|
for m in comment_pat.finditer(raw):
|
|
rel = m.group(1)
|
|
# Skip parts, frontmatter, shelved
|
|
if "/parts/" in rel or "/frontmatter/" in rel or "_shelved" in rel:
|
|
continue
|
|
full = quarto_dir / rel
|
|
if full.exists():
|
|
qmd_files.append(full)
|
|
|
|
return qmd_files
|
|
|
|
# ------------------------------------------------------------------
|
|
# LaTeX manifest
|
|
# ------------------------------------------------------------------
|
|
|
|
@staticmethod
|
|
def _is_latex_manifest(path: Path) -> bool:
|
|
try:
|
|
return _MANIFEST_HEADER in path.read_text(encoding="utf-8")[:200]
|
|
except Exception:
|
|
return False
|
|
|
|
def _find_latex_manifest(
|
|
self, explicit_path: Optional[str], vol: Optional[str]
|
|
) -> Optional[Path]:
|
|
"""Locate the LaTeX figure manifest (*_figures.txt).
|
|
|
|
Search order:
|
|
1. Explicit --manifest path
|
|
2. ``output-dir`` directories declared in the PDF YAML configs
|
|
3. Quarto root directory (fresh from LaTeX, not yet moved)
|
|
"""
|
|
if explicit_path:
|
|
p = Path(explicit_path)
|
|
if not p.is_absolute():
|
|
p = Path.cwd() / p
|
|
return p if p.exists() else None
|
|
|
|
quarto_dir = self.config_manager.book_dir
|
|
candidates: List[Path] = []
|
|
|
|
# Search the output directories declared in the YAML configs
|
|
for output_dir in self._output_dirs_from_configs(vol):
|
|
if output_dir.exists():
|
|
for f in output_dir.glob("*_figures.txt"):
|
|
if self._is_latex_manifest(f):
|
|
candidates.append(f)
|
|
|
|
# Fallback: quarto root (LaTeX writes here during compilation,
|
|
# before the post-render script moves it into the build dir)
|
|
for f in quarto_dir.glob("*_figures.txt"):
|
|
if self._is_latex_manifest(f):
|
|
candidates.append(f)
|
|
|
|
if not candidates:
|
|
return None
|
|
|
|
# Most recently modified wins
|
|
candidates.sort(key=lambda p: p.stat().st_mtime, reverse=True)
|
|
return candidates[0]
|
|
|
|
@staticmethod
|
|
def _parse_latex_manifest(path: Path) -> List[Dict]:
|
|
"""Parse a LaTeX figure manifest into [{number, page}, ...]."""
|
|
figures: List[Dict] = []
|
|
try:
|
|
content = path.read_text(encoding="utf-8")
|
|
except Exception:
|
|
return figures
|
|
for m in _LATEX_FIG_PAT.finditer(content):
|
|
figures.append({"number": m.group(1), "page": m.group(2)})
|
|
return figures
|
|
|
|
# ------------------------------------------------------------------
|
|
# Figure extraction from QMD
|
|
# ------------------------------------------------------------------
|
|
|
|
def _extract_figures(self, path: Path) -> List[Dict]:
|
|
"""Extract all figures from a QMD file, deduplicating by label."""
|
|
try:
|
|
content = path.read_text(encoding="utf-8")
|
|
except Exception:
|
|
return []
|
|
|
|
raw: List[Dict] = []
|
|
|
|
# 1. Fenced divs: ::: {#fig-id fig-cap="..." fig-alt="..."}
|
|
for m in _DIV_FIG.finditer(content):
|
|
attrs = m.group(1)
|
|
label_m = re.search(r"#(fig-[\w-]+)", attrs)
|
|
if not label_m:
|
|
continue
|
|
fig_id = label_m.group(1)
|
|
cap_m = _ATTR_CAP.search(attrs)
|
|
alt_m = _ATTR_ALT.search(attrs)
|
|
caption = self._unescape(cap_m.group(1)) if cap_m else ""
|
|
alt_text = self._unescape(alt_m.group(1)) if alt_m else ""
|
|
raw.append({
|
|
"id": fig_id,
|
|
"label": self._extract_title(caption),
|
|
"caption": caption,
|
|
"alt_text": alt_text,
|
|
"source": "div",
|
|
"pos": m.start(),
|
|
})
|
|
|
|
# 2. Markdown images: {#fig-id fig-alt="..."}
|
|
for m in _IMG_FIG.finditer(content):
|
|
attrs = m.group(2)
|
|
label_m = re.search(r"#(fig-[\w-]+)", attrs)
|
|
if not label_m:
|
|
continue
|
|
fig_id = label_m.group(1)
|
|
caption = m.group(1).strip()
|
|
cap_m = _ATTR_CAP.search(attrs)
|
|
alt_m = _ATTR_ALT.search(attrs)
|
|
if cap_m:
|
|
caption = self._unescape(cap_m.group(1))
|
|
alt_text = self._unescape(alt_m.group(1)) if alt_m else ""
|
|
raw.append({
|
|
"id": fig_id,
|
|
"label": self._extract_title(caption),
|
|
"caption": caption,
|
|
"alt_text": alt_text,
|
|
"source": "image",
|
|
"pos": m.start(),
|
|
})
|
|
|
|
# 3. Code-cell figures: ```{python} with #| label: fig-...
|
|
for m in _CODE_BLOCK_FIG.finditer(content):
|
|
cell_opts_text = m.group(1)
|
|
lbl_m = re.search(r"#\|\s*label:\s*(fig-[\w-]+)", cell_opts_text)
|
|
if not lbl_m:
|
|
continue
|
|
fig_id = lbl_m.group(1)
|
|
cap_m = re.search(r'#\|\s*fig-cap:\s*"([^"]*)"', cell_opts_text)
|
|
alt_m = re.search(r'#\|\s*fig-alt:\s*"([^"]*)"', cell_opts_text)
|
|
caption = cap_m.group(1) if cap_m else ""
|
|
alt_text = alt_m.group(1) if alt_m else ""
|
|
raw.append({
|
|
"id": fig_id,
|
|
"label": self._extract_title(caption),
|
|
"caption": caption,
|
|
"alt_text": alt_text,
|
|
"source": "code-cell",
|
|
"pos": m.start(),
|
|
})
|
|
|
|
# Sort by position in file, then deduplicate by label
|
|
raw.sort(key=lambda x: x["pos"])
|
|
seen: Dict[str, Dict] = {}
|
|
for fig in raw:
|
|
fid = fig["id"]
|
|
if fid in seen:
|
|
# Keep whichever has a richer caption
|
|
if not seen[fid]["caption"] and fig["caption"]:
|
|
seen[fid] = fig
|
|
else:
|
|
seen[fid] = fig
|
|
|
|
return [
|
|
{k: v for k, v in fig.items() if k != "pos"}
|
|
for fig in sorted(seen.values(), key=lambda x: x["pos"])
|
|
]
|
|
|
|
@staticmethod
|
|
def _unescape(s: str) -> str:
|
|
return s.replace('\\"', '"').replace("\\'", "'")
|
|
|
|
@staticmethod
|
|
def _strip_quotes(s: str) -> str:
|
|
s = s.strip()
|
|
if (s.startswith('"') and s.endswith('"')) or (s.startswith("'") and s.endswith("'")):
|
|
s = s[1:-1]
|
|
return s
|
|
|
|
@staticmethod
|
|
def _extract_title(caption: str) -> str:
|
|
"""Extract the bold title from a caption."""
|
|
if not caption:
|
|
return ""
|
|
m = re.match(r"\*\*([^*]+)\*\*", caption)
|
|
if m:
|
|
return m.group(1).rstrip(":.").strip()
|
|
colon = caption.find(":")
|
|
period = caption.find(".")
|
|
if colon > 0 and (period < 0 or colon < period):
|
|
return caption[:colon].strip()
|
|
if period > 0:
|
|
return caption[:period].strip()
|
|
return caption[:60].strip()
|
|
|
|
# ------------------------------------------------------------------
|
|
# Output formatting
|
|
# ------------------------------------------------------------------
|
|
|
|
def _fig_display_number(self, fig: Dict, with_pdf: bool) -> str:
|
|
"""Return the display number for a figure."""
|
|
if with_pdf and fig.get("fig_number"):
|
|
return fig["fig_number"]
|
|
return str(fig.get("seq", ""))
|
|
|
|
def _format_figures(self, figures: List[Dict], fmt: str, with_pdf: bool = False) -> str:
|
|
if fmt == "csv":
|
|
header = "chapter,fig_number,page,label,id,caption,alt_text,source,file"
|
|
lines = [header]
|
|
for f in figures:
|
|
cap = f["caption"].replace('"', '""')
|
|
alt = f["alt_text"].replace('"', '""')
|
|
lbl = f["label"].replace('"', '""')
|
|
fig_num = f.get("fig_number", "")
|
|
page = f.get("page", "")
|
|
lines.append(
|
|
f'"{f["chapter"]}",{fig_num},{page},"{lbl}",{f["id"]},"{cap}","{alt}",{f["source"]},{f["file"]}'
|
|
)
|
|
return "\n".join(lines) + "\n"
|
|
|
|
if fmt == "markdown":
|
|
title = "# Figure List"
|
|
if with_pdf:
|
|
title += " (with PDF numbers)"
|
|
lines = [f"{title}\n"]
|
|
current_chapter = ""
|
|
for f in figures:
|
|
if f["chapter"] != current_chapter:
|
|
current_chapter = f["chapter"]
|
|
lines.append(f"\n## {current_chapter}\n")
|
|
num = self._fig_display_number(f, with_pdf)
|
|
page = f.get("page", "")
|
|
header = f"**Figure {num}**"
|
|
if with_pdf and page:
|
|
header += f" (Page {page})"
|
|
header += f" (`{f['id']}`)"
|
|
lines.append(header)
|
|
if f["label"]:
|
|
lines.append(f" **Title**: {f['label']}")
|
|
if f["caption"]:
|
|
lines.append(f" **Caption**: {f['caption']}")
|
|
if f["alt_text"]:
|
|
lines.append(f" **Alt-text**: {f['alt_text']}")
|
|
lines.append(f" *Source*: {f['source']} | *File*: {f['file']}")
|
|
lines.append("")
|
|
# Summary
|
|
total = len(figures)
|
|
with_cap = sum(1 for f in figures if f["caption"])
|
|
with_alt = sum(1 for f in figures if f["alt_text"])
|
|
lines.append(f"---\n**Total**: {total} figures | Captions: {with_cap}/{total} | Alt-text: {with_alt}/{total}")
|
|
return "\n".join(lines)
|
|
|
|
# Plain text
|
|
lines = []
|
|
current_chapter = ""
|
|
for f in figures:
|
|
if f["chapter"] != current_chapter:
|
|
current_chapter = f["chapter"]
|
|
lines.append(f"\n{'='*70}")
|
|
lines.append(f" {current_chapter}")
|
|
lines.append(f"{'='*70}")
|
|
num = self._fig_display_number(f, with_pdf)
|
|
page = f.get("page", "")
|
|
if with_pdf and page:
|
|
lines.append(f" Figure {num:>6s} (Page {page:>4s}) {f['id']}")
|
|
else:
|
|
lines.append(f" Fig {num:>3s} {f['id']}")
|
|
if f["label"]:
|
|
lines.append(f" Title: {f['label']}")
|
|
has_cap = "YES" if f["caption"] else "MISSING"
|
|
has_alt = "YES" if f["alt_text"] else "MISSING"
|
|
lines.append(f" Caption: {has_cap} | Alt-text: {has_alt}")
|
|
lines.append("")
|
|
total = len(figures)
|
|
with_cap = sum(1 for f in figures if f["caption"])
|
|
with_alt = sum(1 for f in figures if f["alt_text"])
|
|
lines.append(f"Total: {total} figures | Captions: {with_cap}/{total} | Alt-text: {with_alt}/{total}")
|
|
return "\n".join(lines) + "\n"
|
|
|
|
def _print_figures_rich(self, figures: List[Dict], with_pdf: bool = False) -> None:
|
|
table = Table(show_header=True, header_style="bold cyan", box=None)
|
|
if with_pdf:
|
|
table.add_column("Fig #", style="bold", width=8, justify="right")
|
|
table.add_column("Page", style="dim", width=5, justify="right")
|
|
else:
|
|
table.add_column("#", style="dim", width=4, justify="right")
|
|
table.add_column("Label", style="cyan", width=30, no_wrap=True)
|
|
table.add_column("Title", style="white", width=30, no_wrap=True)
|
|
table.add_column("Cap", width=4, justify="center")
|
|
table.add_column("Alt", width=4, justify="center")
|
|
table.add_column("Src", style="dim", width=6)
|
|
|
|
current_chapter = ""
|
|
for f in figures:
|
|
if f["chapter"] != current_chapter:
|
|
current_chapter = f["chapter"]
|
|
name = current_chapter[:30] if len(current_chapter) <= 30 else current_chapter[:28] + "…"
|
|
if with_pdf:
|
|
table.add_row("", "", f"[bold yellow]{name}[/bold yellow]", "", "", "", "")
|
|
else:
|
|
table.add_row("", f"[bold yellow]{name}[/bold yellow]", "", "", "", "")
|
|
|
|
title = f["label"][:28] + "…" if len(f["label"]) > 30 else f["label"]
|
|
cap = "[green]✓[/green]" if f["caption"] else "[red]✗[/red]"
|
|
alt = "[green]✓[/green]" if f["alt_text"] else "[red]✗[/red]"
|
|
num = self._fig_display_number(f, with_pdf)
|
|
|
|
if with_pdf:
|
|
page = f.get("page", "")
|
|
table.add_row(num, page, f["id"], title, cap, alt, f["source"])
|
|
else:
|
|
table.add_row(num, f["id"], title, cap, alt, f["source"])
|
|
|
|
total = len(figures)
|
|
with_cap = sum(1 for f in figures if f["caption"])
|
|
with_alt = sum(1 for f in figures if f["alt_text"])
|
|
|
|
panel_title = "Figure List"
|
|
if with_pdf:
|
|
panel_title += " (with PDF numbers)"
|
|
console.print(Panel(table, title=panel_title, border_style="cyan"))
|
|
console.print(
|
|
f"[bold]Total[/bold]: {total} figures | "
|
|
f"Captions: {with_cap}/{total} | "
|
|
f"Alt-text: {with_alt}/{total}"
|
|
)
|
|
|
|
# ------------------------------------------------------------------
|
|
# Concepts (ported from extract_concepts.py)
|
|
# ------------------------------------------------------------------
|
|
|
|
def _run_concepts(self, root: Path, ns) -> bool:
|
|
"""Extract key concepts from QMD files."""
|
|
files = self._qmd_files(root)
|
|
chapter_files = [f for f in files if "/parts/" not in str(f) and "/frontmatter/" not in str(f)]
|
|
|
|
if not chapter_files:
|
|
console.print("[yellow]No QMD files found.[/yellow]")
|
|
return False
|
|
|
|
bold_pat = re.compile(r"\*\*([^*]+)\*\*")
|
|
fn_def_pat = re.compile(r"\[\^fn-([^\]]+)\]:\s*(.+?)(?=\n\n|\[\^|\Z)", re.DOTALL)
|
|
def_patterns = [
|
|
re.compile(r"(\w[\w\s]+?)\s+is defined as", re.IGNORECASE),
|
|
re.compile(r"(\w[\w\s]+?)\s+refers to", re.IGNORECASE),
|
|
re.compile(r"We define\s+(\w[\w\s]+?)\s+as", re.IGNORECASE),
|
|
]
|
|
heading_pat = re.compile(r"^(#{1,6})\s+(.*)")
|
|
|
|
for path in chapter_files:
|
|
try:
|
|
content = path.read_text(encoding="utf-8")
|
|
except Exception:
|
|
continue
|
|
|
|
lines = content.splitlines()
|
|
chapter = self._chapter_name(path)
|
|
|
|
# Extract H2 topics
|
|
h2_topics = []
|
|
for line in lines:
|
|
m = heading_pat.match(line)
|
|
if m and len(m.group(1)) == 2:
|
|
text = re.sub(r"\{#[^}]+\}", "", m.group(2)).strip()
|
|
if not text.startswith("Purpose"):
|
|
h2_topics.append(text)
|
|
|
|
# Bold terms
|
|
bold_terms = set()
|
|
for m in bold_pat.finditer(content):
|
|
term = m.group(1).strip()
|
|
if len(term) > 2 and not term.startswith("Note"):
|
|
bold_terms.add(term)
|
|
|
|
# Definitions
|
|
definitions = set()
|
|
for pat in def_patterns:
|
|
for m in pat.finditer(content):
|
|
term = m.group(1).strip()
|
|
if len(term) < 50:
|
|
definitions.add(term)
|
|
|
|
# Footnotes
|
|
footnotes = []
|
|
for m in fn_def_pat.finditer(content):
|
|
footnotes.append(m.group(1))
|
|
|
|
# Print
|
|
name = chapter[:40] if len(chapter) <= 40 else chapter[:38] + "…"
|
|
console.print(f"\n[bold cyan]{name}[/bold cyan] [dim]({self._relative(path)})[/dim]")
|
|
|
|
if h2_topics:
|
|
console.print(f" [yellow]Topics:[/yellow] {', '.join(h2_topics[:8])}")
|
|
if bold_terms:
|
|
terms = sorted(bold_terms)[:12]
|
|
console.print(f" [yellow]Key terms:[/yellow] {', '.join(terms)}")
|
|
if definitions:
|
|
defs = sorted(definitions)[:6]
|
|
console.print(f" [yellow]Defines:[/yellow] {', '.join(defs)}")
|
|
if footnotes:
|
|
console.print(f" [yellow]Footnotes:[/yellow] {len(footnotes)}")
|
|
|
|
console.print(f"\n[bold]Scanned {len(chapter_files)} files.[/bold]")
|
|
return True
|
|
|
|
# ------------------------------------------------------------------
|
|
# Headers (ported from extract_headers.py)
|
|
# ------------------------------------------------------------------
|
|
|
|
def _run_headers(self, root: Path, ns) -> bool:
|
|
"""List all section headers with levels."""
|
|
files = self._qmd_files(root)
|
|
chapter_files = [f for f in files if "/parts/" not in str(f)]
|
|
|
|
if not chapter_files:
|
|
console.print("[yellow]No QMD files found.[/yellow]")
|
|
return False
|
|
|
|
heading_pat = re.compile(r"^(#{1,6})\s+(.*)")
|
|
|
|
table = Table(show_header=True, header_style="bold cyan", box=None)
|
|
table.add_column("File", style="dim", width=30, no_wrap=True)
|
|
table.add_column("Lvl", style="cyan", width=5, justify="center")
|
|
table.add_column("Header", style="white", width=50)
|
|
|
|
total = 0
|
|
for path in chapter_files:
|
|
try:
|
|
lines = path.read_text(encoding="utf-8").splitlines()
|
|
except Exception:
|
|
continue
|
|
rel = self._relative(path)
|
|
if len(rel) > 28:
|
|
rel = "…" + rel[-27:]
|
|
for line in lines:
|
|
m = heading_pat.match(line)
|
|
if m:
|
|
level = m.group(1)
|
|
text = m.group(2).strip()
|
|
# Indent based on level for visual hierarchy
|
|
indent = " " * (len(level) - 1)
|
|
table.add_row(rel, level, f"{indent}{text}")
|
|
total += 1
|
|
rel = "" # Only show filename on first header
|
|
|
|
console.print(Panel(table, title="Section Headers", border_style="cyan"))
|
|
console.print(f"[bold]Total:[/bold] {total} headers across {len(chapter_files)} files")
|
|
return True
|
|
|
|
# ------------------------------------------------------------------
|
|
# Acronyms (ported from find_acronyms.py)
|
|
# ------------------------------------------------------------------
|
|
|
|
def _run_acronyms(self, root: Path, ns) -> bool:
|
|
"""Find acronyms in parentheses (e.g., (CNN), (GPU))."""
|
|
from collections import Counter
|
|
|
|
files = self._qmd_files(root)
|
|
if not files:
|
|
console.print("[yellow]No QMD files found.[/yellow]")
|
|
return False
|
|
|
|
acronym_pat = re.compile(r"\(([A-Z]{2,}s?)\)")
|
|
acronym_counts: Dict[str, int] = Counter()
|
|
acronym_files: Dict[str, List[str]] = defaultdict(list)
|
|
|
|
for path in files:
|
|
try:
|
|
content = path.read_text(encoding="utf-8")
|
|
except Exception:
|
|
continue
|
|
found = set()
|
|
for m in acronym_pat.finditer(content):
|
|
acr = m.group(1)
|
|
acronym_counts[acr] += 1
|
|
found.add(acr)
|
|
for acr in found:
|
|
acronym_files[acr].append(self._relative(path))
|
|
|
|
if not acronym_counts:
|
|
console.print("[yellow]No acronyms found.[/yellow]")
|
|
return True
|
|
|
|
table = Table(show_header=True, header_style="bold cyan", box=None)
|
|
table.add_column("Acronym", style="cyan", width=12)
|
|
table.add_column("Count", style="white", width=7, justify="right")
|
|
table.add_column("Files", style="dim", width=50)
|
|
|
|
for acr, count in sorted(acronym_counts.items(), key=lambda x: -x[1]):
|
|
file_list = acronym_files[acr]
|
|
files_str = ", ".join(f.split("/")[-1].replace(".qmd", "") for f in file_list[:5])
|
|
if len(file_list) > 5:
|
|
files_str += f" +{len(file_list) - 5} more"
|
|
table.add_row(acr, str(count), files_str)
|
|
|
|
console.print(Panel(table, title="Acronyms Found", border_style="cyan"))
|
|
console.print(f"[bold]Total:[/bold] {len(acronym_counts)} unique acronyms, {sum(acronym_counts.values())} occurrences")
|
|
return True
|