@cyanheads/pubchem-mcp-server 1.0.1

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Files changed (127) hide show
  1. package/LICENSE +201 -0
  2. package/README.md +236 -0
  3. package/dist/config/index.d.ts +98 -0
  4. package/dist/config/index.js +326 -0
  5. package/dist/index.d.ts +24 -0
  6. package/dist/index.js +214 -0
  7. package/dist/mcp-server/server.d.ts +21 -0
  8. package/dist/mcp-server/server.js +124 -0
  9. package/dist/mcp-server/tools/fetchAssaySummary/index.d.ts +7 -0
  10. package/dist/mcp-server/tools/fetchAssaySummary/index.js +7 -0
  11. package/dist/mcp-server/tools/fetchAssaySummary/logic.d.ts +71 -0
  12. package/dist/mcp-server/tools/fetchAssaySummary/logic.js +96 -0
  13. package/dist/mcp-server/tools/fetchAssaySummary/registration.d.ts +12 -0
  14. package/dist/mcp-server/tools/fetchAssaySummary/registration.js +68 -0
  15. package/dist/mcp-server/tools/fetchCompoundProperties/index.d.ts +7 -0
  16. package/dist/mcp-server/tools/fetchCompoundProperties/index.js +7 -0
  17. package/dist/mcp-server/tools/fetchCompoundProperties/logic.d.ts +131 -0
  18. package/dist/mcp-server/tools/fetchCompoundProperties/logic.js +100 -0
  19. package/dist/mcp-server/tools/fetchCompoundProperties/registration.d.ts +13 -0
  20. package/dist/mcp-server/tools/fetchCompoundProperties/registration.js +52 -0
  21. package/dist/mcp-server/tools/fetchCompoundXrefs/index.d.ts +7 -0
  22. package/dist/mcp-server/tools/fetchCompoundXrefs/index.js +7 -0
  23. package/dist/mcp-server/tools/fetchCompoundXrefs/logic.d.ts +89 -0
  24. package/dist/mcp-server/tools/fetchCompoundXrefs/logic.js +145 -0
  25. package/dist/mcp-server/tools/fetchCompoundXrefs/registration.d.ts +13 -0
  26. package/dist/mcp-server/tools/fetchCompoundXrefs/registration.js +52 -0
  27. package/dist/mcp-server/tools/fetchSubstanceDetails/index.d.ts +7 -0
  28. package/dist/mcp-server/tools/fetchSubstanceDetails/index.js +7 -0
  29. package/dist/mcp-server/tools/fetchSubstanceDetails/logic.d.ts +69 -0
  30. package/dist/mcp-server/tools/fetchSubstanceDetails/logic.js +97 -0
  31. package/dist/mcp-server/tools/fetchSubstanceDetails/registration.d.ts +13 -0
  32. package/dist/mcp-server/tools/fetchSubstanceDetails/registration.js +79 -0
  33. package/dist/mcp-server/tools/getCompoundImage/index.d.ts +7 -0
  34. package/dist/mcp-server/tools/getCompoundImage/index.js +7 -0
  35. package/dist/mcp-server/tools/getCompoundImage/logic.d.ts +42 -0
  36. package/dist/mcp-server/tools/getCompoundImage/logic.js +68 -0
  37. package/dist/mcp-server/tools/getCompoundImage/registration.d.ts +12 -0
  38. package/dist/mcp-server/tools/getCompoundImage/registration.js +57 -0
  39. package/dist/mcp-server/tools/searchAssaysByTarget/index.d.ts +7 -0
  40. package/dist/mcp-server/tools/searchAssaysByTarget/index.js +7 -0
  41. package/dist/mcp-server/tools/searchAssaysByTarget/logic.d.ts +35 -0
  42. package/dist/mcp-server/tools/searchAssaysByTarget/logic.js +64 -0
  43. package/dist/mcp-server/tools/searchAssaysByTarget/registration.d.ts +12 -0
  44. package/dist/mcp-server/tools/searchAssaysByTarget/registration.js +62 -0
  45. package/dist/mcp-server/tools/searchCompoundByIdentifier/index.d.ts +7 -0
  46. package/dist/mcp-server/tools/searchCompoundByIdentifier/index.js +7 -0
  47. package/dist/mcp-server/tools/searchCompoundByIdentifier/logic.d.ts +35 -0
  48. package/dist/mcp-server/tools/searchCompoundByIdentifier/logic.js +59 -0
  49. package/dist/mcp-server/tools/searchCompoundByIdentifier/registration.d.ts +12 -0
  50. package/dist/mcp-server/tools/searchCompoundByIdentifier/registration.js +51 -0
  51. package/dist/mcp-server/tools/searchCompoundsByFormula/index.d.ts +7 -0
  52. package/dist/mcp-server/tools/searchCompoundsByFormula/index.js +7 -0
  53. package/dist/mcp-server/tools/searchCompoundsByFormula/logic.d.ts +38 -0
  54. package/dist/mcp-server/tools/searchCompoundsByFormula/logic.js +75 -0
  55. package/dist/mcp-server/tools/searchCompoundsByFormula/registration.d.ts +12 -0
  56. package/dist/mcp-server/tools/searchCompoundsByFormula/registration.js +62 -0
  57. package/dist/mcp-server/tools/searchCompoundsBySimilarity/index.d.ts +7 -0
  58. package/dist/mcp-server/tools/searchCompoundsBySimilarity/index.js +7 -0
  59. package/dist/mcp-server/tools/searchCompoundsBySimilarity/logic.d.ts +41 -0
  60. package/dist/mcp-server/tools/searchCompoundsBySimilarity/logic.js +82 -0
  61. package/dist/mcp-server/tools/searchCompoundsBySimilarity/registration.d.ts +12 -0
  62. package/dist/mcp-server/tools/searchCompoundsBySimilarity/registration.js +62 -0
  63. package/dist/mcp-server/tools/searchCompoundsByStructure/index.d.ts +7 -0
  64. package/dist/mcp-server/tools/searchCompoundsByStructure/index.js +7 -0
  65. package/dist/mcp-server/tools/searchCompoundsByStructure/logic.d.ts +41 -0
  66. package/dist/mcp-server/tools/searchCompoundsByStructure/logic.js +78 -0
  67. package/dist/mcp-server/tools/searchCompoundsByStructure/registration.d.ts +13 -0
  68. package/dist/mcp-server/tools/searchCompoundsByStructure/registration.js +63 -0
  69. package/dist/mcp-server/transports/auth/core/authContext.d.ts +33 -0
  70. package/dist/mcp-server/transports/auth/core/authContext.js +24 -0
  71. package/dist/mcp-server/transports/auth/core/authTypes.d.ts +17 -0
  72. package/dist/mcp-server/transports/auth/core/authTypes.js +5 -0
  73. package/dist/mcp-server/transports/auth/core/authUtils.d.ts +18 -0
  74. package/dist/mcp-server/transports/auth/core/authUtils.js +45 -0
  75. package/dist/mcp-server/transports/auth/index.d.ts +10 -0
  76. package/dist/mcp-server/transports/auth/index.js +9 -0
  77. package/dist/mcp-server/transports/auth/strategies/jwt/jwtMiddleware.d.ts +27 -0
  78. package/dist/mcp-server/transports/auth/strategies/jwt/jwtMiddleware.js +149 -0
  79. package/dist/mcp-server/transports/auth/strategies/oauth/oauthMiddleware.d.ts +20 -0
  80. package/dist/mcp-server/transports/auth/strategies/oauth/oauthMiddleware.js +124 -0
  81. package/dist/mcp-server/transports/httpErrorHandler.d.ts +26 -0
  82. package/dist/mcp-server/transports/httpErrorHandler.js +73 -0
  83. package/dist/mcp-server/transports/httpTransport.d.ts +21 -0
  84. package/dist/mcp-server/transports/httpTransport.js +208 -0
  85. package/dist/mcp-server/transports/stdioTransport.d.ts +42 -0
  86. package/dist/mcp-server/transports/stdioTransport.js +63 -0
  87. package/dist/services/pubchem/pubchemApiClient.d.ts +52 -0
  88. package/dist/services/pubchem/pubchemApiClient.js +120 -0
  89. package/dist/types-global/errors.d.ts +127 -0
  90. package/dist/types-global/errors.js +126 -0
  91. package/dist/utils/index.d.ts +12 -0
  92. package/dist/utils/index.js +20 -0
  93. package/dist/utils/internal/errorHandler.d.ts +176 -0
  94. package/dist/utils/internal/errorHandler.js +335 -0
  95. package/dist/utils/internal/index.d.ts +9 -0
  96. package/dist/utils/internal/index.js +9 -0
  97. package/dist/utils/internal/logger.d.ts +148 -0
  98. package/dist/utils/internal/logger.js +430 -0
  99. package/dist/utils/internal/requestContext.d.ts +83 -0
  100. package/dist/utils/internal/requestContext.js +72 -0
  101. package/dist/utils/metrics/index.d.ts +7 -0
  102. package/dist/utils/metrics/index.js +7 -0
  103. package/dist/utils/metrics/tokenCounter.d.ts +35 -0
  104. package/dist/utils/metrics/tokenCounter.js +110 -0
  105. package/dist/utils/network/fetchWithTimeout.d.ts +21 -0
  106. package/dist/utils/network/fetchWithTimeout.js +59 -0
  107. package/dist/utils/network/index.d.ts +6 -0
  108. package/dist/utils/network/index.js +5 -0
  109. package/dist/utils/parsing/dateParser.d.ts +73 -0
  110. package/dist/utils/parsing/dateParser.js +107 -0
  111. package/dist/utils/parsing/index.d.ts +8 -0
  112. package/dist/utils/parsing/index.js +8 -0
  113. package/dist/utils/parsing/jsonParser.d.ts +82 -0
  114. package/dist/utils/parsing/jsonParser.js +126 -0
  115. package/dist/utils/scheduling/index.d.ts +6 -0
  116. package/dist/utils/scheduling/index.js +6 -0
  117. package/dist/utils/scheduling/scheduler.d.ts +72 -0
  118. package/dist/utils/scheduling/scheduler.js +152 -0
  119. package/dist/utils/security/idGenerator.d.ts +137 -0
  120. package/dist/utils/security/idGenerator.js +215 -0
  121. package/dist/utils/security/index.d.ts +9 -0
  122. package/dist/utils/security/index.js +9 -0
  123. package/dist/utils/security/rateLimiter.d.ts +108 -0
  124. package/dist/utils/security/rateLimiter.js +179 -0
  125. package/dist/utils/security/sanitization.d.ts +184 -0
  126. package/dist/utils/security/sanitization.js +453 -0
  127. package/package.json +108 -0
package/package.json ADDED
@@ -0,0 +1,108 @@
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+ {
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+ "name": "@cyanheads/pubchem-mcp-server",
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+ "version": "1.0.1",
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+ "description": "A Model Context Protocol (MCP) server providing comprehensive LLM tools for the PubChem PUG REST API.",
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+ "main": "dist/index.js",
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+ "files": [
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+ "dist"
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+ ],
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+ "bin": {
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+ "pubchem-mcp-server": "dist/index.js"
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+ },
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+ "exports": "./dist/index.js",
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+ "types": "dist/index.d.ts",
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+ "type": "module",
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+ "repository": {
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+ "type": "git",
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+ "url": "git+https://github.com/cyanheads/pubchem-mcp-server.git"
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+ },
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+ "bugs": {
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+ "url": "https://github.com/cyanheads/pubchem-mcp-server/issues"
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+ },
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+ "homepage": "https://github.com/cyanheads/pubchem-mcp-server#readme",
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+ "scripts": {
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+ "build": "tsc && node --loader ts-node/esm scripts/make-executable.ts dist/index.js",
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+ "start": "node dist/index.js",
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+ "start:stdio": "MCP_LOG_LEVEL=debug MCP_TRANSPORT_TYPE=stdio node dist/index.js",
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+ "start:http": "MCP_LOG_LEVEL=debug MCP_TRANSPORT_TYPE=http node dist/index.js",
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+ "start:agent": "MCP_LOG_LEVEL=debug node dist/agent/cli/boot.js",
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+ "rebuild": "ts-node --esm scripts/clean.ts && npm run build",
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+ "docs:generate": "typedoc --tsconfig ./tsconfig.typedoc.json",
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+ "depcheck": "npx depcheck",
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+ "tree": "ts-node --esm scripts/tree.ts",
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+ "fetch-spec": "ts-node --esm scripts/fetch-openapi-spec.ts",
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+ "format": "prettier --write \"**/*.{ts,js,json,md,html,css}\"",
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+ "inspector": "npx mcp-inspector --config mcp.json --server pubchem-mcp-server",
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+ "db:duckdb-example": "MCP_LOG_LEVEL=debug tsc && node dist/storage/duckdbExample.js"
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+ },
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+ "dependencies": {
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+ "@duckdb/node-api": "^1.3.1-alpha.23",
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+ "@hono/node-server": "^1.14.4",
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+ "@modelcontextprotocol/sdk": "^1.13.2",
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+ "@supabase/supabase-js": "^2.50.2",
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+ "@types/node": "^24.0.7",
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+ "@types/sanitize-html": "^2.16.0",
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+ "@types/validator": "13.15.2",
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+ "chrono-node": "^2.8.0",
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+ "dotenv": "^16.5.0",
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+ "hono": "^4.8.3",
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+ "ignore": "^7.0.5",
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+ "jose": "^6.0.11",
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+ "limiter": "^3.0.0",
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+ "node-cron": "^4.1.1",
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+ "openai": "^5.8.2",
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+ "partial-json": "^0.1.7",
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+ "sanitize-html": "^2.17.0",
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+ "tiktoken": "^1.0.21",
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+ "ts-node": "^10.9.2",
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+ "typescript": "^5.8.3",
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+ "validator": "13.15.15",
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+ "winston": "^3.17.0",
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+ "winston-transport": "^4.9.0",
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+ "zod": "^3.25.67"
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+ },
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+ "keywords": [
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+ "mcp",
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+ "mcp-server",
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+ "model-context-protocol",
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+ "ai-agent",
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+ "llm",
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+ "pubchem",
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+ "chemistry",
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+ "cheminformatics",
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+ "bioinformatics",
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+ "drug-discovery",
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+ "scientific-computing",
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+ "api-wrapper",
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+ "typescript",
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+ "hono",
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+ "zod"
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+ ],
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+ "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubchem-mcp-server#readme)",
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+ "license": "Apache-2.0",
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+ "publishConfig": {
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+ "access": "public"
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+ },
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+ "funding": [
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+ {
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+ "type": "github",
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+ "url": "https://github.com/sponsors/cyanheads"
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+ },
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+ {
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+ "type": "buy_me_a_coffee",
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+ "url": "https://www.buymeacoffee.com/cyanheads"
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+ }
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+ ],
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+ "engines": {
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+ "node": ">=20.0.0"
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+ },
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+ "devDependencies": {
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+ "@types/js-yaml": "^4.0.9",
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+ "@types/node-cron": "^3.0.11",
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+ "axios": "^1.10.0",
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+ "depcheck": "^1.4.7",
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+ "js-yaml": "^4.1.0",
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+ "prettier": "^3.6.2",
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+ "typedoc": "^0.28.7"
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+ }
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+ }