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Bindery

Audit EPUB body text and repair broken EPUBs with safe, deterministic fixes, validated by epubcheck, with optional in-place replacement in a Calibre library.

Bindery's dry-run library sweep: per-book epubcheck results and a summary table ending in 'no files written'

What it fixes

Bindery makes accidentally broken markup well-formed again. It does not rewrite or reflow content. The default pass applies only a small set of deterministic, semantics-preserving well-formedness fixes that real-world EPUBs (especially Calibre conversions) trip over — nothing else changes without an explicit flag:

  • Unclosed void elements (<link>, <br>, <img>, ...) get self-closed.
  • Undeclared named entities (&nbsp;, &deg;, &eacute;, ...) become numeric character references that every XML parser understands.
  • Bare & (common in toc.ncx) is escaped to &amp;.
  • Junk before the XML prolog (BOM, stray bytes) is stripped.
  • Duplicate xmlns on the root <html> is collapsed to one.
  • NCX-001: toc.ncx dtb:uid is synced to the OPF unique identifier; duplicated NCX playOrder values are resequenced whenever the NCX is processed (part of the always-on NCX pipeline, not a flag).
  • mimetype is rewritten first and stored, fixing the common ordering defect; a missing entry is added and wrong or whitespace-padded content is normalized to the OCF constant.

Opt-in repairs

Everything below is off until its flag is passed (or all at once via --all). They go further than well-formedness — altering structure or adding minimal content — so they never run by default:

  • --fix-ids: rewrite ids that are not valid XML names (start with a digit, contain a colon) in the OPF manifest, updating every reference to them (spine, fallback, media-overlay, the EPUB 2 cover meta), and in the NCX (where old conversions stamp navPoint ids from UUIDs). Touches the OPF, so it is off by default; the dc: metadata is never altered.
  • --add-img-alt: add alt="" to <img> elements missing the required attribute. Renders identically, but it adds markup the author never wrote, and an empty alt tells a screen reader the image is decorative; hence opt-in.
  • --reserialize: rebuild content documents that are still malformed by re-parsing them with html5lib and re-emitting XHTML, closing unclosed <p>/<div>/<span>/<blockquote> that the regex transforms cannot. Runs only on documents that are not already well-formed, so good files are untouched.
  • --strip-bad-attrs: drop attributes that are invalid XML (a name starting with a digit, or a namespaced name whose prefix is never declared, like Office VML v:shapes). Surgical and a no-op on well-formed files.
  • --escape-unknown-entities: escape entity names that are not in the HTML5 table (&foo; becomes &amp;foo;), which renders exactly as browsers already render an unknown entity. Documents whose DOCTYPE carries an internal subset are skipped wholesale, since a subset can declare custom entities.
  • --fix-id-colons: translates illegal colons in id="X:Y" and their matching #X:Y fragment references to valid underscores.
  • --fix-empty-body: appends a non-breaking space &nbsp; to strictly empty body tags to satisfy parser requirements.
  • --fix-missing-title: injects a <title>Unknown</title> fallback in the <head> if missing, handling both empty <title/> self-closing tags and entirely absent tags.
  • --unwrap-block-in-inline: safely unwraps <span> tags that illegally contain a block-level element (e.g. <div> or <p>), leaving the block element intact.
  • --strip-invalid-value: systematically strips invalid value="..." attributes from elements like <div>, <span>, <p>, etc.
  • --fix-page-map: normalizes legacy page-map markup — drops the non-standard page-map="..." attribute from the OPF <spine> and adds class="pages" to classless NCX <pageList> elements (epubcheck rejects both on older HarperCollins / Anna's Archive conversions).
  • --strip-epub3-attrs: scrubs the EPUB3-only attributes epubcheck rejects on an EPUB2 package — page-progression-direction, epub:type, aria-label (a fixed, documented set; rendering is unchanged, and lookalikes like type or the wider aria family survive).
  • --downgrade-epub3-tags: downgrades EPUB3/HTML5 semantic elements to their EPUB2 equivalents — figure/section to div, figcaption to p — keeping existing classes and appending the semantic name (class="figure") as the styling hook. Tag names a stylesheet styles as an element selector are protected book-wide, so styled formatting is never destroyed.
  • --unwrap-illegal-tags: strips completely invalid or deprecated HTML tags that break EPUB3 validation (<st>, <sentence>, <o>, <w>, <pagebreak>) while retaining their inner text. Any of those names styled as an element selector by an EPUB stylesheet (.css entries and inline <style> blocks alike; class/id selectors like .st/#w don't count) is protected for the whole book, guaranteeing format preservation.

Three opt-in fixes are lossy and stand apart from the semantics-preserving rest:

  • --strip-pagination: remove print page numbers and running headers that a PDF/OCR conversion baked into the body text as literal paragraphs (so they reflow into the middle of a sentence: "where the hay cart 16 was taking him"). It removes only that injected furniture, never the author's prose: where a number split a sentence it rejoins the two paragraphs (closing up a word split like compli- / mentary), and it preserves roman chapter numbers, page-list nav anchors, and years. A book is only treated as paginated when it has both a dense run of arabic numbers and several confident mid-sentence interrupts, so a merely chapter-numbered book is left alone. Three safety nets guard every edit (character conservation, tag balance, and an epubcheck no-regression check); any failure leaves the document untouched.
  • --strip-broken-tags: remove leaked HTML closing tags missing their open brackets (e.g. </p>) that render as raw text.
  • --strip-watermarks: remove known producer and distributor watermarks (e.g. OceanofPDF, ABC Amber LIT Converter) and stray marker files. It locates the stamp and deletes the outermost wrapper whose entire visible text is the watermark, ensuring prose that merely mentions the URL is preserved.

All lossy edits are invisible to epubcheck, so they are accepted when the result is no worse rather than measurably better.

The safety contract

Every repair is gated by epubcheck. The acceptance rule is two-mode, because a fatal parse error makes epubcheck stop reading a file and hides every downstream error:

  • If a book had fatals, success means fewer fatals. The error count may rise as previously-hidden schema warnings become visible once the file parses; that is the book going from "won't open" to "opens with nits," not a regression.
  • If a book had no fatals, an error increase is a real regression, so a strict error decrease is required.

Introducing a net-new fatal is always rejected. If epubcheck itself fails to run (crash, timeout, unparsable output), the book is reported as an error and never applied; only an explicit --no-validate skips the gate. Originals are never modified except by an explicit, atomic in-place replace (see below), and even then only after the gate accepts the result.

The lossy modes (--strip-pagination, --strip-broken-tags, and --strip-watermarks) are the exception to the "must improve" rule. Since they remove visible markup rather than correcting XML schema violations, epubcheck counts often remain unchanged. They are accepted when the result is no worse (no net-new fatals or errors), relying on strict programmatic safety nets instead.

Install

Python 3.14+, plus epubcheck on PATH for the gate. Dependencies: tqdm for progress output, plus the pinned VirInvictus libraries vir-tui (TUI rendering) and cquarry (read-only Calibre database access); html5lib remains an optional extra, needed only for --reserialize.

uv tool install bindery-cli                            # core tools
uv tool install "bindery-cli[reserialize]"             # incl. --reserialize

Usage

Three verbs: bindery repair fixes a single EPUB epubcheck-gated, bindery audit reports content flaws without touching anything, and bindery library sweeps a Calibre library tree (dry run by default; --apply replaces accepted books atomically in place). The sections below take each in turn.

Auditing

Bindery includes a comprehensive auditing tool to inspect EPUB body text for non-schema flaws that epubcheck cannot catch. It extracts and analyzes the visible text to detect content issues, producing console reports that can be used to filter your library or feed into bindery repair.

Scan a Calibre library for specific issues:

# Detect non-English content (e.g., Cyrillic or CJK in an English library)
cd ~/docs/Calibre\ Library && bindery audit content

# Find books with hardcoded print page numbers interrupting the text
bindery audit pagenumbers ~/docs/Calibre\ Library

# Find books that are empty or severely truncated
bindery audit emptytext ~/docs/Calibre\ Library

# Find books with severe OCR damage (garbage characters, excessive hyphenation)
bindery audit ocr ~/docs/Calibre\ Library

# Flag books where a single content document is too large for readers to render
bindery audit monolithic ~/docs/Calibre\ Library

# Run all audits and generate a comprehensive CSV
cd ~/docs/Calibre\ Library && bindery audit all

Audits can also be run on a directory of loose .epub files by passing the path as the second argument:

bindery audit pagenumbers /path/to/loose/epubs

Or on one or more library books by Calibre id (comma-separated) — fetched through cquarry's single-entity get_book() (no library-wide scan), with the EPUB resolved via cquarry's own path logic:

cd ~/docs/Calibre\ Library && bindery audit all --id 1234,1235

--id composes with --tag: the book is tagged only if the audit flags it.

Spine-integrity reporting: Both audit and library reports now classify manifest/NCX references that point to absent files. A convention verdict means the ToC is bloated but the present documents form a consecutive chapter span (e.g., the Wandering Inn official-build pattern, safe). A fragment verdict means the span itself is broken.

Archive integrity: every audit fully reads each archive entry (CRC + decompression), so a damaged download is reported CORRUPT — with the first broken entry named — instead of being mislabeled EMPTY by emptytext. library --sweep splits its unreadable bucket into not_a_zip / truncated / encrypted / corrupt_entry, so the right disease is visible without leaving the sweep.

Tagging flagged books (opt-in)

By default an audit writes nothing. With --tag TAG (library mode only), every book the audit flags is tagged in metadata.db through cquarry's trigger-safe write module — useful for piping flagged books back into Calibre views:

cd ~/docs/Calibre\ Library && bindery audit content --tag "Audit Flagged"

The audit itself stays read-only; only the final tagging pass writes, it skips books that already carry the tag, and THIN emptytext advisories are never tagged. Close Calibre first so the write does not fight its lock. Tagged books are recorded in Calibre's metadata_dirtied queue, so the desktop app regenerates their sidecar .opfs (and re-pushes metadata to wireless readers) on its next startup — no manual resync needed.

Repair one book to a new file (gated; writes only if it is an improvement):

bindery repair broken.epub                 # -> "broken (repaired).epub"
bindery repair broken.epub fixed.epub
bindery repair scanned.epub --strip-pagination   # also remove baked-in page numbers

Scan a Calibre library and see what would be fixed, writing nothing:

bindery library ~/docs/Calibre\ Library --only fatals --audit epub_audit.csv

Apply accepted repairs in place, atomically, with backups:

bindery library ~/docs/Calibre\ Library --only fatals --apply --backup ~/bindery-backups

Apply all safe and lossy repairs directly into the Calibre database natively:

bindery library ~/docs/Calibre\ Library --only all --apply --all --install-to-calibre
  • --only {fatals,ncx,all} restricts the candidate set. ncx targets NCX-001 mismatches (detected without epubcheck); fatals needs --audit.
  • --id <ids> limits the sweep to a comma-separated list of Calibre book IDs, skipping the full library walk.
  • --audit CSV (the fatals,errors,warnings,path format produced by an epubcheck sweep) skips clean books so a run is fast. Paths are resolved on both sides, and a CSV that matches nothing triggers a loud warning instead of silently selecting zero books.
  • --sweep replaces the CSV step entirely: it runs a live epubcheck sweep for candidate selection and reuses each result as that book's before-measurement, so no book is checked twice. Bindery launches a transparent, persistent Java daemon (EpubcheckDaemon) to evaluate candidates in the background, eliminating the JVM startup penalty. This reduces validation time from ~5 seconds per book down to ~0.05 seconds, allowing --sweep to scan a 5,000-book library in just 10 minutes. Combine with --only fatals for a self-contained, lightning-fast "find and fix the broken books" run.
  • --json FILE writes a machine-readable report of the whole run (per-book status, before/after counts, applied flag, summary totals). --manual-list FILE writes the paths of every book that was not auto-repaired, one per line, ready for manual follow-up.
  • --apply is required to write; the default is a dry run. --backup DIR mirrors originals before replacing; --backup-inplace writes .epub.bak beside each file.
  • --install-to-calibre resolves the Calibre book id from metadata.db via cquarry (one read-only path→id map per run), so a hand-renamed Author/Title (id)/ directory can never send the repaired file to the wrong book. The directory-name regex is only a no-catalog fallback; with neither, the file is saved atomically in place.
  • --install-to-calibre installs the repaired EPUB through cquarry's write module: the file is placed atomically at the catalogued path (same filename, Calibre's layout never changes) and the format row is re-registered in one transaction, so the stored size stays truthful and the book lands in metadata_dirtied — Calibre regenerates its sidecar .opf on next start. No external calibredb call is involved. It falls back to atomic file replacement if the Calibre database ID cannot be resolved, and a database failure degrades to the in-place save with a warning.
  • --all automatically turns on all opt-in non-fatal fixes and lossy strips (pagination, watermarks, bad attributes, unknown entities, image alt tags, etc.) in a single run.
  • Only the .epub is replaced. metadata.opf, cover.jpg, and metadata.db are left for Calibre's Quality Check sync to reconcile.
  • A per-book progress line goes to stderr (stdout stays a clean report); --quiet suppresses it. A corrupt or unreadable book is reported and skipped, never aborting the sweep.
  • Exit codes: 0 for a clean sweep, 1 for a usage error, 2 when any book was rejected, unreadable, or failed epubcheck (for scripts and cron).
  • repair refuses to overwrite an existing output file unless --force is given.

Companion scripts

scripts/ holds standalone, read-only utilities that are useful for EPUB maintenance but fall outside Bindery's repair contract (fixing what they find would be a content change, which Bindery makes only via the opt-in --strip-pagination):

  • find_missing_images.py: scans a library tree and reports every book whose <img> tags point at files that do not exist inside the archive (a common defect in converted EPUBs). Reads the archives in place; nothing is unpacked or written. The library path is set at the bottom of the script.

Development

./run_tests.sh        # unittest suite

See spec.md for the full contract and roadmap.md for what is planned.

License

MIT. See LICENSE.

Support

If Bindery's useful to you and you'd like to chip in:

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Credits

Author: vrnvctss

License

MIT

Requires

Python >=3.14

Provides Extra

reserialize

Tags

calibre ebook epub epubcheck html-repair repair watermarks

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