chore: pyqual auto-fix iteration

Author: tom-sapletta-com

TODO.md

@@ -1,7 +1,7 @@
 # TODO
 
 **Generated by:** prefact v0.1.30
-**Generated on:** 2026-03-31T16:24:24.128813
+**Generated on:** 2026-03-31T16:48:18.410478
 **Total issues:** 53 active, 0 completed
 
 ---

docs/README.md

@@ -1,7 +1,7 @@
 <!-- code2docs:start --># regix
 
-![version](https://img.shields.io/badge/version-0.1.0-blue) ![python](https://img.shields.io/badge/python-%3E%3D3.9-blue) ![coverage](https://img.shields.io/badge/coverage-unknown-lightgrey) ![functions](https://img.shields.io/badge/functions-157-green)
-> **157** functions | **41** classes | **25** files | CC̄ = 4.9
+![version](https://img.shields.io/badge/version-0.1.0-blue) ![python](https://img.shields.io/badge/python-%3E%3D3.9-blue) ![coverage](https://img.shields.io/badge/coverage-unknown-lightgrey) ![functions](https://img.shields.io/badge/functions-166-green)
+> **166** functions | **41** classes | **25** files | CC̄ = 4.6
 
 > Auto-generated project documentation from source code analysis.
 
@@ -153,7 +153,7 @@ Content outside the markers is preserved when regenerating. Enable this with `sy
 
 ```
 regix/
-├── project    ├── check_regression    ├── gates    ├── exceptions    ├── compare    ├── config    ├── history    ├── cli    ├── git    ├── snapshot    ├── report├── regix/    ├── cache        ├── architecture_backend    ├── smells        ├── docstring_backend        ├── vallm_backend    ├── backends/        ├── radon_backend        ├── coverage_backend        ├── lizard_backend    ├── integrations/    ├── models        ├── structure_backend    ├── benchmark```
+├── project    ├── check_regression    ├── gates    ├── exceptions    ├── compare├── regix/    ├── history    ├── git    ├── cli    ├── snapshot    ├── config    ├── report    ├── cache    ├── smells        ├── architecture_backend        ├── docstring_backend        ├── radon_backend        ├── vallm_backend    ├── backends/        ├── coverage_backend    ├── models    ├── integrations/        ├── lizard_backend        ├── structure_backend    ├── benchmark```
 
 ## API Overview
 
@@ -164,18 +164,16 @@ regix/
 - **`GitDirtyError`** — Raised when the working tree is dirty and the operation requires a clean state.
 - **`BackendError`** — Raised when a backend fails to produce output.
 - **`ConfigError`** — Raised when the configuration file is invalid.
+- **`Regix`** — Main entry point — wraps snapshot, compare, and history.
+- **`CommitInfo`** — Lightweight commit metadata.
 - **`GateThresholds`** — Threshold set for a single tier (hard or target).
 - **`RegressionConfig`** — All user-configurable values for a Regix run.
-- **`CommitInfo`** — Lightweight commit metadata.
-- **`Regix`** — Main entry point — wraps snapshot, compare, and history.
 - **`ArchitectureBackend`** — Computes per-function structural metrics via AST for smell detection.
-- **`DocstringBackend`** — —
-- **`VallmBackend`** — —
+- **`DocstringBackend`** — Measure docstring coverage using the ``ast`` module.
+- **`RadonBackend`** — Maintainability index and cyclomatic complexity via ``radon``.
+- **`VallmBackend`** — LLM-based code quality scoring via the ``vallm`` CLI tool.
 - **`BackendBase`** — Interface that all analysis backends must implement.
-- **`RadonBackend`** — —
 - **`CoverageBackend`** — —
-- **`LizardBackend`** — —
-- **`RegixCollector`** — GateSet-compatible metric collector for pyqual.
 - **`SymbolMetrics`** — All tracked metrics for a single symbol (function, class, or module).
 - **`MetricDelta`** — Change in a single metric between two snapshots.
 - **`ArchSmell`** — An architectural regression smell detected by cross-symbol analysis.
@@ -189,7 +187,9 @@ regix/
 - **`HistoryReport`** — Multi-commit metric timeline.
 - **`GateCheck`** — Single gate threshold check.
 - **`GateResult`** — Aggregate gate evaluation result.
-- **`StructureBackend`** — —
+- **`RegixCollector`** — GateSet-compatible metric collector for pyqual.
+- **`LizardBackend`** — Cyclomatic complexity and function length via the ``lizard`` library.
+- **`StructureBackend`** — AST-based structural metrics: fan_out, call_count, symbol_count.
 - **`BenchmarkResult`** — —
 - **`BenchmarkProbe`** — Abstract benchmark probe.
 - **`ImportProbe`** — Measures import time of a Python module in a fresh process.
@@ -208,13 +208,6 @@ regix/
 - `check_gates(snapshot, config)` — Evaluate absolute quality gates against a single snapshot.
 - `compare(snap_before, snap_after, config)` — Compare two snapshots and produce a regression report.
 - `build_history(depth, ref, workdir, config)` — Walk ``depth`` commits and return a HistoryReport with metric timeline.
-- `compare(ref_a, ref_b, local, config)` — Compare metrics between two git refs or local state.
-- `history(depth, ref, metric, fmt)` — Show metric timeline across N historical commits.
-- `snapshot(ref, fmt, output, config)` — Capture and store a snapshot without comparing.
-- `diff(ref_a, ref_b, threshold, metric)` — Show symbol-by-symbol metric diff (like git diff for metrics).
-- `gates(ref, fail_on, config, workdir)` — Check current state against configured quality gates (absolute thresholds).
-- `status(config, workdir)` — Show Regix configuration and available backends.
-- `init(workdir)` — Create a default regix.yaml in the project root.
 - `resolve_ref(ref, workdir)` — Resolve a symbolic ref to a commit SHA.
 - `list_commits(ref, depth, workdir)` — Return commit history starting from *ref*, newest first.
 - `is_clean(workdir)` — Return True if there are no uncommitted changes.
@@ -223,6 +216,13 @@ regix/
 - `checkout_temporary(ref, workdir)` — Context manager: create a git worktree at *ref* in a temp directory.
 - `read_tree_sources(ref, workdir, suffix)` — Read all files matching *suffix* from a git ref entirely in RAM.
 - `read_local_sources(workdir, files)` — Read source code for *files* from the local working tree into RAM.
+- `compare(ref_a, ref_b, local, config)` — Compare metrics between two git refs or local state.
+- `history(depth, ref, metric, fmt)` — Show metric timeline across N historical commits.
+- `snapshot(ref, fmt, output, config)` — Capture and store a snapshot without comparing.
+- `diff(ref_a, ref_b, threshold, metric)` — Show symbol-by-symbol metric diff (like git diff for metrics).
+- `gates(ref, fail_on, config, workdir)` — Check current state against configured quality gates (absolute thresholds).
+- `status(config, workdir)` — Show Regix configuration and available backends.
+- `init(workdir)` — Create a default regix.yaml in the project root.
 - `capture(ref, workdir, config, backend_names)` — Capture a snapshot at a git ref or the local working tree.
 - `render(report, fmt, output)` — Render a regression report in the specified format.
 - `render_history(report, fmt)` — Render a history report.
@@ -254,7 +254,7 @@ regix/
 📄 `regix.cache` (5 functions)
 📄 `regix.cli` (8 functions)
 📄 `regix.compare` (4 functions)
-📄 `regix.config` (15 functions, 2 classes)
+📄 `regix.config` (24 functions, 2 classes)
 📄 `regix.exceptions` (4 functions, 5 classes)
 📄 `regix.gates` (2 functions)
 📄 `regix.git` (9 functions, 1 classes)

project/analysis.toon.yaml

@@ -7,9 +7,9 @@ HEALTH[8]:
   🟡 CC    compare CC=16 (limit:15)
   🟡 CC    diff CC=15 (limit:15)
   🟡 CC    capture CC=17 (limit:15)
+  🟡 CC    filter CC=15 (limit:15)
   🟡 CC    collect CC=19 (limit:15)
   🟡 CC    detect_smells CC=17 (limit:15)
-  🟡 CC    filter CC=15 (limit:15)
 
 REFACTOR[3]:
   1. split regix/benchmark.py  (god module)

project/calls.mmd

@@ -1,40 +1,40 @@
 flowchart LR
     subgraph regix__Regix
-        regix__Regix__history["history"]
         regix__Regix____init__["__init__"]
+        regix__Regix__history["history"]
         regix__Regix__snapshot["snapshot"]
     end
     subgraph regix__backends
-        regix__backends__get_backend["get_backend"]
         regix__backends__structure_backend__StructureBackend__collect["collect"]
         regix__backends__structure_backend___analyse_function["_analyse_function"]
+        regix__backends__get_backend["get_backend"]
     end
     subgraph regix__benchmark
-        regix__benchmark___make_config_parse_probe["_make_config_parse_probe"]
-        regix__benchmark__BackendProbe__run["run"]
-        regix__benchmark__BenchmarkReporter__print_plain["print_plain"]
-        regix__benchmark___make_gates_probe["_make_gates_probe"]
-        regix__benchmark___make_snapshot_probe["_make_snapshot_probe"]
+        regix__benchmark__BenchmarkReporter__print_json["print_json"]
         regix__benchmark___make_compare_probe["_make_compare_probe"]
+        regix__benchmark___make_gates_probe["_make_gates_probe"]
         regix__benchmark__build_regix_suite["build_regix_suite"]
+        regix__benchmark__BenchmarkReporter__print_plain["print_plain"]
         regix__benchmark__BenchmarkReporter__print["print"]
+        regix__benchmark__BackendProbe__run["run"]
+        regix__benchmark___make_snapshot_probe["_make_snapshot_probe"]
         regix__benchmark__main["main"]
-        regix__benchmark__BenchmarkReporter__print_json["print_json"]
+        regix__benchmark___make_config_parse_probe["_make_config_parse_probe"]
     end
     subgraph regix__cache
+        regix__cache___cache_dir["_cache_dir"]
+        regix__cache___cache_key["_cache_key"]
         regix__cache__lookup["lookup"]
         regix__cache__store["store"]
         regix__cache__clear["clear"]
-        regix__cache___cache_dir["_cache_dir"]
-        regix__cache___cache_key["_cache_key"]
     end
     subgraph regix__cli
+        regix__cli__history["history"]
+        regix__cli___load_config["_load_config"]
         regix__cli__snapshot["snapshot"]
+        regix__cli__diff["diff"]
         regix__cli__gates["gates"]
-        regix__cli___load_config["_load_config"]
         regix__cli__status["status"]
-        regix__cli__history["history"]
-        regix__cli__diff["diff"]
     end
     subgraph regix__compare
         regix__compare__compare["compare"]
@@ -49,15 +49,15 @@ flowchart LR
         regix__gates___passes["_passes"]
     end
     subgraph regix__git
+        regix__git__get_dirty_files["get_dirty_files"]
+        regix__git__read_tree_sources["read_tree_sources"]
         regix__git___run_git["_run_git"]
-        regix__git__is_clean["is_clean"]
+        regix__git__checkout_temporary["checkout_temporary"]
         regix__git__get_changed_files["get_changed_files"]
-        regix__git__get_dirty_files["get_dirty_files"]
         regix__git__resolve_ref["resolve_ref"]
         regix__git__read_local_sources["read_local_sources"]
         regix__git__list_commits["list_commits"]
-        regix__git__read_tree_sources["read_tree_sources"]
-        regix__git__checkout_temporary["checkout_temporary"]
+        regix__git__is_clean["is_clean"]
     end
     subgraph regix__history
         regix__history__build_history["build_history"]
@@ -66,28 +66,28 @@ flowchart LR
         regix__history___linear_slope["_linear_slope"]
     end
     subgraph regix__report
-        regix__report__render["render"]
         regix__report___render_rich["_render_rich"]
+        regix__report__render["render"]
     end
     subgraph regix__smells
-        regix__smells___was_already_hollow["_was_already_hollow"]
+        regix__smells___count_hollow_signals["_count_hollow_signals"]
+        regix__smells___check_stub_regression["_check_stub_regression"]
+        regix__smells___avg_func_length["_avg_func_length"]
+        regix__smells___function_count_drop["_function_count_drop"]
         regix__smells___check_no_delegation["_check_no_delegation"]
-        regix__smells___func_length["_func_length"]
         regix__smells___check_symbol_smells["_check_symbol_smells"]
+        regix__smells___check_hallucination_proxy["_check_hallucination_proxy"]
+        regix__smells___func_length["_func_length"]
+        regix__smells___was_already_hollow["_was_already_hollow"]
         regix__smells___check_god_function["_check_god_function"]
-        regix__smells___avg_func_length["_avg_func_length"]
-        regix__smells___function_count_drop["_function_count_drop"]
-        regix__smells___check_stub_regression["_check_stub_regression"]
-        regix__smells__detect_smells["detect_smells"]
         regix__smells___largest_function["_largest_function"]
-        regix__smells___count_hollow_signals["_count_hollow_signals"]
-        regix__smells___check_hallucination_proxy["_check_hallucination_proxy"]
+        regix__smells__detect_smells["detect_smells"]
     end
     subgraph regix__snapshot
-        regix__snapshot___merge_symbols["_merge_symbols"]
-        regix__snapshot___collect_files["_collect_files"]
         regix__snapshot__capture["capture"]
+        regix__snapshot___merge_symbols["_merge_symbols"]
         regix__snapshot___filter_sources["_filter_sources"]
+        regix__snapshot___collect_files["_collect_files"]
     end
     subgraph scripts__check_regression
         scripts__check_regression__check_regression["check_regression"]
@@ -98,21 +98,6 @@ flowchart LR
     scripts__check_regression__check_regression --> regix__benchmark__BenchmarkReporter__print
     regix__compare___compare_symbol_metrics --> regix__compare___compute_delta
     regix__compare__compare --> regix__smells__detect_smells
-    regix__cli___load_config --> regix__config__RegressionConfig__from_file
-    regix__cli__history --> regix__cli___load_config
-    regix__cli__snapshot --> regix__cli___load_config
-    regix__cli__snapshot --> regix__snapshot__capture
-    regix__cli__diff --> regix__cli___load_config
-    regix__cli__diff --> regix__snapshot__capture
-    regix__cli__gates --> regix__cli___load_config
-    regix__cli__gates --> regix__snapshot__capture
-    regix__cli__gates --> regix__gates__check_gates
-    regix__cli__status --> regix__cli___load_config
-    regix__history___compute_trends --> regix__history___linear_slope
-    regix__history__build_history --> regix__git__list_commits
-    regix__history__build_history --> regix__snapshot__capture
-    regix__history__build_history --> regix__history___compute_trends
-    regix__history__build_history --> regix__history___aggregate_snapshot_metrics
     regix__git__resolve_ref --> regix__git___run_git
     regix__git__list_commits --> regix__git___run_git
     regix__git__is_clean --> regix__git___run_git
@@ -121,10 +106,24 @@ flowchart LR
     regix__git__checkout_temporary --> regix__git__resolve_ref
     regix__git__checkout_temporary --> regix__git___run_git
     regix__git__read_tree_sources --> regix__git__resolve_ref
+    regix__history___compute_trends --> regix__history___linear_slope
+    regix__history__build_history --> regix__git__list_commits
+    regix__history__build_history --> regix__snapshot__capture
+    regix__history__build_history --> regix__history___compute_trends
+    regix__history__build_history --> regix__history___aggregate_snapshot_metrics
     regix__Regix____init__ --> regix__config__RegressionConfig__from_file
     regix__Regix__snapshot --> regix__snapshot__capture
     regix__Regix__history --> regix__history__build_history
-    regix__report__render --> regix__report___render_rich
+    regix__cli___load_config --> regix__config__RegressionConfig__from_file
+    regix__cli__history --> regix__cli___load_config
+    regix__cli__snapshot --> regix__cli___load_config
+    regix__cli__snapshot --> regix__snapshot__capture
+    regix__cli__diff --> regix__cli___load_config
+    regix__cli__diff --> regix__snapshot__capture
+    regix__cli__gates --> regix__cli___load_config
+    regix__cli__gates --> regix__snapshot__capture
+    regix__cli__gates --> regix__gates__check_gates
+    regix__cli__status --> regix__cli___load_config
     regix__snapshot__capture --> regix__snapshot___merge_symbols
     regix__snapshot__capture --> regix__git__resolve_ref
     regix__snapshot__capture --> regix__backends__get_backend
@@ -137,6 +136,7 @@ flowchart LR
     regix__cache__store --> regix__cache___cache_dir
     regix__cache__store --> regix__cache___cache_key
     regix__cache__clear --> regix__cache___cache_dir
+    regix__report__render --> regix__report___render_rich
     regix__smells__detect_smells --> regix__smells___check_god_function
     regix__smells__detect_smells --> regix__smells___check_symbol_smells
     regix__smells___check_symbol_smells --> regix__smells___check_hallucination_proxy

project/calls.png

@@ -17,17 +17,17 @@ flowchart TD
     scripts__check_regression -->|3| regix__benchmark
     regix__snapshot -->|3| regix__git
     regix__benchmark -->|3| regix__snapshot
+    regix__Regix -->|2| regix__config
     regix__cli -->|2| regix__config
     regix__cli -->|2| regix__report
     regix__cli -->|2| regix__backends
-    regix__Regix -->|2| regix__config
     regix__compare -->|1| regix__smells
-    regix__cli -->|1| regix__history
-    regix__cli -->|1| regix__gates
     regix__history -->|1| regix__git
     regix__history -->|1| regix__snapshot
     regix__Regix -->|1| regix__snapshot
     regix__Regix -->|1| regix__history
+    regix__cli -->|1| regix__history
+    regix__cli -->|1| regix__gates
     regix__snapshot -->|1| regix__backends
     regix__benchmark -->|1| regix__backends
     regix__benchmark -->|1| regix__gates