@cyanheads/pubchem-mcp-server 0.6.1 → 0.6.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (58) hide show
  1. package/AGENTS.md +371 -0
  2. package/CLAUDE.md +371 -0
  3. package/README.md +215 -85
  4. package/changelog/0.1.x/0.1.21.md +23 -0
  5. package/changelog/0.1.x/0.1.22.md +14 -0
  6. package/changelog/0.1.x/0.1.23.md +18 -0
  7. package/changelog/0.2.x/0.2.0.md +24 -0
  8. package/changelog/0.2.x/0.2.1.md +14 -0
  9. package/changelog/0.2.x/0.2.2.md +17 -0
  10. package/changelog/0.2.x/0.2.3.md +27 -0
  11. package/changelog/0.2.x/0.2.4.md +27 -0
  12. package/changelog/0.3.x/0.3.0.md +31 -0
  13. package/changelog/0.3.x/0.3.1.md +19 -0
  14. package/changelog/0.4.x/0.4.0.md +15 -0
  15. package/changelog/0.4.x/0.4.1.md +12 -0
  16. package/changelog/0.4.x/0.4.2.md +41 -0
  17. package/changelog/0.4.x/0.4.3.md +18 -0
  18. package/changelog/0.5.x/0.5.0.md +24 -0
  19. package/changelog/0.5.x/0.5.1.md +24 -0
  20. package/changelog/0.5.x/0.5.2.md +21 -0
  21. package/changelog/0.6.x/0.6.0.md +15 -0
  22. package/changelog/0.6.x/0.6.1.md +40 -0
  23. package/changelog/0.6.x/0.6.2.md +29 -0
  24. package/changelog/0.6.x/0.6.3.md +40 -0
  25. package/changelog/template.md +151 -0
  26. package/dist/index.js +4 -0
  27. package/dist/index.js.map +1 -1
  28. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
  29. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +4 -0
  30. package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
  31. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +1 -0
  32. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts.map +1 -1
  33. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +3 -0
  34. package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -1
  35. package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts +1 -0
  36. package/dist/mcp-server/tools/definitions/get-compound-image.tool.d.ts.map +1 -1
  37. package/dist/mcp-server/tools/definitions/get-compound-image.tool.js +3 -0
  38. package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map +1 -1
  39. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +3 -0
  41. package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
  42. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
  43. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +4 -0
  44. package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
  45. package/dist/mcp-server/tools/definitions/index.d.ts +2 -0
  46. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  47. package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
  48. package/dist/mcp-server/tools/definitions/search-assays.tool.js +3 -0
  49. package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
  50. package/dist/mcp-server/tools/definitions/untrusted-text.d.ts.map +1 -1
  51. package/dist/mcp-server/tools/definitions/untrusted-text.js +8 -1
  52. package/dist/mcp-server/tools/definitions/untrusted-text.js.map +1 -1
  53. package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
  54. package/dist/services/pubchem/pubchem-client.js +21 -9
  55. package/dist/services/pubchem/pubchem-client.js.map +1 -1
  56. package/manifest.json +3 -2
  57. package/package.json +21 -10
  58. package/server.json +10 -3
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@cyanheads/pubchem-mcp-server",
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- "version": "0.6.1",
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+ "version": "0.6.3",
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  "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
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  "mcpName": "io.github.cyanheads/pubchem-mcp-server",
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  "type": "module",
@@ -9,12 +9,23 @@
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  "bin": {
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  "pubchem-mcp-server": "dist/index.js"
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  },
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- "files": ["dist/", "README.md", "LICENSE", "server.json", "manifest.json", "Dockerfile"],
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+ "files": [
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+ "changelog/",
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+ "dist/",
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+ "README.md",
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+ "LICENSE",
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+ "CLAUDE.md",
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+ "AGENTS.md",
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+ "Dockerfile",
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+ "server.json",
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+ "manifest.json"
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+ ],
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  "scripts": {
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  "build": "bun scripts/build.ts",
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  "rebuild": "bun scripts/clean.ts && bun scripts/build.ts",
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  "clean": "bun scripts/clean.ts",
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  "devcheck": "bun scripts/devcheck.ts",
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+ "audit:fix": "bun audit fix",
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  "audit:refresh": "rm -f bun.lock && bun install && bun audit",
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  "tree": "bun scripts/tree.ts",
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  "list-skills": "bun scripts/list-skills.ts",
@@ -66,25 +77,25 @@
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  ],
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  "engines": {
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  "node": ">=24.0.0",
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- "bun": ">=1.3.0"
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+ "bun": ">=1.4.0"
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  },
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  "packageManager": "bun@1.4.0",
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  "publishConfig": {
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  "access": "public"
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  },
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  "dependencies": {
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- "@cyanheads/mcp-ts-core": "^0.12.3",
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+ "@cyanheads/mcp-ts-core": "^0.13.6",
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  "pino-pretty": "^13.1.3",
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- "zod": "^4.4.3"
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+ "zod": "^4.6.5"
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  },
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  "devDependencies": {
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- "@biomejs/biome": "2.5.9",
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+ "@biomejs/biome": "2.5.14",
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  "@socketsecurity/bun-security-scanner": "^1.1.2",
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- "@types/node": "26.2.0",
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+ "@types/node": "26.6.1",
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  "depcheck": "^1.4.7",
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- "ignore": "^7.0.6",
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- "tsc-alias": "^1.9.2",
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+ "ignore": "^7.0.9",
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+ "tsc-alias": "^1.9.5",
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  "typescript": "^7.0.2",
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- "vitest": "^4.1.11"
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+ "vitest": "^5.0.1"
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  }
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  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
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  "url": "https://github.com/cyanheads/pubchem-mcp-server",
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  "source": "github"
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  },
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- "version": "0.6.1",
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+ "version": "0.6.3",
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  "remotes": [
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  {
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  "type": "streamable-http",
@@ -19,7 +19,7 @@
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubchem-mcp-server",
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  "runtimeHint": "bun",
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- "version": "0.6.1",
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+ "version": "0.6.3",
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  "packageArguments": [
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  { "type": "positional", "value": "run" },
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  { "type": "positional", "value": "start:stdio" }
@@ -42,12 +42,19 @@
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  "registryBaseUrl": "https://registry.npmjs.org",
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  "identifier": "@cyanheads/pubchem-mcp-server",
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  "runtimeHint": "bun",
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- "version": "0.6.1",
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+ "version": "0.6.3",
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  "packageArguments": [
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  { "type": "positional", "value": "run" },
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  { "type": "positional", "value": "start:http" }
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  ],
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  "environmentVariables": [
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+ {
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+ "name": "MCP_SESSION_MODE",
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+ "description": "HTTP session mode: stateless, stateful, or auto. Stateless is sufficient for PubChem; auto resolves to stateful.",
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+ "format": "string",
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+ "isRequired": false,
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+ "default": "stateless"
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+ },
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  {
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  "name": "MCP_HTTP_HOST",
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  "description": "The hostname for the HTTP server.",