---
phase: 11-manual-ruff-cli-mypy
verified: 2026-02-24T00:00:00Z
status: passed
score: 7/7 must-haves verified
re_verification: false
---

# Phase 11: Manual Ruff + CLI + Mypy Verification Report

**Phase Goal:** `cli.py` is ruff-clean and all 42 mypy errors across 9 files are resolved — the codebase is type-correct under `--strict`
**Verified:** 2026-02-24
**Status:** passed
**Re-verification:** No — initial verification

---

## Goal Achievement

### Observable Truths

| #  | Truth                                                                                      | Status     | Evidence                                                                          |
|----|-------------------------------------------------------------------------------------------|------------|-----------------------------------------------------------------------------------|
| 1  | `uv run ruff check src/corpus_analyzer/cli.py` exits 0 with zero violations              | VERIFIED   | `uv run ruff check src/corpus_analyzer/cli.py` → "All checks passed!"            |
| 2  | `uv run ruff check .` exits 0 (entire codebase)                                           | VERIFIED   | `uv run ruff check .` → "All checks passed!"                                      |
| 3  | `uv run mypy src/` exits 0 — zero errors across all 53 source files                       | VERIFIED   | `uv run mypy src/` → "Success: no issues found in 53 source files" (exit 0)      |
| 4  | All 281 tests pass after fixes                                                             | VERIFIED   | `uv run pytest -q` → "281 passed in 3.31s"                                       |
| 5  | `DEFAULT_SYSTEM_PROMPT` is a `str` at runtime (genuine bug fixed)                         | VERIFIED   | `type(DEFAULT_SYSTEM_PROMPT).__name__` → "str"; `isinstance(..., str)` → True    |
| 6  | `cast(Table, self.db[...])` pattern applied at all Table call sites in database.py        | VERIFIED   | grep confirms 8 occurrences across insert/update/delete_where operations          |
| 7  | `Atom` dataclass promoted to module level in chunked_processor.py                         | VERIFIED   | `class Atom` at line 26 (module level), before `split_on_headings` function       |

**Score:** 7/7 truths verified

---

### Required Artifacts

| Artifact                                          | Requirement | Status   | Details                                                                              |
|---------------------------------------------------|-------------|----------|--------------------------------------------------------------------------------------|
| `src/corpus_analyzer/cli.py`                      | RUFF-07     | VERIFIED | ruff exits 0; B023/B904 fixed; 45 E501 lines wrapped                               |
| `src/corpus_analyzer/core/database.py`            | MYPY-01     | VERIFIED | cast(Table, ...) at 8 call sites; bare dict/list annotations fixed                  |
| `src/corpus_analyzer/llm/chunked_processor.py`    | MYPY-02     | VERIFIED | Atom at module level (line 26); finalize_atom/get_chunk_text/chain_lines annotated  |
| `src/corpus_analyzer/utils/ui.py`                 | MYPY-03     | VERIFIED | Function signatures annotated with Any for duck-typed parameters                    |
| `src/corpus_analyzer/extractors/markdown.py`      | MYPY-04     | VERIFIED | Bare dict parameter replaced with dict[str, Any]                                    |
| `src/corpus_analyzer/extractors/__init__.py`      | MYPY-04     | VERIFIED | Explicit `dict[str, type[MarkdownExtractor] | type[PythonExtractor]]` at line 24   |
| `src/corpus_analyzer/llm/ollama_client.py`        | MYPY-06     | VERIFIED | TYPE_CHECKING guard at line 6; `self.db: CorpusDatabase | None = None` at line 28  |
| `src/corpus_analyzer/ingest/chunker.py`           | MYPY-06     | VERIFIED | current_lines var-annotated as list[str]                                            |
| `src/corpus_analyzer/analyzers/shape.py`          | MYPY-06     | VERIFIED | _generate_recommended_schema return type annotated as dict[str, Any]                |
| `src/corpus_analyzer/llm/rewriter.py`             | MYPY-05     | VERIFIED | process_document fully annotated; DEFAULT_SYSTEM_PROMPT trailing comma removed      |

---

### Key Link Verification

| From                                         | To                         | Via                                              | Status   | Details                                                          |
|----------------------------------------------|----------------------------|--------------------------------------------------|----------|------------------------------------------------------------------|
| `src/corpus_analyzer/core/database.py`       | `sqlite_utils.db.Table`    | `cast(Table, self.db[...])` at every call site   | WIRED    | 8 cast() occurrences confirmed by grep                           |
| `src/corpus_analyzer/llm/chunked_processor.py` | `Atom dataclass`         | Module-level promotion from nested definition    | WIRED    | `class Atom` at line 26 before `split_on_headings`              |
| `src/corpus_analyzer/llm/ollama_client.py`   | `core/database.py`         | TYPE_CHECKING guard for CorpusDatabase type      | WIRED    | `from typing import TYPE_CHECKING` + guard block present         |
| `src/corpus_analyzer/extractors/__init__.py` | `MarkdownExtractor | PythonExtractor` | Explicit dict[str, type[...]] annotation  | WIRED    | Pattern `dict[str, type[Markdown` confirmed at line 24           |
| `src/corpus_analyzer/llm/rewriter.py`        | `DEFAULT_SYSTEM_PROMPT`    | Trailing comma removal — str not tuple           | WIRED    | Runtime type confirmed as str; line 399 references it safely     |
| `src/corpus_analyzer/llm/rewriter.py`        | `OllamaClient.db`          | `adv_rewriter.client.db = db` at line 409       | WIRED    | Attribute exists in ollama_client.py; mypy passes cleanly        |

---

### Requirements Coverage

| Requirement | Source Plan | Description                                                                          | Status    | Evidence                                                          |
|-------------|-------------|--------------------------------------------------------------------------------------|-----------|-------------------------------------------------------------------|
| RUFF-07     | 11-01       | All E501 violations in cli.py fixed (45 lines wrapped)                               | SATISFIED | `ruff check cli.py` exits 0; `ruff check .` exits 0             |
| MYPY-01     | 11-02       | core/database.py zero mypy errors — cast(Table, ...) pattern applied                | SATISFIED | mypy returns empty for database.py; grep confirms cast() pattern  |
| MYPY-02     | 11-03       | llm/chunked_processor.py zero mypy errors — Atom promoted, nested functions typed   | SATISFIED | mypy exits 0; Atom at module level; all nested functions annotated|
| MYPY-03     | 11-04       | utils/ui.py zero mypy errors                                                         | SATISFIED | mypy exits 0 for entire src/                                      |
| MYPY-04     | 11-04       | extractors/markdown.py and extractors/__init__.py zero mypy errors                  | SATISFIED | mypy exits 0; explicit dict type at line 24 of __init__.py       |
| MYPY-05     | 11-05       | llm/rewriter.py zero mypy errors — operator bug fixed; OllamaClient.db added        | SATISFIED | mypy exits 0; DEFAULT_SYSTEM_PROMPT is str; client.db at line 409|
| MYPY-06     | 11-04       | llm/ollama_client.py, ingest/chunker.py, analyzers/shape.py zero mypy errors        | SATISFIED | mypy exits 0 for all 53 source files                              |

No orphaned requirements — all 7 requirement IDs from plan frontmatter are accounted for in REQUIREMENTS.md.

---

### Anti-Patterns Found

| File | Line | Pattern | Severity | Impact |
|------|------|---------|----------|--------|
| `llm/rewriter.py` | 15, 41, 52, 81 | "placeholder" string literals | Info | These are domain logic for detecting placeholder variables in documents — not code stubs |

No blocker or warning anti-patterns found. The "placeholder" occurrences in rewriter.py are intentional domain features (the rewriter detects `$VAR` style placeholders in documentation), not code quality issues.

---

### Human Verification Required

None — all phase goals are mechanically verifiable and confirmed by automated checks.

---

## Summary

Phase 11 achieved its goal fully. The codebase is now:

- **Ruff-clean:** `ruff check .` exits 0 across all 53 source files. cli.py had 45 E501 violations and 2 semantic violations (B023, B904) — all fixed with line wrapping and default-argument capture / `raise ... from None`.
- **Mypy-clean:** `mypy src/` exits 0 with "no issues found in 53 source files". All 42 original errors across 9 files have been resolved: cast(Table, ...) pattern in database.py, Atom dataclass promotion in chunked_processor.py, full annotations on nested functions, TYPE_CHECKING guards, bare generic replacements, and the genuine runtime bug fix in rewriter.py (DEFAULT_SYSTEM_PROMPT was a `tuple[str]` due to a trailing comma).
- **Test suite intact:** All 281 tests pass in 3.31s. No logic changes, only type annotations, structural promotion, and formatting.

---

_Verified: 2026-02-24_
_Verifier: Claude (gsd-verifier)_
