witsoc-bio 1.0.0__tar.gz

witsoc_bio-1.0.0/PKG-INFO

@@ -0,0 +1,18 @@
+Metadata-Version: 2.5
+Name: witsoc-bio
+Version: 1.0.0
+Summary: Witsoc biology domain pack
+Author: Witsoc contributors
+License: Proprietary
+Keywords: biology,causal-inference,open-problems,research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+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: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+The biology domain pack for the Witsoc research architecture. Install it directly only for inspection; the Witsoc skill installs and activates this pinned pack automatically when a biological task is routed.

witsoc_bio-1.0.0/pyproject.toml

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+[build-system]
+requires = ["hatchling>=1.25"]
+build-backend = "hatchling.build"
+
+[project]
+name = "witsoc-bio"
+version = "1.0.0"
+description = "Witsoc biology domain pack"
+readme = {text = "The biology domain pack for the Witsoc research architecture. Install it directly only for inspection; the Witsoc skill installs and activates this pinned pack automatically when a biological task is routed.", content-type = "text/markdown"}
+requires-python = ">=3.10"
+license = {text = "Proprietary"}
+authors = [{name = "Witsoc contributors"}]
+dependencies = []
+keywords = ["biology", "research", "open-problems", "causal-inference"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.scripts]
+witsoc-bio-pack = "witsoc_domain_bio.__main__:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/witsoc_domain_bio"]
+
+[tool.hatch.build.targets.sdist]
+include = ["src/witsoc_domain_bio", "pyproject.toml"]

witsoc_bio-1.0.0/src/witsoc_domain_bio/__init__.py

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+"""Installed resource access for the Witsoc biology domain pack."""
+
+from __future__ import annotations
+
+import json
+from importlib.resources import files
+from typing import Any
+
+__version__ = "1.0.0"
+
+
+def metadata() -> dict[str, Any]:
+    return json.loads(files(__package__).joinpath("pack.json").read_text(encoding="utf-8"))
+
+
+def domain_root():
+    return files(__package__).joinpath("domain")

witsoc_bio-1.0.0/src/witsoc_domain_bio/__main__.py

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+"""Inspect the installed biology pack without invoking the Witsoc core."""
+
+from __future__ import annotations
+
+import json
+
+from . import domain_root, metadata
+
+
+def main() -> int:
+    value = metadata()
+    value["installed_domain_root"] = str(domain_root())
+    print(json.dumps(value, indent=2, sort_keys=True))
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

witsoc_bio-1.0.0/src/witsoc_domain_bio/domain/capabilities.json

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+{
+  "schema": "witsoc.capability-manifest.v1",
+  "owner": "bio",
+  "version": 1,
+  "capabilities": [
+    {
+      "id": "source-status-map",
+      "summary": "Bind biological claims to primary sources, samples, corrections, and contradictions.",
+      "modes": ["SOURCE_SYNTHESIS", "OPEN_DISCOVERY"],
+      "roles": ["explorer", "researcher"],
+      "default": true,
+      "triggers": [],
+      "inputs": ["witsoc.target.v2"],
+      "outputs": ["witsoc.source-map.v2", "witsoc.obstruction.v2"],
+      "requires": ["retrievable source and dataset provenance"],
+      "load": ["domains/bio/doctrine/provenance.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" plan --help", "python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" contract --help"],
+      "cost_class": "small",
+      "priority": 95
+    },
+    {
+      "id": "open-frontier",
+      "summary": "Reduce competing biological mechanisms through bounded discriminating episodes.",
+      "modes": ["OPEN_DISCOVERY"],
+      "roles": ["explorer", "researcher"],
+      "default": true,
+      "triggers": [],
+      "inputs": ["witsoc.target.v2", "witsoc.source-map.v2", "witsoc.research-delta.v1", "witsoc.obstruction.v2"],
+      "outputs": ["witsoc.frontier.v2", "witsoc.research-episode.v1", "witsoc.research-delta.v1", "witsoc.obstruction.v2"],
+      "requires": ["frozen evidence scope", "competing mechanism set"],
+      "load": ["domains/bio/doctrine/open_problem.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" plan --help", "python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" contract --help"],
+      "cost_class": "medium",
+      "priority": 100
+    },
+    {
+      "id": "causal-perturbation",
+      "summary": "Audit intervention response, denominator, confounding, controls, replication, and scope.",
+      "modes": ["OPEN_DISCOVERY", "CLAIM_VERIFICATION", "ARTIFACT_PRODUCTION"],
+      "roles": ["explorer", "generator", "researcher"],
+      "default": false,
+      "triggers": ["perturbation", "knockdown", "knockout", "crispr", "intervention", "causal mechanism"],
+      "inputs": ["witsoc.target.v2", "witsoc.research-episode.v1", "witsoc.candidate.v2"],
+      "outputs": ["witsoc.candidate.v2", "witsoc.receipt.v2", "witsoc.obstruction.v2"],
+      "requires": ["unit-level data and metadata", "negative and positive controls"],
+      "load": ["domains/bio/doctrine/claim_freeze.md", "domains/bio/doctrine/denominators.md", "domains/bio/doctrine/confounders.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/check.py\" --help"],
+      "cost_class": "medium",
+      "priority": 90
+    },
+    {
+      "id": "genetics-to-function",
+      "summary": "Trace variants through fine mapping, molecular consequence, effector, and functional phenotype.",
+      "modes": ["OPEN_DISCOVERY", "CROSS_DOMAIN"],
+      "roles": ["explorer", "researcher"],
+      "default": false,
+      "triggers": ["gwas", "variant", "fine mapping", "allele", "locus", "colocalization", "genetic interaction"],
+      "inputs": ["witsoc.target.v2", "witsoc.source-map.v2", "witsoc.transfer.v2"],
+      "outputs": ["witsoc.candidate.v2", "witsoc.obstruction.v2", "witsoc.transfer.v2"],
+      "requires": ["population and linkage context", "functional discriminator"],
+      "load": ["domains/bio/doctrine/genetics_to_function.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" plan --help"],
+      "cost_class": "medium",
+      "priority": 80
+    },
+    {
+      "id": "structure-function",
+      "summary": "Convert molecular structures into specific, rescuable, orthogonally measured functional predictions.",
+      "modes": ["OPEN_DISCOVERY", "CROSS_DOMAIN"],
+      "roles": ["explorer", "researcher"],
+      "default": false,
+      "triggers": ["structure", "interface", "binding", "domain", "conformation", "mutation", "structure function"],
+      "inputs": ["witsoc.target.v2", "witsoc.source-map.v2", "witsoc.transfer.v2"],
+      "outputs": ["witsoc.candidate.v2", "witsoc.obstruction.v2", "witsoc.transfer.v2"],
+      "requires": ["construct and state provenance", "orthogonal functional readout"],
+      "load": ["domains/bio/doctrine/structure_function.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" plan --help"],
+      "cost_class": "medium",
+      "priority": 75
+    },
+    {
+      "id": "systems-context",
+      "summary": "Resolve state, composition, feedback, compensation, spatial, temporal, and multi-modal context.",
+      "modes": ["OPEN_DISCOVERY", "CLAIM_VERIFICATION", "CROSS_DOMAIN"],
+      "roles": ["explorer", "researcher"],
+      "default": false,
+      "triggers": ["multi-omics", "single-cell", "spatial", "cell state", "tissue", "feedback", "compensation"],
+      "inputs": ["witsoc.target.v2", "witsoc.source-map.v2", "witsoc.candidate.v2"],
+      "outputs": ["witsoc.candidate.v2", "witsoc.obstruction.v2", "witsoc.transfer.v2"],
+      "requires": ["unit alignment across measurements", "context metadata"],
+      "load": ["domains/bio/doctrine/systems_context.md", "domains/bio/doctrine/confounders.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/expression_diagnostics.py\" --help"],
+      "cost_class": "medium",
+      "priority": 75
+    },
+    {
+      "id": "discriminating-design",
+      "summary": "Design controls, estimands, sampling, power, and outcomes that distinguish live mechanisms.",
+      "modes": ["OPEN_DISCOVERY", "ARTIFACT_PRODUCTION"],
+      "roles": ["explorer", "generator", "researcher"],
+      "default": false,
+      "triggers": ["experiment", "study design", "control", "power", "replication", "preregister"],
+      "inputs": ["witsoc.frontier.v2", "witsoc.obstruction.v2", "witsoc.research-episode.v1"],
+      "outputs": ["witsoc.candidate.v2", "witsoc.research-episode.v1"],
+      "requires": ["named competing explanations", "measurement feasibility"],
+      "load": ["domains/bio/doctrine/baselines_and_metrics.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/design.py\" --help", "python3 \"$WITSOC_ROOT/domains/bio/scripts/power.py\" --help"],
+      "cost_class": "small",
+      "priority": 70
+    },
+    {
+      "id": "evidence-adapter",
+      "summary": "Recompute pinned evidence and enforce denominator, provenance, contradiction, confounding, and scope gates.",
+      "modes": ["CLAIM_VERIFICATION", "ARTIFACT_PRODUCTION", "REPAIR", "OPEN_DISCOVERY"],
+      "roles": ["generator", "explorer"],
+      "default": true,
+      "triggers": [],
+      "inputs": ["witsoc.candidate.v2", "witsoc.target.v2"],
+      "outputs": ["witsoc.receipt.v2", "witsoc.obstruction.v2"],
+      "requires": ["pinned inputs and analysis context"],
+      "load": ["domains/bio/doctrine/report_language.md", "domains/bio/doctrine/provenance.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/check.py\" --help"],
+      "cost_class": "medium",
+      "priority": 85
+    },
+    {
+      "id": "cross-domain-transfer",
+      "summary": "Exchange typed models and discriminators while retaining biological scope ownership.",
+      "modes": ["CROSS_DOMAIN"],
+      "roles": ["explorer", "researcher"],
+      "default": true,
+      "triggers": [],
+      "inputs": ["witsoc.transfer.v2", "witsoc.obstruction.v2", "witsoc.candidate.v2"],
+      "outputs": ["witsoc.transfer.v2", "witsoc.obstruction.v2", "witsoc.candidate.v2"],
+      "requires": ["scope and invariant audit"],
+      "load": ["domains/bio/doctrine/two_pack.md"],
+      "commands": ["python3 \"$WITSOC_ROOT/domains/bio/scripts/discovery_ops.py\" plan --help"],
+      "cost_class": "small",
+      "priority": 90
+    }
+  ]
+}

witsoc_bio-1.0.0/src/witsoc_domain_bio/domain/claim.schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "bio-claim-v1",
+  "title": "Frozen perturbation claim",
+  "description": "Extends frame-claim-v1 with everything that can change what a perturbation result MEANS. The rule that makes this worth writing out: freeze every dimension even when the value is unknown. An explicit 'unknown' and a silently omitted field read identically in a report and have entirely different consequences — the first is a stated limit, the second is a limit nobody knows about. A changed value here is a NEW claim with a new hash and its own lineage; it never mutates this one.",
+  "type": "object",
+  "additionalProperties": true,
+  "required": [
+    "claim_id",
+    "exact_statement",
+    "target_sha256",
+    "organism",
+    "claim_class",
+    "biological_context",
+    "perturbation",
+    "assay",
+    "dataset",
+    "claimed_effect",
+    "falsification_conditions",
+    "allowed_scope",
+    "frozen_conditions"
+  ],
+  "properties": {
+    "claim_id": {
+      "type": "string",
+      "minLength": 1
+    },
+    "target_sha256": {
+      "description": "SHA-256 over the canonical form of this claim with this field removed. Recomputed at every gate rather than read back.",
+      "type": "string",
+      "pattern": "^[0-9a-f]{64}$"
+    },
+    "organism": {
+      "type": "string",
+      "minLength": 1
+    },
+    "claim_class": {
+      "description": "Which row of data/claim_classes.json this is. The class sets the ceiling, so an unclassified claim has no ceiling and cannot be audited.",
+      "enum": [
+        "cell_level_association",
+        "guide_conditioned_within_screen",
+        "target_conditioned",
+        "donor_replicated_population",
+        "in_vivo_animal",
+        "organoid_patient_model",
+        "spatial_tissue",
+        "network_causal_method",
+        "model_predictive_superiority",
+        "literature_only"
+      ]
+    },
+    "generalization_axis": {
+      "description": "The axis along which generality is claimed — cell_line, donor, perturbation, context, or none. This decides which leakage findings are fatal rather than cosmetic.",
+      "enum": [
+        "none",
+        "cell_line",
+        "donor",
+        "perturbation",
+        "context",
+        "time",
+        "dose"
+      ]
+    },
+    "biological_context": {
+      "type": "object",
+      "required": [
+        "cell_type",
+        "tissue",
+        "disease_state",
+        "donor_or_model_system"
+      ],
+      "properties": {
+        "cell_type": {
+          "type": "string",
+          "minLength": 1
+        },
+        "tissue": {
+          "type": "string",
+          "minLength": 1
+        },
+        "disease_state": {
+          "type": "string",
+          "minLength": 1
+        },
+        "donor_or_model_system": {
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    },
+    "perturbation": {
+      "type": "object",
+      "required": [
+        "entity",
+        "modality",
+        "dose",
+        "duration",
+        "delivery"
+      ],
+      "properties": {
+        "entity": {
+          "type": "string",
+          "minLength": 1
+        },
+        "modality": {
+          "type": "string",
+          "minLength": 1
+        },
+        "dose": {
+          "type": "string",
+          "minLength": 1
+        },
+        "duration": {
+          "type": "string",
+          "minLength": 1
+        },
+        "delivery": {
+          "type": "string",
+          "minLength": 1
+        },
+        "is_combination": {
+          "description": "True for a combination claim, which makes the additive baseline mandatory — it is the baseline elaborate models most often lose to.",
+          "type": "boolean"
+        }
+      }
+    },
+    "assay": {
+      "type": "object",
+      "required": [
+        "type",
+        "readout",
+        "experimental_unit",
+        "controls",
+        "batches",
+        "replicates"
+      ],
+      "properties": {
+        "type": {
+          "type": "string",
+          "minLength": 1
+        },
+        "readout": {
+          "description": "What was physically measured. Every scope-language check works back from this: a transcriptomic readout cannot reach mechanism, organism, or clinic on its own.",
+          "type": "string",
+          "minLength": 1
+        },
+        "experimental_unit": {
+          "description": "The unit the claim is about. Usually decided implicitly by whatever the analysis groups by, which is exactly why it is frozen here instead.",
+          "type": "string",
+          "minLength": 1
+        },
+        "controls": {
+          "type": "string",
+          "minLength": 1
+        },
+        "batches": {
+          "type": "string",
+          "minLength": 1
+        },
+        "replicates": {
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    },
+    "dataset": {
+      "type": "object",
+      "required": [
+        "id",
+        "version",
+        "source",
+        "preprocessing_state"
+      ],
+      "properties": {
+        "id": {
+          "type": "string",
+          "minLength": 1
+        },
+        "version": {
+          "type": "string",
+          "minLength": 1
+        },
+        "source": {
+          "type": "string",
+          "minLength": 1
+        },
+        "license": {
+          "type": "string"
+        },
+        "preprocessing_state": {
+          "description": "Raw, filtered, normalized, integrated. Two analyses of 'the same dataset' at different preprocessing states are analyses of different data.",
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    },
+    "model_evaluation": {
+      "description": "Present only for a predictive claim. Its absence is what makes the baseline and metric gates not-applicable rather than failed.",
+      "type": "object",
+      "required": [
+        "model",
+        "baseline",
+        "split"
+      ],
+      "properties": {
+        "model": {
+          "type": "string"
+        },
+        "model_version": {
+          "type": "string"
+        },
+        "training_data": {
+          "type": "string"
+        },
+        "baseline": {
+          "type": "string"
+        },
+        "split": {
+          "type": "string"
+        },
+        "evaluation_unit": {
+          "type": "string"
+        }
+      }
+    },
+    "claimed_effect": {
+      "type": "object",
+      "required": [
+        "direction",
+        "magnitude",
+        "endpoint"
+      ],
+      "properties": {
+        "direction": {
+          "enum": [
+            "increase",
+            "decrease",
+            "change",
+            "no_change",
+            "unknown"
+          ]
+        },
+        "magnitude": {
+          "type": "string",
+          "minLength": 1
+        },
+        "endpoint": {
+          "type": "string",
+          "minLength": 1
+        }
+      }
+    },
+    "falsification_conditions": {
+      "description": "What would show this claim is wrong. A claim with no stated way to be wrong cannot be audited: there is nothing for a check to fail.",
+      "type": "array",
+      "minItems": 1,
+      "items": {
+        "type": "string",
+        "minLength": 10
+      }
+    },
+    "allowed_scope": {
+      "description": "The bounds inside which a result would hold. Written before the result, because after it the temptation is to write the bounds that fit.",
+      "type": "string",
+      "minLength": 10
+    },
+    "derived_from": {
+      "description": "The claim hash this one was narrowed, widened, or repaired from. Present whenever a context changed: the lineage is recorded, the old claim is not edited.",
+      "type": "string",
+      "pattern": "^[0-9a-f]{64}$"
+    },
+    "exact_statement": {
+      "description": "The claim in one sentence, in the form: perturbing X with modality P changes response Y in context Z. If it cannot be written this way, it is more than one claim. The frame's claim calls this `exact_statement` and so does this one. It was `statement` until a contract-shape check noticed that a pack declaring `extends: frame-claim-v1` while renaming one of its required fields is not extending it — and that the frame's reducer, reading the name it expects, had been recording an EMPTY statement for every claim this pack froze. The campaign state was unreadable and nothing failed.",
+      "type": "string",
+      "minLength": 20
+    },
+    "frozen_conditions": {
+      "description": "What must not drift, under the name the frame reads. These are the same dimensions this field's own gates already diff against — collecting them here is what lets the FRAME see them too, rather than each pack protecting its target in a vocabulary only it understands.",
+      "type": "object"
+    },
+    "status": {
+      "description": "Inherited from frame-claim-v1; declared here so the extension is checkable."
+    }
+  }
+}