medfence 0.1.0__tar.gz

medfence-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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medfence-0.1.0/PKG-INFO

@@ -0,0 +1,192 @@
+Metadata-Version: 2.4
+Name: medfence
+Version: 0.1.0
+Summary: Deterministic, fail-closed verification harness for clinical LLM outputs
+Author-email: Debanit Panigrahi <d.panigrahi.nitrkl@gmail.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/Debanitrkl/medfence
+Project-URL: Repository, https://github.com/Debanitrkl/medfence
+Project-URL: Issues, https://github.com/Debanitrkl/medfence/issues
+Keywords: llm,verification,clinical,healthcare,hallucination,guardrails,fail-closed,prescription,grounding
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+# medfence
+
+[![ci](https://github.com/Debanitrkl/medfence/actions/workflows/ci.yml/badge.svg)](https://github.com/Debanitrkl/medfence/actions/workflows/ci.yml)
+
+**A deterministic, fail-closed verification harness for clinical LLM outputs.**
+
+LLM extraction is entering clinical workflows (scribes, prescription digitization,
+lab-report parsing) faster than verification infrastructure is being built. Known
+failure modes include fabricated medications, silently altered dosages, mg→mcg unit
+swaps, and invented frequencies. `medfence` is the fence between model output and
+clinical action: pure-function, zero-dependency, every verdict backed by
+machine-checkable evidence.
+
+```python
+from medfence import verify, Extraction, SourceDocument
+
+report = verify(
+    Extraction(artifact_type="prescription", payload=llm_output),
+    SourceDocument(text=ocr_text, modality="ocr", ocr_confidence=0.91),
+)
+report.overall        # Verdict.PASS | Verdict.FAIL | Verdict.ABSTAIN
+report.coverage       # fraction of payload fields actually verified
+report.to_audit_json()  # one hash-chained JSON line per verification
+```
+
+## The three guarantees
+
+1. **Deterministic.** No I/O, no clock, no model calls inside `verify()`. Identical
+   `(source, extraction, rulepack)` → bit-identical report. Verdicts are reproducible
+   by strangers; that is what makes them auditable.
+2. **Fail-closed.** `ABSTAIN` is a first-class verdict, not an error state. "Couldn't
+   check" routes to a human exactly like `FAIL`; it never silently becomes `PASS`.
+   Unknown artifact types, missing reference data, low-confidence OCR → `ABSTAIN`.
+3. **No finding without evidence.** Every verdict carries a source span, a reference
+   bundle key, or a rule id. A check that cannot produce evidence must abstain.
+
+And one deliberate refusal: **medfence never judges clinical appropriateness.**
+`dose_in_range` answers "does 500 mg paracetamol exist as a marketed product?",
+never "should this patient take it?" Fidelity and referential validity are
+mechanically decidable; clinical judgment is not, and pretending otherwise is how
+verification tools become unlicensed medical devices.
+
+## Check families (v0)
+
+**Family G: span grounding ("no span, no claim")**
+Every extracted value must align to a span in the source, *localized to its own
+medication's line*, because whole-document matching invites cross-medication collisions
+(a 250 mg on someone else's line must not ground your altered strength).
+Numbers and units match exact-after-normalization only; fuzzy-matching a dosage
+is how a fence approves a hallucination. `unit_integrity` catches the mg↔mcg
+class specifically. Fully ungrounded medication objects fail `no_orphans`
+(the fabricated-drug detector).
+
+**Family R: reference validity**
+Drug names, marketed strengths, dose forms, and frequency tokens are checked
+against a versioned, content-hashed Indian drug bundle and a closed grammar of
+prescription shorthand (OD, BD, TDS, 1-0-1, SOS, …). Fuzzy lookup is allowed for
+retrieval; a weak hit is `ABSTAIN`, never `PASS`.
+
+## Benchmark
+
+100 documents: 20 synthetic Indian OPD prescriptions × (1 clean + 4 seeded-error
+variants). Reproduce with `python scripts/make_golden.py && python scripts/benchmark.py`.
+
+| error class        |  n | FAIL | ABSTAIN | PASS | caught | **false PASS** |
+|--------------------|---:|-----:|--------:|-----:|-------:|---------------:|
+| fabricated_drug    | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| unit_swap          | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| altered_strength   | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| invented_frequency | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| clean              | 20 |    0 |       0 |   20 |    n/a | (100% clean-pass) |
+
+**Read this honestly:** 100% on a synthetic golden set means the set is easy, not
+that the fence is finished. The seeded errors are clean single-fault injections on
+noise-free text. The numbers that matter will come from real, anonymized,
+OCR-noisy prescriptions. Contributions of anonymized hard cases are the most
+valuable thing you can send this project.
+
+## What v0 deliberately does not do
+
+- Drug-drug interaction checking (v1 candidate, behind an explicit opt-in)
+- Patient-contextual dosing (age/weight/renal): the SaMD line; we stay below it
+- Auto-correction: medfence flags, it never fixes
+- LLM-as-judge fallback: if deterministic checks can't verify it, a human sees it
+- STT/word-timestamp evidence (the `Evidence` type is designed for it; v0 is OCR/text)
+- **Omission detection**: `verify()` checks payload→source fidelity, not
+  source→payload completeness: a medication silently *dropped* by the extractor is
+  not caught. This gap is encoded as a strict-xfail test so it stays visible.
+
+## Reference bundle
+
+v0 ships `refdata-2026.07.0-seed`: ~27 common Indian OPD molecules with brand
+aliases, forms, and marketed strengths, a deliberately small, versioned
+placeholder for a proper CDSCO + NLEM + Jan Aushadhi normalization pass. The
+bundle is content-hashed and the hash is pinned into every report, so verdicts
+remain reproducible as the data grows.
+
+## Testing & validation
+
+The suite is deliberately heavier than the library; for a verification tool,
+the tests *are* the product claim. Beyond unit tests, three layers guard the
+contract:
+
+- **Property-based** (`tests/test_properties.py`, Hypothesis): `verify()` is
+  total, fail-closed, and non-mutating over arbitrary junk payloads; reports are
+  bit-identical; clean-by-construction cases PASS and any corruption of them
+  never does; mg/mcg canonicalization never merges; aggregation matches an
+  independent worst-of oracle and is order-invariant and monotone.
+- **Metamorphic** (`tests/test_metamorphic.py`): ~700 guarded corruptions
+  (digit edits, magnitude shifts, unit swaps, real-but-absent drug insertion,
+  in-grammar frequency swaps, …) applied to every clean golden case at test
+  time; none may PASS. Same fault taxonomy as the golden set, one
+  implementation (`scripts/corruptions.py`), two depths.
+- **Golden gate** (`tests/test_golden_gate.py`): the benchmark as hard
+  assertions; false-PASS == 0 and clean-pass == 100% fail the build, and the
+  committed golden set must match its generator exactly.
+
+Known v0 limitations are encoded as `xfail(strict=True)` tests (duplicate
+medication names, trailing punctuation on frequencies, omission detection):
+executable documentation that flips to a build failure the day the limitation
+is fixed.
+
+```bash
+uv sync --group dev
+uv run pytest                      # full suite (~750 tests, <5 s)
+uv run pytest -m golden            # just the benchmark gate
+```
+
+## Project layout
+
+```
+medfence/
+  contract.py        # types + fail-closed aggregation (the stable core)
+  normalize.py       # deterministic text/unit/number normalization
+  rulepack.py        # bundle loading, thresholds-as-versioned-data
+  checks/grounding.py  # Family G
+  checks/refdata.py    # Family R
+  verify.py          # the single entrypoint
+  data/refdata_seed.json
+scripts/make_golden.py   # regenerate the golden set (deterministic, no RNG)
+scripts/benchmark.py     # the table above (exits 1 on any false PASS)
+scripts/corruptions.py   # shared fault operators (golden set + metamorphic grid)
+tests/               # contract invariants, properties, metamorphic grid, golden gate
+tests/schemas/       # JSON Schema for the audit report (the output contract)
+docs/adr-001-*.md    # the design record
+docs/related-work.md # how this differs from LangExtract, Guardrails, etc.
+```
+
+## Design record & positioning
+
+See `docs/adr-001-clinical-verification-contract-v0.md` for the full contract
+spec, options considered, and the trade-off analysis (notably: why ABSTAIN
+exists, why coverage is a first-class output, and where the SaMD line is drawn).
+For how medfence relates to LangExtract, Guardrails AI, clinical
+self-verification, and the rest of the landscape, see `docs/related-work.md`.
+
+## License
+
+Apache-2.0.
+
+## Quick demo
+
+```bash
+python3 demo.py   # one prescription: PASS, FAIL (mcg swap + fabricated drug), ABSTAIN (low OCR)
+```

medfence-0.1.0/README.md

@@ -0,0 +1,165 @@
+# medfence
+
+[![ci](https://github.com/Debanitrkl/medfence/actions/workflows/ci.yml/badge.svg)](https://github.com/Debanitrkl/medfence/actions/workflows/ci.yml)
+
+**A deterministic, fail-closed verification harness for clinical LLM outputs.**
+
+LLM extraction is entering clinical workflows (scribes, prescription digitization,
+lab-report parsing) faster than verification infrastructure is being built. Known
+failure modes include fabricated medications, silently altered dosages, mg→mcg unit
+swaps, and invented frequencies. `medfence` is the fence between model output and
+clinical action: pure-function, zero-dependency, every verdict backed by
+machine-checkable evidence.
+
+```python
+from medfence import verify, Extraction, SourceDocument
+
+report = verify(
+    Extraction(artifact_type="prescription", payload=llm_output),
+    SourceDocument(text=ocr_text, modality="ocr", ocr_confidence=0.91),
+)
+report.overall        # Verdict.PASS | Verdict.FAIL | Verdict.ABSTAIN
+report.coverage       # fraction of payload fields actually verified
+report.to_audit_json()  # one hash-chained JSON line per verification
+```
+
+## The three guarantees
+
+1. **Deterministic.** No I/O, no clock, no model calls inside `verify()`. Identical
+   `(source, extraction, rulepack)` → bit-identical report. Verdicts are reproducible
+   by strangers; that is what makes them auditable.
+2. **Fail-closed.** `ABSTAIN` is a first-class verdict, not an error state. "Couldn't
+   check" routes to a human exactly like `FAIL`; it never silently becomes `PASS`.
+   Unknown artifact types, missing reference data, low-confidence OCR → `ABSTAIN`.
+3. **No finding without evidence.** Every verdict carries a source span, a reference
+   bundle key, or a rule id. A check that cannot produce evidence must abstain.
+
+And one deliberate refusal: **medfence never judges clinical appropriateness.**
+`dose_in_range` answers "does 500 mg paracetamol exist as a marketed product?",
+never "should this patient take it?" Fidelity and referential validity are
+mechanically decidable; clinical judgment is not, and pretending otherwise is how
+verification tools become unlicensed medical devices.
+
+## Check families (v0)
+
+**Family G: span grounding ("no span, no claim")**
+Every extracted value must align to a span in the source, *localized to its own
+medication's line*, because whole-document matching invites cross-medication collisions
+(a 250 mg on someone else's line must not ground your altered strength).
+Numbers and units match exact-after-normalization only; fuzzy-matching a dosage
+is how a fence approves a hallucination. `unit_integrity` catches the mg↔mcg
+class specifically. Fully ungrounded medication objects fail `no_orphans`
+(the fabricated-drug detector).
+
+**Family R: reference validity**
+Drug names, marketed strengths, dose forms, and frequency tokens are checked
+against a versioned, content-hashed Indian drug bundle and a closed grammar of
+prescription shorthand (OD, BD, TDS, 1-0-1, SOS, …). Fuzzy lookup is allowed for
+retrieval; a weak hit is `ABSTAIN`, never `PASS`.
+
+## Benchmark
+
+100 documents: 20 synthetic Indian OPD prescriptions × (1 clean + 4 seeded-error
+variants). Reproduce with `python scripts/make_golden.py && python scripts/benchmark.py`.
+
+| error class        |  n | FAIL | ABSTAIN | PASS | caught | **false PASS** |
+|--------------------|---:|-----:|--------:|-----:|-------:|---------------:|
+| fabricated_drug    | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| unit_swap          | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| altered_strength   | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| invented_frequency | 20 |   20 |       0 |    0 |   100% |         **0%** |
+| clean              | 20 |    0 |       0 |   20 |    n/a | (100% clean-pass) |
+
+**Read this honestly:** 100% on a synthetic golden set means the set is easy, not
+that the fence is finished. The seeded errors are clean single-fault injections on
+noise-free text. The numbers that matter will come from real, anonymized,
+OCR-noisy prescriptions. Contributions of anonymized hard cases are the most
+valuable thing you can send this project.
+
+## What v0 deliberately does not do
+
+- Drug-drug interaction checking (v1 candidate, behind an explicit opt-in)
+- Patient-contextual dosing (age/weight/renal): the SaMD line; we stay below it
+- Auto-correction: medfence flags, it never fixes
+- LLM-as-judge fallback: if deterministic checks can't verify it, a human sees it
+- STT/word-timestamp evidence (the `Evidence` type is designed for it; v0 is OCR/text)
+- **Omission detection**: `verify()` checks payload→source fidelity, not
+  source→payload completeness: a medication silently *dropped* by the extractor is
+  not caught. This gap is encoded as a strict-xfail test so it stays visible.
+
+## Reference bundle
+
+v0 ships `refdata-2026.07.0-seed`: ~27 common Indian OPD molecules with brand
+aliases, forms, and marketed strengths, a deliberately small, versioned
+placeholder for a proper CDSCO + NLEM + Jan Aushadhi normalization pass. The
+bundle is content-hashed and the hash is pinned into every report, so verdicts
+remain reproducible as the data grows.
+
+## Testing & validation
+
+The suite is deliberately heavier than the library; for a verification tool,
+the tests *are* the product claim. Beyond unit tests, three layers guard the
+contract:
+
+- **Property-based** (`tests/test_properties.py`, Hypothesis): `verify()` is
+  total, fail-closed, and non-mutating over arbitrary junk payloads; reports are
+  bit-identical; clean-by-construction cases PASS and any corruption of them
+  never does; mg/mcg canonicalization never merges; aggregation matches an
+  independent worst-of oracle and is order-invariant and monotone.
+- **Metamorphic** (`tests/test_metamorphic.py`): ~700 guarded corruptions
+  (digit edits, magnitude shifts, unit swaps, real-but-absent drug insertion,
+  in-grammar frequency swaps, …) applied to every clean golden case at test
+  time; none may PASS. Same fault taxonomy as the golden set, one
+  implementation (`scripts/corruptions.py`), two depths.
+- **Golden gate** (`tests/test_golden_gate.py`): the benchmark as hard
+  assertions; false-PASS == 0 and clean-pass == 100% fail the build, and the
+  committed golden set must match its generator exactly.
+
+Known v0 limitations are encoded as `xfail(strict=True)` tests (duplicate
+medication names, trailing punctuation on frequencies, omission detection):
+executable documentation that flips to a build failure the day the limitation
+is fixed.
+
+```bash
+uv sync --group dev
+uv run pytest                      # full suite (~750 tests, <5 s)
+uv run pytest -m golden            # just the benchmark gate
+```
+
+## Project layout
+
+```
+medfence/
+  contract.py        # types + fail-closed aggregation (the stable core)
+  normalize.py       # deterministic text/unit/number normalization
+  rulepack.py        # bundle loading, thresholds-as-versioned-data
+  checks/grounding.py  # Family G
+  checks/refdata.py    # Family R
+  verify.py          # the single entrypoint
+  data/refdata_seed.json
+scripts/make_golden.py   # regenerate the golden set (deterministic, no RNG)
+scripts/benchmark.py     # the table above (exits 1 on any false PASS)
+scripts/corruptions.py   # shared fault operators (golden set + metamorphic grid)
+tests/               # contract invariants, properties, metamorphic grid, golden gate
+tests/schemas/       # JSON Schema for the audit report (the output contract)
+docs/adr-001-*.md    # the design record
+docs/related-work.md # how this differs from LangExtract, Guardrails, etc.
+```
+
+## Design record & positioning
+
+See `docs/adr-001-clinical-verification-contract-v0.md` for the full contract
+spec, options considered, and the trade-off analysis (notably: why ABSTAIN
+exists, why coverage is a first-class output, and where the SaMD line is drawn).
+For how medfence relates to LangExtract, Guardrails AI, clinical
+self-verification, and the rest of the landscape, see `docs/related-work.md`.
+
+## License
+
+Apache-2.0.
+
+## Quick demo
+
+```bash
+python3 demo.py   # one prescription: PASS, FAIL (mcg swap + fabricated drug), ABSTAIN (low OCR)
+```

medfence-0.1.0/medfence/__init__.py

@@ -0,0 +1,25 @@
+from .contract import (
+    Evidence,
+    Extraction,
+    Finding,
+    Severity,
+    SourceDocument,
+    Verdict,
+    VerificationReport,
+)
+from .rulepack import Rulepack, load_rulepack
+from .verify import verify
+
+__all__ = [
+    "Evidence",
+    "Extraction",
+    "Finding",
+    "Rulepack",
+    "Severity",
+    "SourceDocument",
+    "Verdict",
+    "VerificationReport",
+    "load_rulepack",
+    "verify",
+]
+__version__ = "0.1.0"