tablassert 7.3.6__tar.gz → 7.4.1__tar.gz

{tablassert-7.3.6 → tablassert-7.4.1}/AGENTS.md

@@ -4,7 +4,7 @@ Guidance for AI coding agents working in this repository.
 
 ## Project Overview
 
-Tablassert is a Python package (>=3.11) for tabular data assertion, normalization, and quality control. It builds declarative knowledge graphs from tabular data, exporting NCATS Translator-compliant KGX NDJSON. Uses **Polars** DataFrames, **DuckDB** for entity resolution, and **ONNX/BioBERT** for quality control. CLI built with **Typer**. Models built with **Pydantic v2**.
+Tablassert is a Python package (>=3.11) for tabular data assertion, normalization, and optional quality control. It builds declarative knowledge graphs from tabular data, exporting NCATS Translator-compliant KGX NDJSON. Uses **Polars** DataFrames, **DuckDB** for entity resolution, and **ONNX/BioBERT** for QC when enabled. CLI built with **cyclopts**. Models built with **Pydantic v2**.
 
 ## Quick Reference
 
@@ -31,17 +31,18 @@ Tablassert is a Python package (>=3.11) for tabular data assertion, normalizatio
 
 ```
 src/tablassert/
-  cli.py          # Typer CLI (entry point: tablassert.cli:CLI)
+  cli.py          # cyclopts CLI (entry point: tablassert.cli:APP)
   lib.py          # Core logic: encodings, data loading, Tcode(Section) class
   models.py       # Pydantic v2 models (TablaBase base class)
   enums.py        # str, Enum subclasses (Tokens, Repositories, Comparisons, etc.)
-  fullmap.py      # NER / entity resolution (DuckDB, 12 shards)
+  fullmap.py      # NER / entity resolution (DuckDB, 10 shards)
   qc.py           # Quality control (ONNX/BioBERT, sentence_transformers)
   nlp.py          # Text normalization (level_one: strip+lowercase, level_two: regex)
   ingests.py      # YAML ingestion: from_yaml(), to_sections(), fastmerge()
-  downloader.py   # Playwright-based file downloads with retries
+  downloader.py   # httpx-based file downloads with retries
+  progress.py     # Rich progress bars for pipeline stages
   utils.py        # Hashing (xxhash), STORE path, namespace UUIDs
-  log.py          # loguru logger → .logassert/logassert.log
+  log.py          # loguru logger → .logassert/tablassert.log; cat() helper for category tagging
   __init__.py     # Empty file (lazy loading is per-module, not here)
 docs/             # MkDocs documentation source
 mkdocs.yml        # MkDocs configuration
@@ -51,8 +52,9 @@ tests/            # Test directory (at repo root)
 
 - `conftest.py` provides a `fixtures_path` fixture returning `Path(__file__).parent / "fixtures"`.
 - pytest configured via `pyproject.toml` `[tool.pytest.ini_options]` with `testpaths = ["tests"]`.
+- pytest markers: `network` requires internet; `gpu` requires `CUDAExecutionProvider`.
 - Test fixtures: `tests/fixtures/` contains YAML files for Section model tests.
-- Test modules: `test_enums.py`, `test_fullmap.py`, `test_ingests.py`, `test_lib.py`, `test_models.py`, `test_nlp.py`, `test_utils.py`.
+- Test modules: `test_downloader.py`, `test_enums.py`, `test_fullmap.py`, `test_ingests.py`, `test_lib.py`, `test_models.py`, `test_nlp.py`, `test_utils.py`.
 
 ## Code Style
 
@@ -69,9 +71,8 @@ tests/            # Test directory (at repo root)
   else:
       pl = Lazy.load("polars")
   ```
-- Lazy-loaded deps: `polars`, `duckdb`, `orjson`, `typer`, `xxhash`, `polars_hash`, `yaml`
-- Direct (non-lazy) heavy deps: `sqlite_utils`, `rapidfuzz`, `pydantic`, `loguru`, `yaml.CLoader`
-- Previously-optional deps now in core: `sentence_transformers`, `onnxruntime`, `sklearn`, `playwright`, `pyexcel` — lazy-loaded when present
+- Lazy-loaded deps: `polars`, `duckdb`, `orjson`, `xxhash`, `polars_hash`, `yaml`, `httpx`, `pyexcel`, `onnxruntime`, `sentence_transformers`
+- Direct (non-lazy) heavy deps: `sqlite_utils`, `rapidfuzz`, `pydantic`, `loguru`, `cyclopts`, `rich`, `yaml.CLoader`
 - Some modules mix direct and lazy imports for the same package (e.g., `ingests.py` does `from yaml import CLoader` directly, then lazy-loads `yaml` for `yaml.load()`)
 - Import order: standard library → blank line → third-party → blank line → local
 - Use `from __future__ import annotations` to enable deferred evaluation
@@ -130,13 +131,13 @@ All enums live in `enums.py` and extend `str, Enum`. Key enums: `Tokens`, `Repos
 
 - Use `RuntimeError` for exceptional cases (no custom exception classes currently)
 - Use `logger.warning()` for non-fatal issues (e.g., empty subgraphs)
-- Logger: `from tablassert.log import logger`
+- Logger: `from tablassert.log import logger` (or `cat()` for category-tagged logger)
 
 ### Other Conventions
 
 - `operator.add` for Polars string concatenation on columns (not `+` directly)
-- CLI entry point: `tablassert.cli:CLI` (Typer app with `pretty_exceptions_show_locals=False`)
-- Use `rich.progress` for progress tracking in CLI
+- CLI entry point: `tablassert.cli:APP` (cyclopts app)
+- Use `rich.progress` for progress tracking in CLI (via `progress.py` which wraps Rich Live/Progress)
 - Data side-effects stored in hidden directories: `.logassert/`, `.storassert/`, `.onnxassert/`
 
 ## Tools
@@ -151,12 +152,13 @@ All enums live in `enums.py` and extend `str, Enum`. Key enums: `Tokens`, `Repos
 ## Optional Dependency Groups
 
 Defined in `pyproject.toml` `[project.optional-dependencies]`:
-- `rtcompat` — `polars[rtcompat]` (runtime-compatible Polars build for CPUs without required instructions)
-- `rt` — alias for `rtcompat`
+- `rt` — `polars[rtcompat]` (runtime-compatible Polars build for CPUs without required instructions)
+- `qc` — `onnxruntime` (CPU QC runtime)
+- `qc-cuda` — `onnxruntime-gpu` (CUDA QC runtime; single GPU on device 0)
 
-All other dependencies (ML, web, Excel) are now in core `dependencies`.
+All other ML, web, and Excel dependencies are in core `dependencies`; the ONNX Runtime choice is extra-driven.
 
-Install with: `uv sync` or `pip install tablassert`
+Install with: `uv sync`, `uv sync --extra qc`, `uv sync --extra qc-cuda`, or `pip install tablassert[...]`
 
 ## CI Workflows
 
@@ -164,7 +166,3 @@ Install with: `uv sync` or `pip install tablassert`
 - **MkDocs deploy** (`.github/workflows/docs.yml`): builds docs and deploys to GitHub Pages on push to `main`
 - **Docker publish** (`.github/workflows/docker.yml`): builds and pushes image to GHCR on tag push (`v*`)
 - **Autotag** (`.github/workflows/autotag.yml`): automatic version tagging
-
-## Key Dependencies
-
-polars, duckdb, orjson, pydantic, typer, xxhash, loguru, rapidfuzz, scikit-learn, sqlite-utils, pyyaml, lazy-loader, polars-hash, fastexcel, pyarrow, optimum-onnx

{tablassert-7.3.6 → tablassert-7.4.1}/CHANGELOG.md

@@ -2,6 +2,32 @@
 
 All notable changes to this project are documented in this file.
 
+## 7.4.1 - 2026-05-05
+
+### Bug Fixes
+- Fixed `AttributeError: 'str' object has no attribute 'value'` raised by `format_section_oneline()` in `progress.py` during the BUILDING TCODE stage. The `Section` model sets `use_enum_values=True`, so `Tcode.status` is already a plain string — removed the stale `.value` access.
+
+## 7.4.0 - 2026-05-05
+
+### Changes
+- Renamed CLI commands for brevity: `build-knowledge-graph` → `build`, `verify-table-configuration-syntax` → `validate`. Version display moved from `tablassert version` subcommand to `tablassert --version` flag.
+- Added `qc` parameter to `resolve_many()` for optional QC auditing during standalone batch resolution. ONNX Runtime provider is auto-detected via `get_qc_provider()`.
+- Added `has_qc_runtime()` helper to `qc.py` for ONNX Runtime detection.
+- Added `empty_matches()` helper to `fullmap.py` for empty result fallback.
+- Added `DownloadReceipt` dataclass, `DownloadError`/`DownloadValidationError` exception classes, and `classify()`/`validate_download()`/`modernize_xls()` to `downloader.py`.
+- Updated log format to include timestamps: `{time:YYYY-MM-DD HH:mm:ss}`.
+
+### Bug Fixes
+- Fixed tutorial table configuration using header names as `encoding` values instead of Excel column letters (`A`, `B`, `C`, `D`).
+
+### Documentation
+- Updated all documentation to reflect renamed CLI commands.
+- Fixed tutorial and example YAML configurations to use Excel column letter references (`A`, `B`, `C`, `D`) for `method: column` encodings instead of header names, matching the headerless source reading behavior.
+- Fixed `encoding` values in `docs/examples/` gallery configurations.
+- Updated `resolve_many()` API reference with new `qc` parameter and auto-detected QC provider.
+- Fixed CITATION.cff version (7.2.2 → 7.4.0).
+- Fixed CONTRIBUTING.md lazy-loaded package list (`typer` → `cyclopts`, added missing packages).
+
 ## 7.3.6 - 2026-04-29
 
 ### Documentation
@@ -109,7 +135,7 @@ All notable changes to this project are documented in this file.
 ## 7.0.1 - 2026-03-17
 
 ### Documentation
-- Updated installation docs to reflect `pyproject.toml` extras and added `tablassert[rtcompat]` guidance for systems without required default Polars CPU instructions.
+- Updated installation docs to reflect `pyproject.toml` extras and added `tablassert[rt]` guidance for systems without required default Polars CPU instructions.
 
 ## 7.0.0 - 2026-03-17
 

{tablassert-7.3.6 → tablassert-7.4.1}/CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "If you use Tablassert, please cite it as below."
 type: software
 title: Tablassert
-version: 7.2.2
+version: 7.4.0
 license: Apache-2.0
 repository-code: https://github.com/SkyeAv/Tablassert
 abstract: Tablassert is a highly performant declarative knowledge graph backend for bioinformatics that extracts knowledge assertions from tabular data, performs entity resolution and data quality control, and exports NCATS Translator-compliant Knowledge Graph Exchange (KGX) NDJSON.

{tablassert-7.3.6 → tablassert-7.4.1}/CONTRIBUTING.md

@@ -25,7 +25,7 @@ uv sync
 All ML, web, and Excel dependencies are included in the core install. The only optional extra is a runtime-compatible Polars build for CPUs without required instructions:
 
 ```bash
-uv sync --extra rtcompat   # polars[rtcompat]
+uv sync --extra rt   # polars[rtcompat]
 ```
 
 ## Development Workflow
@@ -143,7 +143,7 @@ else:
     pl = Lazy.load("polars")
 ```
 
-Lazy-loaded packages: `polars`, `duckdb`, `orjson`, `typer`, `xxhash`, `polars_hash`, `yaml`
+Lazy-loaded packages: `polars`, `duckdb`, `orjson`, `xxhash`, `polars_hash`, `yaml`, `httpx`, `pyexcel`, `onnxruntime`, `sentence_transformers`
 
 Import order: standard library → blank line → third-party → blank line → local
 

{tablassert-7.3.6 → tablassert-7.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tablassert
-Version: 7.3.6
+Version: 7.4.1
 Summary: Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.
 Project-URL: Homepage, https://github.com/SkyeAv/Tablassert
 Project-URL: Source, https://github.com/SkyeAv/Tablassert
@@ -24,14 +24,15 @@ Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.11
+Requires-Dist: cyclopts>=1.0.0
 Requires-Dist: duckdb>=1.5.0
 Requires-Dist: fastexcel>=0.19.0
+Requires-Dist: httpx>=0.28.1
 Requires-Dist: lazy-loader>=0.5
 Requires-Dist: loguru>=0.7.3
-Requires-Dist: onnxruntime>=1.24.4
 Requires-Dist: optimum-onnx>=0.1.0
 Requires-Dist: orjson>=3.11.7
-Requires-Dist: playwright>=1.58.0
+Requires-Dist: playwright<1.59,>=1.58.0
 Requires-Dist: polars-hash>=0.5.6
 Requires-Dist: polars>=1.39.0
 Requires-Dist: pyarrow>=23.0.1
@@ -39,15 +40,17 @@ Requires-Dist: pydantic>=2.12.5
 Requires-Dist: pyexcel>=0.7.4
 Requires-Dist: pyyaml>=6.0.3
 Requires-Dist: rapidfuzz>=3.14.3
+Requires-Dist: rich>=13.0.0
 Requires-Dist: scikit-learn>=1.8.0
 Requires-Dist: sentence-transformers>=5.3.0
 Requires-Dist: sqlite-utils>=3.39
-Requires-Dist: typer>=0.21.2
 Requires-Dist: xxhash>=3.6.0
+Provides-Extra: qc
+Requires-Dist: onnxruntime>=1.24.4; extra == 'qc'
+Provides-Extra: qc-cuda
+Requires-Dist: onnxruntime-gpu>=1.24.4; extra == 'qc-cuda'
 Provides-Extra: rt
-Requires-Dist: polars[rtcompat]>=1.39.0; extra == 'rt'
-Provides-Extra: rtcompat
-Requires-Dist: polars[rtcompat]>=1.39.0; extra == 'rtcompat'
+Requires-Dist: polars[rtcompat]>=1.40.1; extra == 'rt'
 Description-Content-Type: text/markdown
 
 # Tablassert
@@ -57,11 +60,11 @@ Description-Content-Type: text/markdown
 [![License](https://img.shields.io/pypi/l/tablassert.svg)](https://github.com/SkyeAv/Tablassert/blob/main/LICENSE)
 [![Docs](https://img.shields.io/github/deployments/SkyeAv/Tablassert/github-pages?label=docs)](https://skyeav.github.io/Tablassert/)
 
-Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.
+Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution built in and optional quality control.
 
 ```bash
 pip install tablassert
-tablassert build-knowledge-graph config.yaml
+tablassert build config.yaml
 ```
 
 **[Full Documentation](https://skyeav.github.io/Tablassert/)** — installation guides, tutorials, configuration reference, and API docs.
@@ -72,12 +75,16 @@ tablassert build-knowledge-graph config.yaml
 pip install tablassert
 ```
 
-All dependencies (ML, web, Excel support) are included in the base install. An optional extra is available for CPU compatibility:
+Base install includes web and Excel support. Optional extras are available for CPU compatibility and QC runtime selection:
 
 ```bash
-pip install "tablassert[rtcompat]"  # Polars build for CPUs without required instructions
+pip install "tablassert[rt]"       # Polars build for CPUs without required instructions
+pip install "tablassert[qc]"       # Enable QC with CPU ONNX Runtime
+pip install "tablassert[qc-cuda]"  # Enable QC with CUDA ONNX Runtime on GPU 0
 ```
 
+QC is disabled by default at the graph level. Set `qc: true` in a graph config to enable the audit stage.
+
 <details>
 <summary><strong>Docker</strong></summary>
 
@@ -88,32 +95,39 @@ docker run --rm \
   -v /path/to/config:/data \
   -v /path/to/datassert:/datassert \
   ghcr.io/skyeav/tablassert:latest \
-  build-knowledge-graph /data/graph-config.yaml
+  build /data/graph-config.yaml
 ```
 
 </details>
 
 ## Quick Demo
 
-```bash
-# Build a knowledge graph from a YAML configuration
-$ tablassert build-knowledge-graph graph-config.yaml
-⠋ Loading Tables...
-⠋ Extracting Sections...
-⠋ Building TCode...
-⠋ Collecting Instructions...
-⠋ Building Subgraphs...
-⠋ Compiling Graph...
-✓ Finished!
+```python
+from pathlib import Path
+from tablassert.lib import resolve_many
+
+# Resolve gene names to CURIEs against a datassert database
+results = resolve_many(
+    col="gene",
+    entities=["TP53", "BRCA1", "EGFR"],
+    datassert=Path("/path/to/datassert"),
+    taxon="9606",
+)
+
+for row in results:
+    print(f"{row['original gene']} → {row['gene']} ({row['gene name']})")
+# TP53 → HGNC:11998 (TP53)
+# BRCA1 → HGNC:1100 (BRCA1)
+# EGFR → HGNC:3236 (EGFR)
 ```
 
-Define your entities and relationships in YAML, point tablassert at your data, and get NCATS Translator-compliant KGX NDJSON out the other side — no code required. Intermediate section artifacts are staged in `.storassert/` during the build.
+Point `resolve_many()` at a datassert database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup, NLP preprocessing, or DuckDB connection management required. For full pipeline builds with YAML configuration, use `tablassert build config.yaml`.
 
 ## Key Features
 
 - **Declarative Configuration** — YAML-based, no code required
 - **Entity Resolution** — Maps text to biological entities (genes, diseases, chemicals)
-- **Quality Control** — Three-stage validation (exact → fuzzy → BERT embeddings)
+- **Quality Control** — Optional three-stage validation (exact → fuzzy → BERT embeddings)
 - **KGX Compliance** — NCATS Translator-compatible NDJSON output
 - **Performance** — Lazy evaluation pipelines with Polars and DuckDB-accelerated entity resolution
 

{tablassert-7.3.6 → tablassert-7.4.1}/README.md

@@ -5,11 +5,11 @@
 [![License](https://img.shields.io/pypi/l/tablassert.svg)](https://github.com/SkyeAv/Tablassert/blob/main/LICENSE)
 [![Docs](https://img.shields.io/github/deployments/SkyeAv/Tablassert/github-pages?label=docs)](https://skyeav.github.io/Tablassert/)
 
-Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in.
+Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution built in and optional quality control.
 
 ```bash
 pip install tablassert
-tablassert build-knowledge-graph config.yaml
+tablassert build config.yaml
 ```
 
 **[Full Documentation](https://skyeav.github.io/Tablassert/)** — installation guides, tutorials, configuration reference, and API docs.
@@ -20,12 +20,16 @@ tablassert build-knowledge-graph config.yaml
 pip install tablassert
 ```
 
-All dependencies (ML, web, Excel support) are included in the base install. An optional extra is available for CPU compatibility:
+Base install includes web and Excel support. Optional extras are available for CPU compatibility and QC runtime selection:
 
 ```bash
-pip install "tablassert[rtcompat]"  # Polars build for CPUs without required instructions
+pip install "tablassert[rt]"       # Polars build for CPUs without required instructions
+pip install "tablassert[qc]"       # Enable QC with CPU ONNX Runtime
+pip install "tablassert[qc-cuda]"  # Enable QC with CUDA ONNX Runtime on GPU 0
 ```
 
+QC is disabled by default at the graph level. Set `qc: true` in a graph config to enable the audit stage.
+
 <details>
 <summary><strong>Docker</strong></summary>
 
@@ -36,32 +40,39 @@ docker run --rm \
   -v /path/to/config:/data \
   -v /path/to/datassert:/datassert \
   ghcr.io/skyeav/tablassert:latest \
-  build-knowledge-graph /data/graph-config.yaml
+  build /data/graph-config.yaml
 ```
 
 </details>
 
 ## Quick Demo
 
-```bash
-# Build a knowledge graph from a YAML configuration
-$ tablassert build-knowledge-graph graph-config.yaml
-⠋ Loading Tables...
-⠋ Extracting Sections...
-⠋ Building TCode...
-⠋ Collecting Instructions...
-⠋ Building Subgraphs...
-⠋ Compiling Graph...
-✓ Finished!
+```python
+from pathlib import Path
+from tablassert.lib import resolve_many
+
+# Resolve gene names to CURIEs against a datassert database
+results = resolve_many(
+    col="gene",
+    entities=["TP53", "BRCA1", "EGFR"],
+    datassert=Path("/path/to/datassert"),
+    taxon="9606",
+)
+
+for row in results:
+    print(f"{row['original gene']} → {row['gene']} ({row['gene name']})")
+# TP53 → HGNC:11998 (TP53)
+# BRCA1 → HGNC:1100 (BRCA1)
+# EGFR → HGNC:3236 (EGFR)
 ```
 
-Define your entities and relationships in YAML, point tablassert at your data, and get NCATS Translator-compliant KGX NDJSON out the other side — no code required. Intermediate section artifacts are staged in `.storassert/` during the build.
+Point `resolve_many()` at a datassert database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup, NLP preprocessing, or DuckDB connection management required. For full pipeline builds with YAML configuration, use `tablassert build config.yaml`.
 
 ## Key Features
 
 - **Declarative Configuration** — YAML-based, no code required
 - **Entity Resolution** — Maps text to biological entities (genes, diseases, chemicals)
-- **Quality Control** — Three-stage validation (exact → fuzzy → BERT embeddings)
+- **Quality Control** — Optional three-stage validation (exact → fuzzy → BERT embeddings)
 - **KGX Compliance** — NCATS Translator-compatible NDJSON output
 - **Performance** — Lazy evaluation pipelines with Polars and DuckDB-accelerated entity resolution
 

{tablassert-7.3.6 → tablassert-7.4.1}/docs/api/lib.md

@@ -19,6 +19,7 @@ def resolve_many(
     prioritize: Optional[list[Categories]] = None,
     avoid: Optional[list[Categories]] = None,
     column_context: bool = True,
+    qc: bool = False,
 ) -> list[dict[str, Any]]
 ```
 
@@ -71,6 +72,10 @@ Controls category-frequency tie-breaking when multiple matches exist for a term.
 
 This is useful when resolving a column of related entities (e.g., all genes) — the shared context helps disambiguate terms that map to multiple categories.
 
+**`qc: bool` (default: `False`)**
+
+When `True`, runs the QC audit stage after entity resolution. The QC pipeline validates mappings through a three-stage audit: exact match, fuzzy matching via rapidfuzz, and BioBERT sentence embeddings with cosine similarity. Requires a QC runtime to be installed (`tablassert[qc]` or `tablassert[qc-cuda]`). The ONNX Runtime provider is auto-detected based on the installed package — CUDA is preferred when `onnxruntime-gpu` is available, otherwise CPU is used.
+
 ### Return Value
 
 Returns a `list[dict[str, Any]]` — one dictionary per resolved entity. The list is produced by calling `polars.DataFrame.to_dicts()` on the collected resolution output.
@@ -230,7 +235,7 @@ Both levels are queried during resolution. Level one (exact case-insensitive mat
 
 ## Integration
 
-`resolve_many()` is a self-contained entry point. It does not require any prior setup beyond having a datassert database available. For full pipeline builds, use the CLI (`tablassert build-knowledge-graph`) which orchestrates resolution through the `Tcode` class.
+`resolve_many()` is a self-contained entry point. It does not require any prior setup beyond having a datassert database available. For full pipeline builds, use the CLI (`tablassert build`) which orchestrates resolution through the `Tcode` class.
 
 ## Next Steps
 

{tablassert-7.3.6 → tablassert-7.4.1}/docs/api/qc.md

@@ -2,6 +2,8 @@
 
 The `qc` module validates entity resolution mappings through a multi-stage pipeline: exact matching, fuzzy matching, and BERT semantic similarity.
 
+QC runtime support is optional. Install `tablassert[qc]` for CPU inference or `tablassert[qc-cuda]` for CUDA inference on GPU 0.
+
 ## fullmap_audit()
 
 Primary quality control function that filters entity mappings based on confidence criteria.
@@ -14,7 +16,9 @@ def fullmap_audit(
   col: str,
   section_hash: str,
   config_file: str,
-  out: str = "passed"
+  out: str = "passed",
+  log: bool = True,
+  provider: Optional[Literal["cpu", "cuda"]] = None
 ) -> pl.LazyFrame
 ```
 
@@ -44,6 +48,14 @@ Name of the boolean column indicating validation status.
 
 Rows with `out=True` passed QC, `out=False` failed.
 
+**`log: bool` (default: `True`)**
+
+Controls whether failed QC rows are logged.
+
+**`provider: Optional[Literal["cpu", "cuda"]]`**
+
+Optional runtime override. Use `"cpu"` to force CPU inference, `"cuda"` to require CUDA inference, or `None` to auto-select from the installed QC runtime.
+
 **`section_hash: str` / `config_file: str`**
 
 Context fields used in QC failure logs for traceability.
@@ -119,13 +131,13 @@ return similarity >= 0.2
 
 **Model:** `pritamdeka/BioBERT-mnli-snli-scinli-scitail-mednli-stsb`
 
-**Backend:** ONNX Runtime (CPU)
+**Backend:** ONNX Runtime (`CPUExecutionProvider` or `CUDAExecutionProvider`)
 
 **Optimizations:**
 - Graph optimization level: ALL
 - ONNX session caching
 
-Lazy-loaded on first `fullmap_audit()` call that reaches the embedding stage, then reused for subsequent calls.
+Lazy-loaded on first `fullmap_audit()` call that reaches the embedding stage, then reused per provider for subsequent calls.
 
 ### Model Caching
 
@@ -163,7 +175,8 @@ validated = fullmap_audit(
   lf,
   col="subject",
   section_hash="tutorial-section",
-  config_file="tutorial-table.yaml"
+  config_file="tutorial-table.yaml",
+  provider="cpu"
 )
 
 # Only rows that passed QC remain
@@ -205,7 +218,7 @@ Output: 990 rows (700 + 250 + 40)
 
 ### Integration with Pipeline
 
-QC is applied after entity resolution:
+QC is applied after entity resolution when graph or API QC is enabled:
 
 1. **Entity resolution** (`resolve()`) - Maps text to CURIEs
 2. **Quality control** (`fullmap_audit()`) - Validates mappings

{tablassert-7.3.6 → tablassert-7.4.1}/docs/changelog.md

@@ -4,10 +4,10 @@ The canonical release history lives in the repository root at [`CHANGELOG.md`](h
 
 ## Current Release Notes
 
-## 7.3.6 - 2026-04-29
+## 7.4.1 - 2026-05-05
 
-### Documentation
+### Bug Fixes
 
-- Documented that `publication` must start with `PMC` followed by digits when `repo` is `"PMC"`.
+- Fixed crash in the BUILDING TCODE progress display caused by `format_section_oneline()` calling `.value` on `Tcode.status`, which is a plain string under `use_enum_values=True`.
 
 For older releases and the full project history, open the root `CHANGELOG.md` in the repository.

{tablassert-7.3.6 → tablassert-7.4.1}/docs/cli.md

@@ -1,6 +1,6 @@
 # CLI Reference
 
-Tablassert provides three commands.
+Tablassert provides two commands.
 
 ## version
 
@@ -9,29 +9,29 @@ Display the current Tablassert package version.
 ### Synopsis
 
 ```bash
-tablassert version
+tablassert --version
 ```
 
 ### Example
 
 ```bash
-tablassert version
+tablassert --version
 ```
 
 ### Description
 
-Prints the installed Tablassert version to stdout and exits.
+Prints the installed Tablassert version to stdout and exits. This is a flag on the main `tablassert` command, not a subcommand.
 
 ---
 
-## build-knowledge-graph
+## build
 
 Build A KGX Compliant Knowledge Graph From A Graph Configuration File
 
 ### Synopsis
 
 ```bash
-tablassert build-knowledge-graph <graph_configuration_file>
+tablassert build <graph_configuration_file>
 ```
 
 ### Options
@@ -43,7 +43,7 @@ tablassert build-knowledge-graph <graph_configuration_file>
 ### Example
 
 ```bash
-tablassert build-knowledge-graph /path/to/MOKGV6.yaml
+tablassert build /path/to/MOKGV6.yaml
 ```
 
 ### Description
@@ -68,14 +68,14 @@ See [Graph Configuration](configuration/graph.md) for details on the YAML schema
 
 ---
 
-## verify-table-configuration-syntax
+## validate
 
 Verify The Syntax Of A Declarative Table Configuration File
 
 ### Synopsis
 
 ```bash
-tablassert verify-table-configuration-syntax <table_configuration_file>
+tablassert validate <table_configuration_file>
 ```
 
 ### Options
@@ -87,7 +87,7 @@ tablassert verify-table-configuration-syntax <table_configuration_file>
 ### Example
 
 ```bash
-tablassert verify-table-configuration-syntax /path/to/table-config.yaml
+tablassert validate /path/to/table-config.yaml
 ```
 
 ### Description
@@ -108,27 +108,27 @@ See [Table Configuration](configuration/table.md) for details on the YAML schema
 ### Check Version
 
 ```bash
-tablassert version
+tablassert --version
 ```
 
 ### Build Knowledge Graph
 
 ```bash
-tablassert build-knowledge-graph my-graph.yaml
+tablassert build my-graph.yaml
 ```
 
 ### Validate Table Configuration
 
 ```bash
-tablassert verify-table-configuration-syntax table-config.yaml
+tablassert validate table-config.yaml
 ```
 
 ## Workflow
 
 1. **Create table configuration** - Define data sources and transformations
 2. **Create graph configuration** - Define output name, table configs, databases
-3. **Validate table config** - `tablassert verify-table-configuration-syntax table.yaml`
-4. **Build knowledge graph** - `tablassert build-knowledge-graph graph.yaml`
+3. **Validate table config** - `tablassert validate table.yaml`
+4. **Build knowledge graph** - `tablassert build graph.yaml`
 5. **Process executes:**
    - Downloads files from URLs (if needed)
    - Applies transformations to each table