Releases · docxology/template

20 Mar 22:20

v3.0.0

f0edf91

Latest

f0edf91 feat: add Zenodo publication DOI and citation info
ff38ead A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication
1cc241d update
2a1292e remove
a2a025e update
fb97834 update
7963c55 Update README.md
8feb9e5 update
2265924 desloppify: remove deprecated aliases, narrow exception types
ea9bb14 fix: remove unused Path imports in test files; change _DANGEROUS_PATTERNS to tuple
53c0078 fix: masked-exception-fixes cluster (narrow exception types, promote debug→warning)
15ca548 fix: quick-convention-fixes cluster (emoji logging, stdlib logging, security/config/retry/prompt cleanup)
e9669d0 test: add 16 tests for pipeline_types (PipelineConfig, PipelineStageResult, StageSpec)
eaf35df desloppify: add direct tests for 3 transitive-only modules (session 8)
ff992f9 desloppify: fix error-pattern-consistency cluster (session 8)
538e020 desloppify: add tests for template helpers and review analysis modules
9529617 desloppify: add tests for install_commands and _pdf_latex_helpers modules
4ccd4eb desloppify: fix review queue — explicit fallback warning, resolved false positives
5d08b20 desloppify: remove unused imports of ManuscriptQualityReview, ManuscriptMethodologyReview
fbc46a5 desloppify: extract create_parser(), add ETA tests, use real parser in CLI tests
4bb27c0 desloppify: avoid mid-function config re-read in extract_manuscript_text
60e0adc desloppify: logic clarity, timeout constant, plotly dead code, double env check
bab41a5 desloppify: fix naming, type safety, error context, os.path migration
166b6bc desloppify: fix api surface documentation and config reload issues
56411c5 desloppify: consolidate prompt-system sentinels; remove noisy logging; improve docstrings
22a3120 desloppify: flatten stream_short/stream_long 3-layer chain
1665c1d desloppify: strip llm/init.py facade; remove forwarding wrappers
6cf5bb1 refactor: strip unused re-export facade from infrastructure/project/init.py
4a22a22 test: add offline tests for retry loop and warmup_model branches
77190ad refactor: inline trivial wrapper methods and improve docstrings
eacdf7c fix: narrow bare except Exception to OSError in tmp-file write patterns
7a96feb fix: rename misleading function names and fix broken test import
50b2788 fix: remove impossible OverflowError, param order bug, and stale migration shims
ba4aac4 desloppify: fix logic bugs, quick-wins, test-quality, incomplete-migrations
0e96f2a desloppify: narrow broad except Exception to specific types in tests and src
1da4321 desloppify: fix validate_structure return type and chain streaming exceptions
0d53148 desloppify: strip bloated docstrings, rename format_benchmark_report
4b508de desloppify: fix type safety and init coupling issues
1228f20 desloppify: fix elegance issues from deferred-elegance cluster
6c7d922 desloppify: fix logic/naming/security issues from review batch
7571641 desloppify: fix contracts, conventions, deprecation
9525c16 desloppify: fix unused imports in test files
a2fcf08 fix test_security.py: update SecurityHeaders references to module-level functions
193acc6 fix: remove unused imports in test files; add coverage_cleanup tests
77a64ce fix: rename ZenodoClient.upload_file bucket→deposition_id, fix URL path; update security.py Union→str|Path
6d04e9f desloppify: add tests for 5 untested modules (fix-test-coverage cluster)
aa9918e desloppify: fix 16 findings across 6 clusters (sessions 5-6)
86827a5 desloppify: fix 5 T1 review issues
f964526 desloppify: fix unused import and annotation quality
8c21c22 desloppify: consolidate functools imports in security.py

Full Changelog: 0.6...v3.0.0

Assets 2

10 Mar 23:19

docxology

0.6

0131a97

v0.6 — Desloppify: Code Health Campaign

🧹 Code Health: Desloppify Campaign

The largest code-quality improvement cycle since the template's inception. 162 commits across 948 files, systematically eliminating technical debt from all 8 infrastructure packages through 26 rounds of blind review.

Fixes

Import hygiene — Removed unused imports across 20+ files; eliminated sys.path mutations from CLI modules; proper TYPE_CHECKING guards throughout
Exception handling — Narrowed broad except Exception / bare except clauses in integrity.py, logging_utils, config_loader, and llm modules; fixed silent JSONDecodeError swallowing; restored exception context with raise ... from exc
Dead code removal — Deleted orphaned coverage_reporter.py (zero importers); removed stub/passthrough wrapper methods across 10+ modules; eliminated dead HTML-entities dict from InputSanitizer
Type annotations — Modernised legacy typing imports (List[x] → list[x], Optional[x] → x | None) across 30+ modules; added TypedDict returns for integrity results; annotated CLI re-exports
API surface — Consolidated LLMConfig env-read wrappers (ABS-001); merged duplicate PerformanceMetrics naming conflict; removed ProjectLogger pure-forwarder abstraction; eliminated calculate_file_hash re-export from publishing boundary
Bug fixes — Fixed inverted scan_errors bool in doc scanner; fixed stall-detection dead branch in pipeline reporter; fixed config_files path bug in config_cli; fixed clean_output_directory return type; fixed broken accessor imports after core.py hub elimination
Structural — Eliminated infrastructure/core/core.py hub; extracted _build_stage_list to remove stage-list duplication; moved MultiProjectResult to TYPE_CHECKING to break reporting→core circular dependency
Logging — Removed noisy debug logs from LLM and environment modules; downgraded verbose entry logs; added get_logger to logic modules lacking structured logging
Docstrings — Stripped AI-generated boilerplate from 40+ functions; removed restating comments and banner comments
Tests — Fixed test name collisions; added deterministic tests for validate_review_quality and exception types; added integration tests to testpaths; removed orphan test files
Dependencies — Removed scipy from infrastructure env check; resolved stale psutil guards; moved matplotlib to optional dep group

Quality Gates

Gate	Status
Desloppify blind reviews	26 rounds
Commits	162
Files changed	948
`ruff check`	✅ 0 errors
`mypy --strict`	✅ 0 errors (all 8 packages)
`bandit -ll`	✅ 0 MEDIUM+ findings
`pip-audit`	✅ Blocking gate
`pytest`	✅ All pass

Documentation

Updated CHANGELOG.md with full v0.6.0 entry
Updated docs/development/roadmap.md with desloppify results and refreshed quality metrics
Updated docs/audit/documentation-review-report.md for v0.6 scope

See CHANGELOG.md for full details.

Assets 2