tablassert 8.0.0__tar.gz → 8.0.1__tar.gz

{tablassert-8.0.0 → tablassert-8.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tablassert
-Version: 8.0.0
+Version: 8.0.1
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
@@ -71,16 +71,11 @@ tablassert build-kg config.yaml
 pip install tablassert
 ```
 
-The base install includes everything needed to build knowledge graphs from CSV/TSV sources. Optional extras are available for CPU compatibility and quality control:
-
-```bash
-pip install "tablassert[rt]"  # Polars build for CPUs without the required instructions
-pip install "tablassert[qc]"  # Enable QC (torch + sentence-transformers BioBERT, scikit-learn)
-```
-
-Excel (`.xlsx`) inputs are read through Polars' `calamine` engine and additionally require `python-calamine` (`pip install python-calamine`).
-
-QC is opt-in: pass `--qc` to `build-kg` to run the three-stage audit (exact → fuzzy → BioBERT). See the [CLI Reference](https://skyeav.github.io/Tablassert/cli/) for the full flag reference.
+The base install builds knowledge graphs from CSV/TSV/Excel sources. Optional extras (`rt`, `qc`,
+`agent`) add CPU-compatible Polars, the three-stage QC audit, and the autonomous agent — see the
+[Installation guide](https://skyeav.github.io/Tablassert/installation/) for the full matrix. QC is opt-in
+at build time (`build-kg --qc`); see the [CLI Reference](https://skyeav.github.io/Tablassert/cli/) for the
+complete flag reference.
 
 ## Quick Demo
 
@@ -88,30 +83,20 @@ QC is opt-in: pass `--qc` to `build-kg` to run the three-stage audit (exact →
 from pathlib import Path
 from tablassert.lib import resolve_many
 
-# Resolve gene names to CURIEs against a fullmap database
-results = resolve_many(
-    col="gene",
-    entities=["TP53", "BRCA1", "EGFR"],
-    fullmap=Path("/path/to/fullmap"),
-    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)
+results = resolve_many(col="gene", entities=["TP53", "BRCA1"], fullmap=Path("/path/to/fullmap"), taxon="9606")
+# [{"original_gene": "TP53", "gene": "HGNC:11998", "gene_name": "TP53", ...}, ...]
 ```
 
-Point `resolve_many()` at a fullmap database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup or NLP preprocessing required. For full pipeline builds with YAML configuration, use `tablassert build-kg config.yaml`.
+Point `resolve_many()` at a fullmap database to resolve any iterable of entity strings to CURIEs — no
+LazyFrame setup or NLP preprocessing required. See the
+[Batch Resolution API](https://skyeav.github.io/Tablassert/api/lib/) for the full reference; for
+YAML-configured pipeline builds use `tablassert build-kg config.yaml`.
 
 ## Key Features
 
-- **Declarative Configuration** — YAML-based, no code required
-- **Entity Resolution** — Maps text to biological entities (genes, diseases, chemicals)
-- **Quality Control** — Optional three-stage validation (exact → fuzzy → BERT embeddings)
-- **KGX Compliance** — NCATS Translator-compatible NDJSON output
-- **Performance** — Lazy evaluation pipelines with Polars and an embedded redb-accelerated entity resolution database
+Declarative YAML configs, built-in entity resolution, optional three-stage QC, and KGX-compliant NDJSON
+output — with lazy Polars pipelines over an embedded redb resolution database. See the
+[documentation](https://skyeav.github.io/Tablassert/) for the full feature overview and use-case gallery.
 
 ## Developing
 

tablassert-8.0.1/README.md

@@ -0,0 +1,70 @@
+# Tablassert
+
+[![PyPI](https://img.shields.io/pypi/v/tablassert.svg)](https://pypi.org/project/tablassert/)
+[![Python](https://img.shields.io/pypi/pyversions/tablassert.svg)](https://pypi.org/project/tablassert/)
+[![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 built in and optional quality control.
+
+```bash
+pip install tablassert
+tablassert build-kg config.yaml
+```
+
+**[Full Documentation](https://skyeav.github.io/Tablassert/)** — installation guides, tutorials, configuration reference, and API docs.
+
+## Installation
+
+```bash
+pip install tablassert
+```
+
+The base install builds knowledge graphs from CSV/TSV/Excel sources. Optional extras (`rt`, `qc`,
+`agent`) add CPU-compatible Polars, the three-stage QC audit, and the autonomous agent — see the
+[Installation guide](https://skyeav.github.io/Tablassert/installation/) for the full matrix. QC is opt-in
+at build time (`build-kg --qc`); see the [CLI Reference](https://skyeav.github.io/Tablassert/cli/) for the
+complete flag reference.
+
+## Quick Demo
+
+```python
+from pathlib import Path
+from tablassert.lib import resolve_many
+
+results = resolve_many(col="gene", entities=["TP53", "BRCA1"], fullmap=Path("/path/to/fullmap"), taxon="9606")
+# [{"original_gene": "TP53", "gene": "HGNC:11998", "gene_name": "TP53", ...}, ...]
+```
+
+Point `resolve_many()` at a fullmap database to resolve any iterable of entity strings to CURIEs — no
+LazyFrame setup or NLP preprocessing required. See the
+[Batch Resolution API](https://skyeav.github.io/Tablassert/api/lib/) for the full reference; for
+YAML-configured pipeline builds use `tablassert build-kg config.yaml`.
+
+## Key Features
+
+Declarative YAML configs, built-in entity resolution, optional three-stage QC, and KGX-compliant NDJSON
+output — with lazy Polars pipelines over an embedded redb resolution database. See the
+[documentation](https://skyeav.github.io/Tablassert/) for the full feature overview and use-case gallery.
+
+## Developing
+
+```bash
+uv sync --group dev --extra qc
+uv run maturin develop --manifest-path rust/Cargo.toml
+make check
+```
+
+See **[CONTRIBUTING.md](CONTRIBUTING.md)** for the full development loop, quality gates, and pull request guidelines.
+
+## License
+
+[Apache License 2.0](LICENSE)
+
+## Contributors
+
+[Skye Lane Goetz](mailto:sgoetz@isbscience.org) — Institute for Systems Biology
+
+[Gwênlyn Glusman](mailto:gglusman@isbscience.org) — Institute for Systems Biology
+
+Jared C. Roach — Institute for Systems Biology

{tablassert-8.0.0 → tablassert-8.0.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "tablassert"
-version = "8.0.0"
+version = "8.0.1"
 description = "Extract knowledge assertions from tabular data into NCATS Translator-compliant KGX NDJSON — declaratively, with entity resolution and quality control built in."
 authors = [
     { name = "Skye Lane Goetz", email = "sgoetz@isbscience.org" }

{tablassert-8.0.0 → tablassert-8.0.1}/src/tablassert/agent.py

@@ -352,8 +352,7 @@ def candidate_tables(files: list[Path]) -> list[Path]:
     """Return EVERY downloaded data-table file, raising ``FileNotFoundError`` when there is none.
 
     The supervisor presents all candidates to the agent (which chooses among them and among Excel
-    worksheets); the fail-fast guard matters for the ``--no-fetch`` snapshot path, where no fetch gate
-    has already run.
+    worksheets); the fail-fast guard raises when a fetch yields no data tables.
     """
     tables: list[Path] = [path for path in files if is_table_file(path.name)]
     if not tables:
@@ -1598,7 +1597,6 @@ def build_agent(
     instructions: str = INSTRUCTIONS,
     max_steps: int = 20,
     planning_interval: int = 3,
-    executor_type: str = "local",
     additional_authorized_imports: list[str] | None = None,
     step_callbacks: list[Callable[[object, object], None]] | None = None,
     final_answer_checks: list[Callable[..., bool]] | None = None,
@@ -1613,10 +1611,7 @@ def build_agent(
     yields an empty tool list: the supervisor builds the fullmap-bound tools (US-009) and passes
     them in, since they need a fullmap this factory does not have.
 
-    SECURITY: ``executor_type="local"`` runs model-written code in-process and is NOT a security
-    boundary; ``executor_type="docker"`` is the HARDENED option (sandboxed executor). Pass
-    ``executor_type`` straight through (``local``/``docker``/``e2b``). ``verbosity_level`` (a
-    smolagents ``LogLevel``) is forwarded only when not None.
+    ``verbosity_level`` (a smolagents ``LogLevel``) is forwarded only when not None.
     """
     _require("smolagents")
     from smolagents import CodeAgent  # local import keeps module import lazy  # pyright: ignore[reportMissingImports]
@@ -1634,7 +1629,7 @@ def build_agent(
         "additional_authorized_imports": imports,
         "step_callbacks": callbacks,
         "final_answer_checks": checks,
-        "executor_type": executor_type,
+        "executor_type": "local",
     }
     if verbosity_level is not None:
         agent_kwargs["verbosity_level"] = verbosity_level
@@ -1975,14 +1970,11 @@ def run_supervisor(
     *,
     fullmap: Path,
     build_model_factory: Callable[[], object],
-    map_threshold: float = 0.8,
-    qc_threshold: float = 0.9,
+    map_threshold: float = 0.25,
     max_improve_iters: int = 3,
     max_steps: int = 20,
-    state_dir: Path = Path(".tablassert-agent"),
-    executor: str = "local",
+    state_dir: Path = Path(".tablassert") / "agent",
     workdir: Path | None = None,
-    fetch: bool = True,
     name: str = "agent",
     version: str = "0.0.1",
 ) -> dict[str, object]:
@@ -1990,8 +1982,7 @@ def run_supervisor(
 
     For each pmc id (resume-aware: terminal DONE/MAPPED/SKIPPED records are skipped):
       1. mark RUNNING + checkpoint; fetch the latest-version article payload (``fetch_pmc_article``, the
-         single seam tests monkeypatch; or a pre-fetched snapshot when ``fetch`` is False) and present ALL
-         candidate tables + the main-text path to the agent;
+         single seam tests monkeypatch) and present ALL candidate tables + the main-text path to the agent;
       2. run the INNER agent (``build_agent`` + ``build_model_factory()``) whose schema-gated
          final answer is the initial Section config;
       3. ``build_and_audit`` it for coverage, then run the deterministic IMPROVE loop
@@ -2036,14 +2027,7 @@ def run_supervisor(
             rec.attempts += 1
             save_state(state_dir, state)
 
-            files: list[Path]
-            if fetch:
-                files = fetch_pmc_article(pmc_id, pmc_download_dir(art_root, pmc_id))
-            else:  # --no-fetch: resolve an already-fetched snapshot (the `fetch` param was previously dead)
-                snapshot: Path = pmc_download_dir(art_root, pmc_id)
-                files = sorted(path for path in snapshot.rglob("*") if path.is_file())
-                if not files:
-                    raise FileNotFoundError(f"--no-fetch but no snapshot files under {snapshot}.")
+            files: list[Path] = fetch_pmc_article(pmc_id, pmc_download_dir(art_root, pmc_id))
             tables: list[Path] = candidate_tables(files)
             table_list: str = "\n".join(f"  - {path}" for path in tables)
             article_xml: Path | None = next((path for path in files if path.suffix.lower() in {".xml", ".nxml"}), None)
@@ -2053,7 +2037,6 @@ def run_supervisor(
                 model=build_model_factory(),
                 tools=make_tools(fullmap=fullmap, table_path=tables[0], name=name, version=version),
                 max_steps=max_steps,
-                executor_type=executor,
                 step_callbacks=[make_step_callback(metrics)],
                 verbosity_level=verbosity,
             )
@@ -2159,7 +2142,6 @@ def run_supervisor(
 
     state.metrics = {
         "map_threshold": map_threshold,
-        "qc_threshold": qc_threshold,
         "mapped": mapped,
         "skipped": skipped,
         "mean_best_coverage": mean_best,

{tablassert-8.0.0 → tablassert-8.0.1}/src/tablassert/cli.py

@@ -492,13 +492,13 @@ def _download_detail(downloaded: int, total: int) -> str:
 
 @APP.command(name="build-kg")
 def build_kg(
-    configuration_file: Path,
+    configuration_file: Annotated[Path, cyclopts.Parameter(name=["--configuration-file", "-f"])],
     release: Annotated[bool, cyclopts.Parameter(name=["--release", "-r"], negative="")] = False,
     qc: Annotated[bool, cyclopts.Parameter(name=["--qc", "-q"], negative="")] = False,
     log: Annotated[bool, cyclopts.Parameter(name=["--log", "-l"], negative="")] = False,
     head: Annotated[bool, cyclopts.Parameter(name=["--head", "-hd"], negative="")] = False,
     table_config: Annotated[bool, cyclopts.Parameter(name=["--table-config", "-tc"], negative="")] = False,
-    fullmap: Annotated[Path, cyclopts.Parameter(name=["--fullmap", "-f"])] = Path("./fullmap"),
+    fullmap: Annotated[Path, cyclopts.Parameter(name=["--fullmap", "-fm"])] = Path("./fullmap"),
 ) -> None:
     """Build a knowledge graph from a YAML configuration file.
 
@@ -536,13 +536,10 @@ def agent(
     api_base: Annotated[str | None, cyclopts.Parameter(name=["--api-base", "-ab"])] = None,
     api_key: Annotated[str | None, cyclopts.Parameter(name=["--api-key", "-ak"])] = None,
     max_steps: Annotated[int, cyclopts.Parameter(name=["--max-steps", "-ms"])] = 20,
-    map_threshold: Annotated[float, cyclopts.Parameter(name=["--map-threshold", "-mt"])] = 0.8,
-    qc_threshold: Annotated[float, cyclopts.Parameter(name=["--qc-threshold", "-qt"])] = 0.9,
+    map_threshold: Annotated[float, cyclopts.Parameter(name=["--map-threshold", "-mt"])] = 0.25,
     max_improve_iters: Annotated[int, cyclopts.Parameter(name=["--max-improve-iters", "-mi"])] = 3,
-    state_dir: Annotated[Path, cyclopts.Parameter(name=["--state-dir", "-sd"])] = Path(".tablassert-agent"),
-    executor: Annotated[Literal["local", "docker"], cyclopts.Parameter(name=["--executor", "-e"])] = "local",
+    state_dir: Annotated[Path, cyclopts.Parameter(name=["--state-dir", "-sd"])] = Path(".tablassert") / "agent",
     backend: Annotated[Literal["openai", "litellm"], cyclopts.Parameter(name=["--backend", "-b"])] = "openai",
-    no_fetch: Annotated[bool, cyclopts.Parameter(name=["--no-fetch", "-nf"], negative="")] = False,
 ) -> None:
     """Autonomously derive, build, audit, and improve KG configs from PMC articles.
 
@@ -556,8 +553,7 @@ def agent(
     Model config comes from ``--model-id``/``--api-base``/``--api-key`` OR the ``TABLASSERT_AGENT_MODEL_ID``
     / ``TABLASSERT_AGENT_API_BASE`` / ``TABLASSERT_AGENT_API_KEY`` environment variables (explicit flags win).
     Secrets are NEVER hardcoded or defaulted: a missing value fails loud (exit 2) BEFORE any model is built.
-    ``--executor docker`` is the hardened, sandboxed code-execution option (``local`` runs in-process and is
-    not a security boundary). Requires the ``[agent]`` extra (``pip install tablassert[agent]``).
+    Requires the ``[agent]`` extra (``pip install tablassert[agent]``).
 
     Args:
         pmc_ids: One or more PMC article ids (positional).
@@ -567,12 +563,9 @@ def agent(
         api_key: API key (falls back to ``TABLASSERT_AGENT_API_KEY``).
         max_steps: Max inner-agent steps per article.
         map_threshold: Coverage an article must reach to be MAPPED.
-        qc_threshold: Target QC pass rate.
         max_improve_iters: Max deterministic improve iterations per article.
         state_dir: Checkpoint/resume directory.
-        executor: Code-execution backend; ``docker`` is the hardened sandbox.
         backend: Model backend (``openai`` or ``litellm``).
-        no_fetch: Skip PMC download (use already-fetched snapshot tables).
     """
     from tablassert import agent as agent_mod
 
@@ -596,12 +589,9 @@ def agent(
         fullmap=fullmap,
         build_model_factory=build_model_factory,
         map_threshold=map_threshold,
-        qc_threshold=qc_threshold,
         max_improve_iters=max_improve_iters,
         max_steps=max_steps,
         state_dir=state_dir,
-        executor=executor,
-        fetch=not no_fetch,
     )
 
     metrics_raw: object = result.get("metrics")

{tablassert-8.0.0 → tablassert-8.0.1}/src/tablassert/errors.py

@@ -18,7 +18,6 @@ TablassertErrorCodes = Literal[
     "regex-bad-replacement",
     "encoding-bad-remove-entry",
     "graph-bad-infores",
-    "override-bad-infores",
     "override-bad-publication",
     "override-bad-upstream-infores",
     "provenance-bad-pmc-id",

{tablassert-8.0.0 → tablassert-8.0.1}/src/tablassert/lib.py

@@ -712,7 +712,7 @@ class Tcode(Section):
             then the trim/format/write finalize ops.
         """
         override = self.provenance.override
-        primary_knowledge_source = (override.infores if override else None) or self.infores or (infores(self.name) if self.name else None)
+        primary_knowledge_source: str | None = self.infores or (infores(self.name) if self.name else None)
         upstream_ids = override.upstream_resource_ids if override else upstream_resource_ids(self.provenance.repo)
         knowledge_level = override.knowledge_level if override else self.provenance.knowledge_level
         agent_type = override.agent_type if override else self.provenance.agent_type

{tablassert-8.0.0 → tablassert-8.0.1}/src/tablassert/models.py

@@ -288,16 +288,14 @@ class ManualProvenance(TablaBase):
 
     When present under :class:`Provenance`, these values replace the legacy
     repo/publication-derived provenance while keeping the same KL/AT defaults.
+    The edge ``primary_knowledge_source`` always derives from the graph-level
+    ``infores`` (or ``infores:<graph-name>``); manual infores CURIEs belong in
+    ``upstream_resource_ids``.
     """
 
-    infores: str | None = Field(
-        None,
-        description="Optional per-section primary knowledge source infores CURIE; defaults to the graph infores when omitted.",
-        examples=["infores:my-kg"],
-    )
     upstream_resource_ids: list[str] = Field(
         default_factory=list,
-        description="Upstream source infores CURIEs emitted instead of the repo-derived source map.",
+        description="Manual upstream source infores CURIEs emitted instead of the repo-derived source map; the sanctioned place for manual infores.",
         examples=[["infores:my-upstream"]],
     )
     publications: list[str] | None = Field(
@@ -310,13 +308,6 @@ class ManualProvenance(TablaBase):
     )
     agent_type: AgentTypes = Field(AgentTypes.DATA_ANALYSIS_PIPELINE, description="Biolink KL/AT agent type responsible for produced edges.")
 
-    @field_validator("infores", mode="after")
-    @classmethod
-    def infores_curie(cls, infores: str | None) -> str | None:
-        if infores is None:
-            return None
-        return validate_infores_curie(infores, "override-bad-infores")
-
     @field_validator("upstream_resource_ids", mode="after")
     @classmethod
     def upstream_infores_curies(cls, values: list[str]) -> list[str]:

tablassert-8.0.0/README.md

@@ -1,85 +0,0 @@
-# Tablassert
-
-[![PyPI](https://img.shields.io/pypi/v/tablassert.svg)](https://pypi.org/project/tablassert/)
-[![Python](https://img.shields.io/pypi/pyversions/tablassert.svg)](https://pypi.org/project/tablassert/)
-[![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 built in and optional quality control.
-
-```bash
-pip install tablassert
-tablassert build-kg config.yaml
-```
-
-**[Full Documentation](https://skyeav.github.io/Tablassert/)** — installation guides, tutorials, configuration reference, and API docs.
-
-## Installation
-
-```bash
-pip install tablassert
-```
-
-The base install includes everything needed to build knowledge graphs from CSV/TSV sources. Optional extras are available for CPU compatibility and quality control:
-
-```bash
-pip install "tablassert[rt]"  # Polars build for CPUs without the required instructions
-pip install "tablassert[qc]"  # Enable QC (torch + sentence-transformers BioBERT, scikit-learn)
-```
-
-Excel (`.xlsx`) inputs are read through Polars' `calamine` engine and additionally require `python-calamine` (`pip install python-calamine`).
-
-QC is opt-in: pass `--qc` to `build-kg` to run the three-stage audit (exact → fuzzy → BioBERT). See the [CLI Reference](https://skyeav.github.io/Tablassert/cli/) for the full flag reference.
-
-## Quick Demo
-
-```python
-from pathlib import Path
-from tablassert.lib import resolve_many
-
-# Resolve gene names to CURIEs against a fullmap database
-results = resolve_many(
-    col="gene",
-    entities=["TP53", "BRCA1", "EGFR"],
-    fullmap=Path("/path/to/fullmap"),
-    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)
-```
-
-Point `resolve_many()` at a fullmap database and resolve any iterable of entity strings to CURIEs — no LazyFrame setup or NLP preprocessing required. For full pipeline builds with YAML configuration, use `tablassert build-kg config.yaml`.
-
-## Key Features
-
-- **Declarative Configuration** — YAML-based, no code required
-- **Entity Resolution** — Maps text to biological entities (genes, diseases, chemicals)
-- **Quality Control** — Optional three-stage validation (exact → fuzzy → BERT embeddings)
-- **KGX Compliance** — NCATS Translator-compatible NDJSON output
-- **Performance** — Lazy evaluation pipelines with Polars and an embedded redb-accelerated entity resolution database
-
-## Developing
-
-```bash
-uv sync --group dev --extra qc
-uv run maturin develop --manifest-path rust/Cargo.toml
-make check
-```
-
-See **[CONTRIBUTING.md](CONTRIBUTING.md)** for the full development loop, quality gates, and pull request guidelines.
-
-## License
-
-[Apache License 2.0](LICENSE)
-
-## Contributors
-
-[Skye Lane Goetz](mailto:sgoetz@isbscience.org) — Institute for Systems Biology
-
-[Gwênlyn Glusman](mailto:gglusman@isbscience.org) — Institute for Systems Biology
-
-Jared C. Roach — Institute for Systems Biology