- Bibliography heading now accepts bold markers (## **BIBLIOGRAPHY**),
alternative names (Works Cited, References), and numbered sub-headings
within the section.
- Original heading text preserved in output instead of hardcoded
"## Bibliography".
- New find_blockquote_notes() parser for PDF-to-markdown footnote format
(> N text), wired into CLI as third fallback after pandoc and numbered.
- PDF junk filtered from bibliography entries: bare page numbers,
blockquote footnotes, download banners, CC license URLs, and short
running headers.
Extend the v2 parser and CLI to handle [N] text footnote definitions
in addition to pandoc-style [^marker]: text. The numbered format is
what docx-to-text conversion of footnoted Word documents produces.
The user's "Anti-Communist Formations of LIS" draft uses this format
for all 107 of its notes; without this support, v2 was structurally
incapable of running on real-world docx-derived inputs.
src/cmos/parser.py:
- Add NoteDefinition.original_prefix field so reassembly can
round-trip the source's marker syntax (pandoc input → pandoc
output, numbered input → numbered output) without consumers
needing to know which format was matched.
- Update find_notes() to populate original_prefix as "[^N]: ".
- Add find_numbered_notes() targeting "[N] text" definitions.
Marker must be all digits (rejects [Smith 2020], [foo], etc.);
caret prefix is rejected (rejects pandoc-style cleanly).
src/cmos/cli.py:
- reformat_notes now auto-detects format: tries find_notes first,
falls back to find_numbered_notes if no pandoc definitions found.
Uses definition.original_prefix for reassembly so both formats
round-trip correctly.
tests/test_parser.py:
- 11 new tests for find_numbered_notes covering: single/multiple
definitions, multi-digit markers, line number recording, trailing
whitespace stripping, ignoring pandoc/non-numeric markers, original
prefix recording, and the actual Anti-Communist draft format.
- 1 new test for find_notes original_prefix population.
tests/test_cli.py:
- 2 new tests for reformat_notes auto-detect: numbered input round-
trips as numbered output, pandoc input still round-trips as pandoc.
Total suite: 136/136 (was 123, +13 net new). v1 untouched, 96/96
v1 tests still passing.
Real-draft validation: ran cmos format-notes against the 107-note
Anti-Communist Formations of LIS draft (108 calls in parallel via
the existing concurrency=8 thread pool, completed cleanly). Output
saved to /tmp (not committed). All 107 notes preserved through the
pipeline; ~30-40 first-occurrence full notes produced clean CMOS 18
note form; ~30 shortened-form refs correctly left unchanged;
2 real bugs surfaced for the next iteration (empty input → conver-
sational reply, Ibid → empty string), plus several lower-priority
issues (substantive note truncation, retry waste on shortened
forms, lossy month dropping). Not addressed in this chunk per the
"collect signal, don't fix" plan.
Wire the v2 note formatter into the CLI so it can be invoked on
real markdown drafts. The format-notes subcommand mirrors v1's
format subcommand: parser → formatter → reassemble, with concurrent
API calls.
src/cmos/cli.py:
- Import find_notes and format_note_entry alongside the existing
v1 imports.
- Add reformat_notes(text, formatter, concurrency) that finds
pandoc-style markdown footnote definitions via find_notes,
formats each definition's text via the v2 note formatter (or
an injected fake), and substitutes the formatted text back into
the original line position. Non-definition lines preserved
byte-for-byte. Returns text unchanged when no definitions found.
- Register the format-notes argparse subparser with the same
--concurrency flag as v1's format.
- Dispatch args.command == "format-notes" to reformat_notes.
- Module docstring updated to document both subcommands.
tests/test_cli.py:
- 7 new tests for reformat_notes covering: in-place substitution,
order preservation under concurrency, prose preservation,
reference markers staying verbatim, no-op on empty input,
trailing newline preservation.
- Extended test_python_dash_m_invocation_actually_runs_main to
also assert "format-notes" appears in --help, catching accidental
subcommand removal.
Path B integrity: formatter.py, note_formatter.py, parser.py,
linter.py, harness/score.py all unchanged. No LINTER_VERSION
bump. 96/96 v1 tests still passing. Total suite: 123/123.
Real-API end-to-end smoke test on a temp draft with 2 footnote
definitions: both reformatted byte-for-byte, prose and headings
preserved, ## Conclusion section after the notes preserved.
Without `if __name__ == "__main__": sys.exit(main())` at the bottom
of cli.py, `python -m cmos.cli format <path>` imports the module
but never invokes main(), so the process silently exits 0 with
empty stdout — indistinguishable from a successful run that
produced no output. Discovered during real-draft testing on
2026-04-11.
Adds a regression test that subprocesses the CLI with --help and
asserts on stdout content. argparse --help exits 0 in both broken
and fixed states; stdout content is the only discriminator.
Both invocation paths now work:
- uv run cmos format <path> (pyproject script entry)
- uv run python -m cmos.cli format <path> (module invocation)
reformat_draft now uses concurrent.futures.ThreadPoolExecutor with a
default of 8 workers. OpenAI SDK calls are synchronous but network-
bound, so threads release the GIL during I/O and give real speedup.
ThreadPoolExecutor.map preserves input order regardless of completion
order, so output is deterministic.
Empirical: HML draft (134 entries) went from ~25 min serial to 1m55s
with concurrency=12. ~12x speedup; further increases hit OpenAI rate
limits.
CLI gains a --concurrency flag (default 8) for tuning per draft size /
rate limit headroom. concurrency=1 forces serial execution for
debugging. New test asserts that order is preserved when concurrent
calls finish out of input order (uses a sleep-by-index fake formatter).
Initial phase-1 baseline of the karpathy/autoresearch-style loop.
The formatter module is the inner-loop artifact; parser and linter
are infra. The linter carries a LINTER_VERSION hash (v0.2.0) that
will force a re-baseline on any rule change.
Components:
- harness/diff.py: case-sensitive field-level substring diff
- harness/score.py: three-axis scoring (field, linter, canary exact)
- src/cmos/linter.py: 9 CMOS 18 structural rules, each Purdue/CMOS cited
- src/cmos/parser.py: locate ## Bibliography section, split entries
- src/cmos/formatter.py: prompt + OpenAI call with caller injection
- src/cmos/cli.py: cmos format path/to/draft.md
- scripts/run_loop.py: loop runner with --fake mode for no-API runs
- exemplars/: 3 canary seed exemplars (book, journal w/DOI, web),
sourced from chicagomanualofstyle.org quick guide
Tests: 48 passing. Fake-mode baseline scalar = 0.000 on the 3 seed
exemplars (identity caller fails the linter on every rule). This is
the floor the real GPT-5 formatter needs to improve from.
Mark Eaton