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fix: resolve v0.4.0 audit — CI, Action, cache/fail-on bugs, packaging#10

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musharna merged 2 commits into
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worktree-audit-fixes-2026-07-01
Jul 1, 2026
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fix: resolve v0.4.0 audit — CI, Action, cache/fail-on bugs, packaging#10
musharna merged 2 commits into
mainfrom
worktree-audit-fixes-2026-07-01

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@musharna musharna commented Jul 1, 2026

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Resolves the full v0.4.0 audit (Critical 1–9 + quick wins; net-new features intentionally out of scope). Every claim was verified against live source before patching.

Critical

  1. CI green — merged the test-collection fix (tests/__init__.py + py3.9 annotation imports) and moved FakeClient into tests/conftest.py instead of cross-importing test modules. Bare pytest now collects and passes.
  2. Action works on its defaults — CLI accepts multiple paths and walks directories for *.bib/*.md (hidden dirs skipped), so paths: . works as documented. Findings are attributed with their filename (text path:Lnn, JSON file) when >1 file is scanned. release.yml now force-moves the v1 major tag on each release.
  3. Cache determinism — DoiCache.get() reads back is_preprint/has_preprint_relation; a preprint from a warm cache is downgraded identically to a cold lookup (was an intermittent false-positive Tier B year failure).
  4. --fail-on validated — a typo like --fail-on retractions used to silently no-op the CI gate; it now errors at parse time (like --cross-check).

Important

  1. Markdown/DOI-list entries (no parsed title) no longer emit a misleading "possibly wrong DOI" on author mismatch — neutral message instead.
  2. DOIs are URL-encoded before being spliced into CrossRef/OpenAlex/doi.org URLs (a # no longer truncates into a different query).
  3. .claude/ git-ignored + excluded from the sdist (was leaking worktrees into uv build); verified the built sdist is clean. Added Typing :: Typed.
  4. release.yml gains a test gate (build needs test) — no publish on red; Action inputs passed via env: (no shell injection) and the install is pinned.
  5. --json --dry-run emits valid JSON; test_semantic_live.py gains the live marker and the weekly workflow sets GHOSTCITE_LIVE=1.

Quick wins

CITATION.cff → 0.4.0 · README pre-commit rev → v0.4.0 + pass_filenames: true · example outputs gain the retractions: line · action fail-on default gains title · fetch-retractions shown in --help · CI matrix +3.10/3.12 · schema_version in --json · CHANGELOG [Unreleased] section.

Deliberately skipped

  • Committing uv.lock — it's intentionally .gitignored (library-lockfile decision left to you).
  • Net-new features (GitHub annotations, --ignore-doi, config file, concurrency, library README) — out of scope per request.

Verification

305 passed / 5 skipped, ruff + mypy + ruff format --check clean, coverage 90.6% (>85 gate). Built sdist confirmed to contain no .claude/ / worktree files. Real-execution walkthroughs: ghostcite ., --json --dry-run, --fail-on typo, and markdown neutral-message all behave as intended.

🤖 Generated with Claude Code

musharna and others added 2 commits June 22, 2026 20:43
@musharna @claude
fix(tests): repair CI test collection on Python 3.9 and 3.13
b8cae7e 
Two independent matrix breakages (the version `CI` job was red on main
since 06-20; `Live tests` was unaffected):

- Py3.9: `tests/test_preprint.py` and `tests/test_venue.py` used
  `list[str] | None` / `str | None` in function default-arg annotations,
  which 3.9 evaluates at definition time -> TypeError (GenericAlias | None).
  Add `from __future__ import annotations` so annotations stay strings.
- Py3.13: `tests/test_cli_semantic.py` imports `from tests.test_cli import
  FakeClient`, but `tests/` was not an importable package. Add empty
  `tests/__init__.py`.

Verified: `pytest -m "not live"` passes on 3.9 and 3.13 (290 passed,
2 skipped), ruff clean.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HjKoaVFk7CFQfdkS18TWHm
@musharna @claude
fix: resolve v0.4.0 audit — CI, Action, cache/fail-on bugs, packaging
884cb7a 
Addresses the full v0.4.0 audit (Critical 1-9 + quick wins).

Correctness fixes:
- cache: get() now reads back is_preprint/has_preprint_relation, so a preprint
  served from a warm cache is downgraded identically to a cold lookup (was an
  intermittent false-positive Tier B year failure).
- --fail-on: validate tier names at parse time — a typo (e.g. "retractions")
  used to silently empty the fail-set and turn the CI gate into a no-op.
- compare: markdown/DOI-list entries (no parsed title) no longer emit a
  misleading "possibly wrong DOI" on author mismatch — neutral message instead.
- crossref/openalex: URL-encode DOIs before splicing into request URLs so a DOI
  containing '#' isn't truncated into a different query.
- cli: --json --dry-run now emits valid JSON.

Action / multi-file input:
- CLI accepts multiple paths and walks directories for *.bib/*.md (hidden dirs
  skipped), so the Action's default `paths: .` works as documented. Findings are
  attributed with their filename (text path:Lnn, JSON `file`) when >1 file.
- action.yml: pass inputs via env (no shell interpolation), pin the install,
  default fail-on gains `title`.
- release.yml: force-move the `v1` major tag to each release commit.
- pre-commit hook: pass_filenames now that the CLI takes multiple files.

CI / packaging:
- release.yml gains a test gate (build needs test) — no publish on red.
- .claude/ git-ignored + excluded from sdist (was leaking worktrees into
  `uv build`); added Typing :: Typed classifier; CI matrix +3.10/3.12.
- test_semantic_live.py gains the `live` marker; live-tests sets GHOSTCITE_LIVE=1.

Test collection / housekeeping:
- merged the CI-collection fix (tests/__init__.py + py3.9 annotation imports);
  FakeClient moved to tests/conftest.py instead of cross-importing test modules.

Docs: CITATION.cff->0.4.0, README pre-commit rev->v0.4.0, example outputs gain
the retractions: line, fetch-retractions shown in --help, schema_version added
to --json, CHANGELOG [Unreleased] section.

305 passed / 5 skipped, ruff+mypy+format clean, coverage 90.6%.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AS7DtpsXwhB2eevQyqFxxe
@musharna musharna marked this pull request as ready for review July 1, 2026 23:24
@musharna musharna merged commit 54879d9 into main Jul 1, 2026
10 checks passed
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