academic-research-kernel 2.0.0__py3-none-any.whl

academic_research_kernel/__init__.py

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+"""Installed deterministic academic research kernel."""
+from ._version import __version__

academic_research_kernel/__main__.py

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+from .cli import main
+
+raise SystemExit(main())

academic_research_kernel/_version.py

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+"""Canonical product release version (independent of skill/schema versions)."""
+__version__ = "2.0.0"

academic_research_kernel/artifact-adapter-matrix.json

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+{
+  "protocol": "artifact-adapter-matrix-1.0",
+  "total_adapters": 14,
+  "adapters": [
+    {
+      "adapter_id": "adapter-academic-source-verification",
+      "adapter_version": "1.0.0",
+      "tier": 1,
+      "is_lossless": true,
+      "accepted_producers": [
+        "academic-source-verification"
+      ],
+      "accepted_schemas": [
+        "academic-evidence-1.0",
+        "evidence-receipt-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-research-object-identity",
+      "adapter_version": "1.0.0",
+      "tier": 1,
+      "is_lossless": true,
+      "accepted_producers": [
+        "research-object-identity"
+      ],
+      "accepted_schemas": [
+        "lineage-receipt-1.0",
+        "research-object-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-claim-evidence-graph",
+      "adapter_version": "1.0.0",
+      "tier": 1,
+      "is_lossless": true,
+      "accepted_producers": [
+        "claim-evidence-graph"
+      ],
+      "accepted_schemas": [
+        "ceg-snapshot-1.0",
+        "claim-evidence-graph-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-decision-ledger",
+      "adapter_version": "1.0.0",
+      "tier": 1,
+      "is_lossless": true,
+      "accepted_producers": [
+        "decision-ledger"
+      ],
+      "accepted_schemas": [
+        "decision-ledger-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-quantitative-paper-audit",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "quantitative-paper-audit"
+      ],
+      "accepted_schemas": [
+        "quantitative-audit-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-research-reproducibility",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "research-reproducibility"
+      ],
+      "accepted_schemas": [
+        "reproduction-receipt-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-cross-review-five",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "cross-review-five"
+      ],
+      "accepted_schemas": [
+        "cross-review-2.0",
+        "cross-review-finding-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-systematic-review",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "systematic-review-meta-analysis"
+      ],
+      "accepted_schemas": [
+        "meta-analysis-1.0",
+        "screening-matrix-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-literature-analysis",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "literature-analysis"
+      ],
+      "accepted_schemas": [
+        "canonical-work-1.0",
+        "corpus-matrix-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-literature-watch",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "literature-watch"
+      ],
+      "accepted_schemas": [
+        "literature-delta-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-retraction-watch",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "retraction-watch"
+      ],
+      "accepted_schemas": [
+        "retraction-alert-1.0",
+        "retraction-delta-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-math-computation",
+      "adapter_version": "1.0.0",
+      "tier": 2,
+      "is_lossless": false,
+      "accepted_producers": [
+        "math-computation"
+      ],
+      "accepted_schemas": [
+        "computation-receipt-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-academic-writing",
+      "adapter_version": "1.0.0",
+      "tier": 3,
+      "is_lossless": false,
+      "accepted_producers": [
+        "academic-writing"
+      ],
+      "accepted_schemas": [
+        "manuscript-opaque-1.0",
+        "submission-package-1.0"
+      ]
+    },
+    {
+      "adapter_id": "adapter-opaque-fallback",
+      "adapter_version": "1.0.0",
+      "tier": 3,
+      "is_lossless": false,
+      "accepted_producers": [],
+      "accepted_schemas": []
+    }
+  ]
+}

academic_research_kernel/cli.py

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+"""Small installation/stdio boundary; no research workflow orchestration."""
+import argparse
+import importlib
+from importlib import metadata, resources, util
+import json
+import os
+import platform
+import sys
+
+from ._version import __version__
+
+REQUIRED = ('jsonschema', 'numpy', 'scipy', 'statsmodels')
+OPTIONAL = ('sympy', 'matplotlib', 'sklearn', 'networkx', 'lifelines', 'arch', 'pingouin', 'torch', 'cupy')
+SERVICES = ('OPENALEX_API_KEY', 'UNPAYWALL_EMAIL', 'SCITE_API_KEY', 'WOS_API_KEY',
+            'SCOPUS_API_KEY', 'DIMENSIONS_API_KEY')
+
+
+def doctor():
+    """Offline installation check. Values of external configuration never leave here."""
+    report = {'version': __version__, 'python': {'executable': sys.executable,
+              'version': platform.python_version()}, 'package_location': str(resources.files('academic_research_kernel')),
+              'required_dependencies': {}, 'optional_dependencies': {},
+              'external_services': {key: 'configured' if os.environ.get(key) else 'unconfigured (optional)' for key in SERVICES},
+              'errors': []}
+    for name in REQUIRED:
+        try:
+            importlib.import_module(name)
+            report['required_dependencies'][name] = metadata.version(name)
+        except Exception as exc:
+            report['required_dependencies'][name] = 'unavailable'
+            report['errors'].append(f'{name}: {type(exc).__name__}')
+    for name in OPTIONAL:
+        report['optional_dependencies'][name] = 'available' if util.find_spec(name) else 'not installed (optional)'
+    try:
+        from jsonschema import Draft202012Validator
+        schemas = list(resources.files('academic_research_kernel').joinpath('schemas').iterdir())
+        schemas = [p for p in schemas if p.name.endswith('.json')]
+        if len(schemas) != 23:
+            raise ValueError('incomplete schema inventory')
+        for path in schemas:
+            Draft202012Validator.check_schema(json.loads(path.read_text(encoding='utf-8')))
+        report['schema_resources'] = {'status': 'ok', 'count': len(schemas)}
+        matrix = resources.files('academic_research_kernel').joinpath('artifact-adapter-matrix.json')
+        json.loads(matrix.read_text(encoding='utf-8'))
+    except Exception as exc:
+        report['schema_resources'] = {'status': 'error'}
+        report['errors'].append(f'resources: {type(exc).__name__}')
+    try:
+        from . import mcp_server
+        report['mcp'] = {'importable': True, 'tool_count': len(mcp_server.TOOLS)}
+        if len(mcp_server.TOOLS) != 12:
+            raise ValueError('unexpected tool count')
+        pct = mcp_server.handle_tool_call('academic_check_percentage', {'count': 10, 'percent': 50, 'sample_size': 20})
+        if pct.get('consistent') is not True:
+            raise ValueError('statistics check failed')
+    except Exception as exc:
+        report['mcp'] = {'importable': False}
+        report['errors'].append(f'MCP: {type(exc).__name__}')
+    report['status'] = 'ok' if not report['errors'] else 'error'
+    return report
+
+
+def main(argv=None):
+    if not (3, 10) <= sys.version_info[:2] < (3, 15):
+        print('academic-research-kernel requires Python 3.10–3.14; use uvx --python 3.12 academic-research-kernel.', file=sys.stderr)
+        return 2
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument('--version', action='version', version=__version__)
+    commands = parser.add_subparsers(dest='command', required=True)
+    check = commands.add_parser('doctor', help='offline environment diagnostic')
+    check.add_argument('--json', action='store_true', help='machine-readable JSON')
+    commands.add_parser('mcp', help='serve the existing 12 MCP tools over stdio')
+    args = parser.parse_args(argv)
+    if args.command == 'doctor':
+        report = doctor()
+        if args.json:
+            print(json.dumps(report, indent=2))
+        else:
+            print(f'academic-research-kernel {__version__}: {report["status"]}')
+            for key, value in report.items():
+                if key not in ('version', 'status'):
+                    print(f'{key}: {json.dumps(value, ensure_ascii=False)}')
+        return 0 if report['status'] == 'ok' else 1
+    try:
+        from .mcp_server import main as serve
+    except ImportError:
+        print('Incomplete runtime installation. Run academic-research-kernel doctor.', file=sys.stderr)
+        return 1
+    serve()
+    return 0