XspecT 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

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Files changed (80) hide show
  1. xspect/classify.py +32 -0
  2. xspect/file_io.py +3 -9
  3. xspect/filter_sequences.py +56 -0
  4. xspect/main.py +52 -30
  5. xspect/mlst_feature/mlst_helper.py +102 -13
  6. xspect/mlst_feature/pub_mlst_handler.py +32 -6
  7. xspect/model_management.py +1 -15
  8. xspect/models/probabilistic_filter_mlst_model.py +160 -32
  9. xspect/models/probabilistic_filter_model.py +1 -0
  10. xspect/models/result.py +18 -6
  11. xspect/ncbi.py +8 -6
  12. xspect/train.py +13 -5
  13. xspect/web.py +173 -0
  14. xspect/xspect-web/.gitignore +24 -0
  15. xspect/xspect-web/README.md +54 -0
  16. xspect/xspect-web/components.json +21 -0
  17. xspect/xspect-web/dist/assets/index-CMG4V7fZ.js +290 -0
  18. xspect/xspect-web/dist/assets/index-jIKg1HIy.css +1 -0
  19. xspect/xspect-web/dist/index.html +14 -0
  20. xspect/xspect-web/dist/vite.svg +1 -0
  21. xspect/xspect-web/eslint.config.js +28 -0
  22. xspect/xspect-web/index.html +13 -0
  23. xspect/xspect-web/package-lock.json +6865 -0
  24. xspect/xspect-web/package.json +58 -0
  25. xspect/xspect-web/pnpm-lock.yaml +4317 -0
  26. xspect/xspect-web/public/vite.svg +1 -0
  27. xspect/xspect-web/src/App.tsx +29 -0
  28. xspect/xspect-web/src/api.tsx +62 -0
  29. xspect/xspect-web/src/assets/react.svg +1 -0
  30. xspect/xspect-web/src/components/classification-form.tsx +284 -0
  31. xspect/xspect-web/src/components/classify.tsx +18 -0
  32. xspect/xspect-web/src/components/data-table.tsx +78 -0
  33. xspect/xspect-web/src/components/dropdown-checkboxes.tsx +63 -0
  34. xspect/xspect-web/src/components/dropdown-slider.tsx +42 -0
  35. xspect/xspect-web/src/components/filter-form.tsx +423 -0
  36. xspect/xspect-web/src/components/filter.tsx +15 -0
  37. xspect/xspect-web/src/components/header.tsx +46 -0
  38. xspect/xspect-web/src/components/landing.tsx +7 -0
  39. xspect/xspect-web/src/components/models-details.tsx +138 -0
  40. xspect/xspect-web/src/components/models.tsx +53 -0
  41. xspect/xspect-web/src/components/result-chart.tsx +44 -0
  42. xspect/xspect-web/src/components/result.tsx +155 -0
  43. xspect/xspect-web/src/components/spinner.tsx +30 -0
  44. xspect/xspect-web/src/components/ui/accordion.tsx +64 -0
  45. xspect/xspect-web/src/components/ui/button.tsx +59 -0
  46. xspect/xspect-web/src/components/ui/card.tsx +92 -0
  47. xspect/xspect-web/src/components/ui/chart.tsx +351 -0
  48. xspect/xspect-web/src/components/ui/command.tsx +175 -0
  49. xspect/xspect-web/src/components/ui/dialog.tsx +135 -0
  50. xspect/xspect-web/src/components/ui/dropdown-menu.tsx +255 -0
  51. xspect/xspect-web/src/components/ui/file-upload.tsx +1459 -0
  52. xspect/xspect-web/src/components/ui/form.tsx +165 -0
  53. xspect/xspect-web/src/components/ui/input.tsx +21 -0
  54. xspect/xspect-web/src/components/ui/label.tsx +24 -0
  55. xspect/xspect-web/src/components/ui/navigation-menu.tsx +168 -0
  56. xspect/xspect-web/src/components/ui/popover.tsx +46 -0
  57. xspect/xspect-web/src/components/ui/select.tsx +183 -0
  58. xspect/xspect-web/src/components/ui/separator.tsx +26 -0
  59. xspect/xspect-web/src/components/ui/slider.tsx +61 -0
  60. xspect/xspect-web/src/components/ui/switch.tsx +29 -0
  61. xspect/xspect-web/src/components/ui/table.tsx +113 -0
  62. xspect/xspect-web/src/components/ui/tabs.tsx +64 -0
  63. xspect/xspect-web/src/index.css +120 -0
  64. xspect/xspect-web/src/lib/utils.ts +6 -0
  65. xspect/xspect-web/src/main.tsx +10 -0
  66. xspect/xspect-web/src/types.tsx +34 -0
  67. xspect/xspect-web/src/utils.tsx +6 -0
  68. xspect/xspect-web/src/vite-env.d.ts +1 -0
  69. xspect/xspect-web/tsconfig.app.json +32 -0
  70. xspect/xspect-web/tsconfig.json +13 -0
  71. xspect/xspect-web/tsconfig.node.json +24 -0
  72. xspect/xspect-web/vite.config.ts +24 -0
  73. {xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/METADATA +7 -8
  74. xspect-0.5.0.dist-info/RECORD +85 -0
  75. {xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/WHEEL +1 -1
  76. xspect/fastapi.py +0 -102
  77. xspect-0.4.0.dist-info/RECORD +0 -24
  78. {xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/entry_points.txt +0 -0
  79. {xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/licenses/LICENSE +0 -0
  80. {xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/top_level.txt +0 -0
xspect/xspect-web/package.json ADDED
@@ -0,0 +1,58 @@
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+ {
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+ "name": "xspect-web",
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+ "private": true,
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+ "version": "0.0.0",
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+ "type": "module",
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+ "scripts": {
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+ "dev": "vite",
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+ "build": "tsc -b && vite build",
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+ "lint": "eslint .",
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+ "preview": "vite preview"
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+ },
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+ "dependencies": {
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+ "@hookform/resolvers": "^5.0.1",
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+ "@radix-ui/react-accordion": "^1.2.10",
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+ "@radix-ui/react-dialog": "^1.1.13",
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+ "@radix-ui/react-dropdown-menu": "^2.1.14",
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+ "@radix-ui/react-label": "^2.1.4",
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+ "@radix-ui/react-navigation-menu": "^1.2.10",
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+ "@radix-ui/react-popover": "^1.1.13",
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+ "@radix-ui/react-select": "^2.2.4",
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+ "@radix-ui/react-separator": "^1.1.6",
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+ "@radix-ui/react-slider": "^1.3.4",
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+ "@radix-ui/react-slot": "^1.2.0",
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+ "@radix-ui/react-switch": "^1.2.4",
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+ "@radix-ui/react-tabs": "^1.1.11",
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+ "@tailwindcss/vite": "^4.1.4",
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+ "@tanstack/react-table": "^8.21.3",
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+ "axios": "^1.9.0",
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+ "class-variance-authority": "^0.7.1",
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+ "clsx": "^2.1.1",
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+ "cmdk": "^1.1.1",
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+ "lucide-react": "^0.503.0",
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+ "react": "^19.0.0",
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+ "react-dom": "^19.0.0",
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+ "react-hook-form": "^7.56.2",
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+ "react-router-dom": "^7.5.3",
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+ "recharts": "^2.15.3",
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+ "tailwind-merge": "^3.2.0",
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+ "tailwindcss": "^4.1.4",
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+ "zod": "^3.24.4"
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+ },
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+ "devDependencies": {
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+ "@eslint/js": "^9.22.0",
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+ "@types/node": "^22.15.18",
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+ "@types/react": "^19.0.10",
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+ "@types/react-dom": "^19.0.4",
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+ "@vitejs/plugin-react": "^4.3.4",
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+ "eslint": "^9.22.0",
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+ "eslint-plugin-react-hooks": "^5.2.0",
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+ "eslint-plugin-react-refresh": "^0.4.19",
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+ "globals": "^16.0.0",
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+ "ts-node": "^10.9.2",
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+ "tw-animate-css": "^1.2.8",
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+ "typescript": "~5.7.2",
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+ "typescript-eslint": "^8.26.1",
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+ "vite": "^6.3.1"
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+ }
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+ }