@ahmed-g-gad/apothem 0.1.1

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Files changed (674) hide show
  1. package/CHANGELOG.md +60 -0
  2. package/LICENSE +21 -0
  3. package/LICENSES/MIT.txt +18 -0
  4. package/LICENSES/PSF-2.0.txt +47 -0
  5. package/README.md +549 -0
  6. package/bin/README.md +37 -0
  7. package/bin/apothem.mjs +78 -0
  8. package/package.json +75 -0
  9. package/pyproject.toml +347 -0
  10. package/src/apothem/README.md +52 -0
  11. package/src/apothem/__init__.py +66 -0
  12. package/src/apothem/__main__.py +28 -0
  13. package/src/apothem/_vendor/.keep +0 -0
  14. package/src/apothem/_vendor/__init__.py +25 -0
  15. package/src/apothem/_vendor/attr/__init__.py +104 -0
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  20. package/src/apothem/_vendor/attr/_config.py +31 -0
  21. package/src/apothem/_vendor/attr/_funcs.py +497 -0
  22. package/src/apothem/_vendor/attr/_make.py +3406 -0
  23. package/src/apothem/_vendor/attr/_next_gen.py +674 -0
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  27. package/src/apothem/_vendor/attr/converters.py +162 -0
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  38. package/src/apothem/_vendor/attr.LICENSE +21 -0
  39. package/src/apothem/_vendor/attrs/__init__.py +72 -0
  40. package/src/apothem/_vendor/attrs/__init__.pyi +314 -0
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  46. package/src/apothem/_vendor/attrs/validators.py +3 -0
  47. package/src/apothem/_vendor/attrs.LICENSE +21 -0
  48. package/src/apothem/_vendor/jsonschema/__init__.py +120 -0
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  67. package/src/apothem/_vendor/jsonschema/benchmarks/useless_keywords.py +32 -0
  68. package/src/apothem/_vendor/jsonschema/benchmarks/validator_creation.py +14 -0
  69. package/src/apothem/_vendor/jsonschema/cli.py +292 -0
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  71. package/src/apothem/_vendor/jsonschema/protocols.py +230 -0
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  76. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/metaschema.json +42 -0
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  90. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/unevaluated +15 -0
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  92. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft3/metaschema.json +172 -0
  93. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft4/metaschema.json +149 -0
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  95. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft7/metaschema.json +166 -0
  96. package/src/apothem/_vendor/jsonschema_specifications.LICENSE +19 -0
  97. package/src/apothem/_vendor/referencing/__init__.py +7 -0
  98. package/src/apothem/_vendor/referencing/_attrs.py +31 -0
  99. package/src/apothem/_vendor/referencing/_attrs.pyi +21 -0
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  103. package/src/apothem/_vendor/referencing/py.typed +0 -0
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  105. package/src/apothem/_vendor/referencing/typing.py +61 -0
  106. package/src/apothem/_vendor/referencing.LICENSE +19 -0
  107. package/src/apothem/_vendor/rpds/__init__.py +251 -0
  108. package/src/apothem/_vendor/typing_extensions.LICENSE +279 -0
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  116. package/src/apothem/_vendor/yaml/emitter.py +1137 -0
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  126. package/src/apothem/_vendor/yaml/serializer.py +110 -0
  127. package/src/apothem/_vendor/yaml/tokens.py +103 -0
  128. package/src/apothem/_vendor/yaml.LICENSE +20 -0
  129. package/src/apothem/agents/README.md +60 -0
  130. package/src/apothem/agents/codebase-explorer.md +91 -0
  131. package/src/apothem/agents/convention-auditor.md +93 -0
  132. package/src/apothem/agents/dependency-auditor.md +97 -0
  133. package/src/apothem/agents/fact-checker.md +84 -0
  134. package/src/apothem/agents/mcp-builder.md +86 -0
  135. package/src/apothem/agents/memory-auditor.md +93 -0
  136. package/src/apothem/agents/prompt-evaluator.md +87 -0
  137. package/src/apothem/agents/quality-gate.md +103 -0
  138. package/src/apothem/agents/refactor-surgeon.md +74 -0
  139. package/src/apothem/agents/research-scout.md +73 -0
  140. package/src/apothem/agents/security-scanner.md +83 -0
  141. package/src/apothem/agents/test-runner.md +84 -0
  142. package/src/apothem/audit/README.md +73 -0
  143. package/src/apothem/audit/_scan_lib.py +182 -0
  144. package/src/apothem/audit/analyze_graph.py +260 -0
  145. package/src/apothem/audit/build_capability_graph.py +607 -0
  146. package/src/apothem/audit/build_inventory.py +657 -0
  147. package/src/apothem/audit/build_plans_provenance.py +997 -0
  148. package/src/apothem/audit/check_links.py +389 -0
  149. package/src/apothem/audit/classify_artifacts.py +381 -0
  150. package/src/apothem/audit/deprecated-tokens.txt +10 -0
  151. package/src/apothem/audit/execute_plans_migration.py +491 -0
  152. package/src/apothem/audit/known-projects.txt +15 -0
  153. package/src/apothem/audit/render_capability_index.py +467 -0
  154. package/src/apothem/audit/render_inventory.py +405 -0
  155. package/src/apothem/audit/scan_ai_surfaces.py +1125 -0
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  194. package/src/apothem/cli/reference_export.py +126 -0
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  585. package/src/apothem/rules/planning-techniques.md +130 -0
  586. package/src/apothem/rules/pre-emission-gate-bars.md +86 -0
  587. package/src/apothem/rules/pre-emission-gate.md +54 -0
  588. package/src/apothem/rules/production-ready-prs-surfaces.md +162 -0
  589. package/src/apothem/rules/production-ready-prs.md +83 -0
  590. package/src/apothem/rules/propagation.md +63 -0
  591. package/src/apothem/rules/recommend-next-step.md +106 -0
  592. package/src/apothem/rules/refactoring-discipline.md +76 -0
  593. package/src/apothem/rules/session-closure.md +44 -0
  594. package/src/apothem/rules/sota-elevation-exemplars.md +76 -0
  595. package/src/apothem/rules/sota-elevation.md +52 -0
  596. package/src/apothem/rules/source-accessibility.md +58 -0
  597. package/src/apothem/rules/surgical-manipulation.md +48 -0
  598. package/src/apothem/rules/systemic-participation-relations.md +108 -0
  599. package/src/apothem/rules/systemic-participation.md +70 -0
  600. package/src/apothem/rules/ten-dimension-check-dimensions.md +52 -0
  601. package/src/apothem/rules/ten-dimension-check.md +59 -0
  602. package/src/apothem/rules/token-budget-discipline.md +81 -0
  603. package/src/apothem/rules/token-efficiency-rewrite-protocol.md +79 -0
  604. package/src/apothem/rules/token-efficiency-rewrite.md +77 -0
  605. package/src/apothem/rules/tool-use-discipline.md +48 -0
  606. package/src/apothem/rules/visual-leverage.md +102 -0
  607. package/src/apothem/schemas/NOTICE.md +9 -0
  608. package/src/apothem/schemas/README.md +104 -0
  609. package/src/apothem/schemas/__init__.py +176 -0
  610. package/src/apothem/schemas/advisory-finding.schema.json +111 -0
  611. package/src/apothem/schemas/agent.schema.json +106 -0
  612. package/src/apothem/schemas/authorship-header.txt +1 -0
  613. package/src/apothem/schemas/cohort-manifest.yaml +248 -0
  614. package/src/apothem/schemas/cohort-metadata-vocabulary.yaml +168 -0
  615. package/src/apothem/schemas/cohort.schema.json +113 -0
  616. package/src/apothem/schemas/command.schema.json +68 -0
  617. package/src/apothem/schemas/compatibility-matrix.yaml +432 -0
  618. package/src/apothem/schemas/context-fragment.schema.json +64 -0
  619. package/src/apothem/schemas/freshness-token-denylist.txt +51 -0
  620. package/src/apothem/schemas/handoff-manifest.yaml +353 -0
  621. package/src/apothem/schemas/header-exceptions.txt +141 -0
  622. package/src/apothem/schemas/header-visibility.yaml +39 -0
  623. package/src/apothem/schemas/learning-signal.schema.json +46 -0
  624. package/src/apothem/schemas/memory-record.schema.json +61 -0
  625. package/src/apothem/schemas/output-style.schema.json +40 -0
  626. package/src/apothem/schemas/plan.schema.json +51 -0
  627. package/src/apothem/schemas/plugin.schema.json +83 -0
  628. package/src/apothem/schemas/profile.example.yaml +70 -0
  629. package/src/apothem/schemas/profile.minimal.yaml +6 -0
  630. package/src/apothem/schemas/profile.schema.json +396 -0
  631. package/src/apothem/schemas/reference-token-denylist.txt +25 -0
  632. package/src/apothem/schemas/skill.schema.json +75 -0
  633. package/src/apothem/skills/README.md +93 -0
  634. package/src/apothem/skills/dependency-upgrade/SKILL.md +105 -0
  635. package/src/apothem/skills/dev-toolkit/SKILL.md +120 -0
  636. package/src/apothem/skills/diagram-authoring/SKILL.md +113 -0
  637. package/src/apothem/skills/document-authoring/SKILL.md +118 -0
  638. package/src/apothem/skills/ecosystem-audit/SKILL.md +108 -0
  639. package/src/apothem/skills/ecosystem-audit/references/audit-fortress.md +85 -0
  640. package/src/apothem/skills/ecosystem-audit/references/procedure.md +162 -0
  641. package/src/apothem/skills/eval-harness/SKILL.md +88 -0
  642. package/src/apothem/skills/incident-runbook/SKILL.md +92 -0
  643. package/src/apothem/skills/multi-source-research/SKILL.md +90 -0
  644. package/src/apothem/skills/plan-suite/SKILL.md +118 -0
  645. package/src/apothem/skills/plan-suite/master_template.md +1324 -0
  646. package/src/apothem/skills/projectify/SKILL.md +117 -0
  647. package/src/apothem/skills/prompt-engineering/SKILL.md +122 -0
  648. package/src/apothem/skills/refactor-extract/SKILL.md +85 -0
  649. package/src/apothem/skills/research-suite/SKILL.md +170 -0
  650. package/src/apothem/skills/research-suite/references/directory-structure.md +47 -0
  651. package/src/apothem/skills/research-suite/references/lifecycle.md +67 -0
  652. package/src/apothem/skills/research-suite/references/principal-investigator-framework.md +37 -0
  653. package/src/apothem/skills/research-suite/references/rigor-mandates.md +30 -0
  654. package/src/apothem/skills/research-suite/research_template.md +476 -0
  655. package/src/apothem/skills/secret-rotation/SKILL.md +87 -0
  656. package/src/apothem/skills/source-synthesis/SKILL.md +92 -0
  657. package/src/apothem/skills/surgical-guard/SKILL.md +118 -0
  658. package/src/apothem/skills/test-authoring/SKILL.md +85 -0
  659. package/src/apothem/skills/vuln-triage/SKILL.md +91 -0
  660. package/src/apothem/skills/workflow/SKILL.md +139 -0
  661. package/src/apothem/statuslines/README.md +26 -0
  662. package/src/apothem/statuslines/__init__.py +20 -0
  663. package/src/apothem/statuslines/conformity.json +5 -0
  664. package/src/apothem/statuslines/render.py +334 -0
  665. package/src/apothem/statuslines/statusline.md +50 -0
  666. package/src/apothem/templates/README.md +43 -0
  667. package/src/apothem/templates/agents-md-template.md +80 -0
  668. package/src/apothem/templates/consideration-log.md +39 -0
  669. package/src/apothem/templates/expertise-gap-log.md +56 -0
  670. package/src/apothem/templates/master-index-template.md +93 -0
  671. package/src/apothem/templates/potency-map.md +53 -0
  672. package/src/apothem/templates/preservation-audit.md +60 -0
  673. package/src/apothem/templates/question-resolution-audit.md +52 -0
  674. package/src/apothem/templates/trace-matrix-template.md +77 -0
@@ -0,0 +1,281 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Verify a canonical .editorconfig is present at the project root.
4
+
5
+ Why this enforcement exists. The supply-chain SOTA-rigor
6
+ cohort requires every repository to ship a ratified ``.editorconfig`` so
7
+ every contributor's editor materializes whitespace, indentation, line
8
+ ending, charset, and final-newline conventions identically regardless of
9
+ local editor configuration. Silent drift at the editor layer surfaces as
10
+ mixed-line-ending diffs, trailing-whitespace noise, and indent-character
11
+ mismatches that cost reviewer attention; a ratified ``.editorconfig`` at
12
+ the repo root pre-empts the entire class of failures. This standalone
13
+ validator confirms the file exists with the canonical contract
14
+ (``root = true`` declaration, the global ``[*]`` section with the six
15
+ canonical keys, the ``[*.{yml,yaml,json}]`` two-space override for
16
+ data-shaped files, and the ``[*.md]`` trailing-whitespace exemption for
17
+ Markdown's two-space hard-break convention).
18
+
19
+ Scope. Standalone corpus-level validator. Reads ``<root>/.editorconfig``
20
+ from a single ``main(root)`` entry point and exits 0 (PASS) or 2 (FAIL)
21
+ with a structured JSON report listing every drift class observed.
22
+ Invoked via ``python -m apothem.conformity.gate --all .`` or
23
+ ``python -m apothem.conformity.gate --check editorconfig-presence-grep
24
+ <root>``.
25
+ """
26
+
27
+ from __future__ import annotations
28
+
29
+ import json
30
+ import re
31
+ import sys
32
+ from dataclasses import asdict, dataclass, field
33
+ from pathlib import Path
34
+ from typing import Final
35
+
36
+ GREP_NAME: Final[str] = "editorconfig-presence-grep"
37
+ RULE_ANCHOR: Final[str] = "supply-chain SOTA-rigor §editorconfig"
38
+ EXIT_PASS: Final[int] = 0
39
+ EXIT_FAIL: Final[int] = 2
40
+
41
+ EDITORCONFIG_FILENAME: Final[str] = ".editorconfig"
42
+
43
+ # The canonical key/value pairs every conformant ``[*]`` section carries.
44
+ # Each value is the verbatim literal the editorconfig spec admits for the
45
+ # key; the matcher compares case-insensitively for value tokens but the
46
+ # key itself is matched literally per the editorconfig grammar.
47
+ GLOBAL_REQUIRED_KEYS: Final[dict[str, str]] = {
48
+ "charset": "utf-8",
49
+ "indent_style": "space",
50
+ "indent_size": "4",
51
+ "end_of_line": "lf",
52
+ "insert_final_newline": "true",
53
+ "trim_trailing_whitespace": "true",
54
+ }
55
+
56
+ # Per-language overrides. Each entry maps the section header (literal
57
+ # bracketed string) to the (key, expected-value) pair the section MUST
58
+ # declare for the override to be canonical.
59
+ PER_LANGUAGE_OVERRIDES: Final[dict[str, dict[str, str]]] = {
60
+ "[*.{yml,yaml,json}]": {"indent_size": "2"},
61
+ "[*.md]": {"trim_trailing_whitespace": "false"},
62
+ }
63
+
64
+ # Matches a section header line such as ``[*]`` or ``[*.md]``. Trailing
65
+ # inline comments (``[*] ; comment``) are tolerated by the editorconfig
66
+ # grammar; we strip them before classification.
67
+ SECTION_RE: Final[re.Pattern[str]] = re.compile(r"^\s*(\[[^\]]+\])\s*(?:[;#].*)?$")
68
+
69
+ # Matches a ``key = value`` declaration inside a section. The
70
+ # editorconfig grammar admits whitespace on either side of the ``=`` and
71
+ # a trailing comment introduced by ``;`` or ``#``.
72
+ KEY_VALUE_RE: Final[re.Pattern[str]] = re.compile(
73
+ r"^\s*([A-Za-z_][A-Za-z0-9_]*)\s*=\s*([^;#]+?)\s*(?:[;#].*)?$"
74
+ )
75
+
76
+ # The ``root = true`` declaration. Matched anywhere in the file (it lives
77
+ # above the first section header by convention but the spec admits any
78
+ # pre-section position).
79
+ ROOT_DECLARATION_RE: Final[re.Pattern[str]] = re.compile(
80
+ r"^\s*root\s*=\s*true\s*(?:[;#].*)?$",
81
+ re.IGNORECASE | re.MULTILINE,
82
+ )
83
+
84
+
85
+ @dataclass(frozen=True)
86
+ class Finding:
87
+ """One editorconfig drift observation."""
88
+
89
+ drift_class: str
90
+ detail: str
91
+ rule: str = RULE_ANCHOR
92
+
93
+
94
+ @dataclass(frozen=True)
95
+ class GrepResult:
96
+ grep: str
97
+ path: str | None
98
+ passed: bool
99
+ findings: list[Finding] = field(default_factory=list)
100
+
101
+ def to_json(self) -> str:
102
+ payload = {
103
+ "grep": self.grep,
104
+ "path": self.path,
105
+ "passed": self.passed,
106
+ "findings": [asdict(f) for f in self.findings],
107
+ }
108
+ return json.dumps(payload, indent=2)
109
+
110
+
111
+ def _parse_sections(text: str) -> dict[str, dict[str, str]]:
112
+ """Parse an editorconfig body into ``{section-header: {key: value}}``.
113
+
114
+ The pre-section preamble (where ``root = true`` lives) is collected
115
+ under the empty-string key so callers can inspect it uniformly.
116
+ """
117
+ sections: dict[str, dict[str, str]] = {"": {}}
118
+ current = ""
119
+ for raw_line in text.splitlines():
120
+ line = raw_line.rstrip()
121
+ if not line or line.lstrip().startswith((";", "#")):
122
+ continue
123
+ section_match = SECTION_RE.match(line)
124
+ if section_match is not None:
125
+ current = section_match.group(1)
126
+ sections.setdefault(current, {})
127
+ continue
128
+ kv_match = KEY_VALUE_RE.match(line)
129
+ if kv_match is not None:
130
+ key = kv_match.group(1)
131
+ value = kv_match.group(2).strip().lower()
132
+ sections[current][key] = value
133
+ return sections
134
+
135
+
136
+ def check(root: Path) -> GrepResult:
137
+ """Verify ``<root>/.editorconfig`` carries the canonical contract.
138
+
139
+ Pre-conditions: ``root`` is the project root (the directory holding
140
+ ``pyproject.toml`` or its closest ancestor).
141
+ Post-conditions: ``result.passed`` is True iff the editorconfig file
142
+ exists with the ``root = true`` declaration, the six canonical
143
+ ``[*]`` keys at their ratified values, and the two per-language
144
+ overrides at their ratified values.
145
+ """
146
+ findings: list[Finding] = []
147
+ target = root / EDITORCONFIG_FILENAME
148
+ if not target.is_file():
149
+ findings.append(
150
+ Finding(
151
+ drift_class="file-absent",
152
+ detail=(
153
+ f"no .editorconfig at {target}; author a canonical file "
154
+ "per the supply-chain SOTA-rigor contract"
155
+ ),
156
+ )
157
+ )
158
+ return GrepResult(
159
+ grep=GREP_NAME,
160
+ path=str(root),
161
+ passed=False,
162
+ findings=findings,
163
+ )
164
+
165
+ try:
166
+ text = target.read_text(encoding="utf-8")
167
+ except (OSError, UnicodeDecodeError) as exc:
168
+ findings.append(
169
+ Finding(
170
+ drift_class="file-absent",
171
+ detail=f"could not read {target}: {exc!r}",
172
+ )
173
+ )
174
+ return GrepResult(
175
+ grep=GREP_NAME,
176
+ path=str(root),
177
+ passed=False,
178
+ findings=findings,
179
+ )
180
+
181
+ if ROOT_DECLARATION_RE.search(text) is None:
182
+ findings.append(
183
+ Finding(
184
+ drift_class="missing-root-declaration",
185
+ detail=(
186
+ "no `root = true` declaration; the editorconfig spec "
187
+ "requires this token to halt the upward walk for "
188
+ "ancestor .editorconfig files"
189
+ ),
190
+ )
191
+ )
192
+
193
+ sections = _parse_sections(text)
194
+
195
+ global_section = sections.get("[*]")
196
+ if global_section is None:
197
+ findings.append(
198
+ Finding(
199
+ drift_class="missing-global-section",
200
+ detail="no `[*]` section; the global override is mandatory",
201
+ )
202
+ )
203
+ else:
204
+ for key, expected in GLOBAL_REQUIRED_KEYS.items():
205
+ if key not in global_section:
206
+ findings.append(
207
+ Finding(
208
+ drift_class="missing-global-section",
209
+ detail=(
210
+ f"[*] section is missing required key {key!r} "
211
+ f"(expected value: {expected!r})"
212
+ ),
213
+ )
214
+ )
215
+ continue
216
+ actual = global_section[key]
217
+ if actual != expected.lower():
218
+ findings.append(
219
+ Finding(
220
+ drift_class="wrong-value",
221
+ detail=(
222
+ f"[*].{key} = {actual!r}; expected "
223
+ f"{expected!r} per the canonical contract"
224
+ ),
225
+ )
226
+ )
227
+
228
+ for header, required in PER_LANGUAGE_OVERRIDES.items():
229
+ section = sections.get(header)
230
+ if section is None:
231
+ findings.append(
232
+ Finding(
233
+ drift_class="missing-per-language-override",
234
+ detail=(
235
+ f"no {header} section; canonical contract requires "
236
+ f"this override declaring {required!r}"
237
+ ),
238
+ )
239
+ )
240
+ continue
241
+ for key, expected in required.items():
242
+ if key not in section:
243
+ findings.append(
244
+ Finding(
245
+ drift_class="missing-per-language-override",
246
+ detail=(
247
+ f"{header} section is missing key {key!r} "
248
+ f"(expected value: {expected!r})"
249
+ ),
250
+ )
251
+ )
252
+ continue
253
+ actual = section[key]
254
+ if actual != expected.lower():
255
+ findings.append(
256
+ Finding(
257
+ drift_class="wrong-value",
258
+ detail=(
259
+ f"{header}.{key} = {actual!r}; expected "
260
+ f"{expected!r} per the canonical contract"
261
+ ),
262
+ )
263
+ )
264
+
265
+ return GrepResult(
266
+ grep=GREP_NAME,
267
+ path=str(root),
268
+ passed=not findings,
269
+ findings=findings,
270
+ )
271
+
272
+
273
+ def main(root: Path) -> int:
274
+ result = check(root)
275
+ print(result.to_json())
276
+ return EXIT_PASS if result.passed else EXIT_FAIL
277
+
278
+
279
+ if __name__ == "__main__":
280
+ target = Path(sys.argv[1]) if len(sys.argv) >= 2 else Path.cwd()
281
+ sys.exit(main(target))