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

xspect/xspect-web/src/components/ui/switch.tsx

@@ -0,0 +1,29 @@
+import * as React from "react"
+import * as SwitchPrimitive from "@radix-ui/react-switch"
+
+import { cn } from "@/lib/utils"
+
+function Switch({
+  className,
+  ...props
+}: React.ComponentProps<typeof SwitchPrimitive.Root>) {
+  return (
+    <SwitchPrimitive.Root
+      data-slot="switch"
+      className={cn(
+        "peer data-[state=checked]:bg-primary data-[state=unchecked]:bg-input focus-visible:border-ring focus-visible:ring-ring/50 dark:data-[state=unchecked]:bg-input/80 inline-flex h-[1.15rem] w-8 shrink-0 items-center rounded-full border border-transparent shadow-xs transition-all outline-none focus-visible:ring-[3px] disabled:cursor-not-allowed disabled:opacity-50",
+        className
+      )}
+      {...props}
+    >
+      <SwitchPrimitive.Thumb
+        data-slot="switch-thumb"
+        className={cn(
+          "bg-background dark:data-[state=unchecked]:bg-foreground dark:data-[state=checked]:bg-primary-foreground pointer-events-none block size-4 rounded-full ring-0 transition-transform data-[state=checked]:translate-x-[calc(100%-2px)] data-[state=unchecked]:translate-x-0"
+        )}
+      />
+    </SwitchPrimitive.Root>
+  )
+}
+
+export { Switch }

xspect/xspect-web/src/components/ui/table.tsx

@@ -0,0 +1,113 @@
+import * as React from "react"
+import { cn } from "@/lib/utils"
+
+function Table({ className, ...props }: React.ComponentProps<"table">) {
+  return (
+    <div
+      data-slot="table-container"
+      className="relative w-full overflow-x-auto"
+    >
+      <table
+        data-slot="table"
+        className={cn("w-full caption-bottom text-sm rounded-md border", className)}
+        {...props}
+      />
+    </div>
+  )
+}
+
+function TableHeader({ className, ...props }: React.ComponentProps<"thead">) {
+  return (
+    <thead
+      data-slot="table-header"
+      className={cn("[&_tr]:border-b", className)}
+      {...props}
+    />
+  )
+}
+
+function TableBody({ className, ...props }: React.ComponentProps<"tbody">) {
+  return (
+    <tbody
+      data-slot="table-body"
+      className={cn("[&_tr:last-child]:border-0", className)}
+      {...props}
+    />
+  )
+}
+
+function TableFooter({ className, ...props }: React.ComponentProps<"tfoot">) {
+  return (
+    <tfoot
+      data-slot="table-footer"
+      className={cn(
+        "bg-muted/50 border-t font-medium [&>tr]:last:border-b-0",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TableRow({ className, ...props }: React.ComponentProps<"tr">) {
+  return (
+    <tr
+      data-slot="table-row"
+      className={cn(
+        "hover:bg-muted/50 data-[state=selected]:bg-muted border-b transition-colors",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TableHead({ className, ...props }: React.ComponentProps<"th">) {
+  return (
+    <th
+      data-slot="table-head"
+      className={cn(
+        "bg-gray-100 text-foreground h-10 px-2 text-left align-middle font-medium whitespace-nowrap [&:has([role=checkbox])]:pr-0 [&>[role=checkbox]]:translate-y-[2px]",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TableCell({ className, ...props }: React.ComponentProps<"td">) {
+  return (
+    <td
+      data-slot="table-cell"
+      className={cn(
+        "p-2 align-middle whitespace-nowrap [&:has([role=checkbox])]:pr-0 [&>[role=checkbox]]:translate-y-[2px]",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TableCaption({
+  className,
+  ...props
+}: React.ComponentProps<"caption">) {
+  return (
+    <caption
+      data-slot="table-caption"
+      className={cn("text-muted-foreground mt-4 text-sm", className)}
+      {...props}
+    />
+  )
+}
+
+export {
+  Table,
+  TableHeader,
+  TableBody,
+  TableFooter,
+  TableHead,
+  TableRow,
+  TableCell,
+  TableCaption,
+}

xspect/xspect-web/src/components/ui/tabs.tsx

@@ -0,0 +1,64 @@
+import * as React from "react"
+import * as TabsPrimitive from "@radix-ui/react-tabs"
+
+import { cn } from "@/lib/utils"
+
+function Tabs({
+  className,
+  ...props
+}: React.ComponentProps<typeof TabsPrimitive.Root>) {
+  return (
+    <TabsPrimitive.Root
+      data-slot="tabs"
+      className={cn("flex flex-col gap-2", className)}
+      {...props}
+    />
+  )
+}
+
+function TabsList({
+  className,
+  ...props
+}: React.ComponentProps<typeof TabsPrimitive.List>) {
+  return (
+    <TabsPrimitive.List
+      data-slot="tabs-list"
+      className={cn(
+        "bg-muted text-muted-foreground inline-flex h-9 w-fit items-center justify-center rounded-lg p-[3px]",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TabsTrigger({
+  className,
+  ...props
+}: React.ComponentProps<typeof TabsPrimitive.Trigger>) {
+  return (
+    <TabsPrimitive.Trigger
+      data-slot="tabs-trigger"
+      className={cn(
+        "data-[state=active]:bg-background dark:data-[state=active]:text-foreground focus-visible:border-ring focus-visible:ring-ring/50 focus-visible:outline-ring dark:data-[state=active]:border-input dark:data-[state=active]:bg-input/30 text-foreground dark:text-muted-foreground inline-flex h-[calc(100%-1px)] flex-1 items-center justify-center gap-1.5 rounded-md border border-transparent px-2 py-1 text-sm font-medium whitespace-nowrap transition-[color,box-shadow] focus-visible:ring-[3px] focus-visible:outline-1 disabled:pointer-events-none disabled:opacity-50 data-[state=active]:shadow-sm [&_svg]:pointer-events-none [&_svg]:shrink-0 [&_svg:not([class*='size-'])]:size-4",
+        className
+      )}
+      {...props}
+    />
+  )
+}
+
+function TabsContent({
+  className,
+  ...props
+}: React.ComponentProps<typeof TabsPrimitive.Content>) {
+  return (
+    <TabsPrimitive.Content
+      data-slot="tabs-content"
+      className={cn("flex-1 outline-none", className)}
+      {...props}
+    />
+  )
+}
+
+export { Tabs, TabsList, TabsTrigger, TabsContent }

xspect/xspect-web/src/index.css

@@ -0,0 +1,120 @@
+@import "tailwindcss";
+@import "tw-animate-css";
+
+@custom-variant dark (&:is(.dark *));
+
+@theme inline {
+  --radius-sm: calc(var(--radius) - 4px);
+  --radius-md: calc(var(--radius) - 2px);
+  --radius-lg: var(--radius);
+  --radius-xl: calc(var(--radius) + 4px);
+  --color-background: var(--background);
+  --color-foreground: var(--foreground);
+  --color-card: var(--card);
+  --color-card-foreground: var(--card-foreground);
+  --color-popover: var(--popover);
+  --color-popover-foreground: var(--popover-foreground);
+  --color-primary: var(--primary);
+  --color-primary-foreground: var(--primary-foreground);
+  --color-secondary: var(--secondary);
+  --color-secondary-foreground: var(--secondary-foreground);
+  --color-muted: var(--muted);
+  --color-muted-foreground: var(--muted-foreground);
+  --color-accent: var(--accent);
+  --color-accent-foreground: var(--accent-foreground);
+  --color-destructive: var(--destructive);
+  --color-border: var(--border);
+  --color-input: var(--input);
+  --color-ring: var(--ring);
+  --color-chart-1: var(--chart-1);
+  --color-chart-2: var(--chart-2);
+  --color-chart-3: var(--chart-3);
+  --color-chart-4: var(--chart-4);
+  --color-chart-5: var(--chart-5);
+  --color-sidebar: var(--sidebar);
+  --color-sidebar-foreground: var(--sidebar-foreground);
+  --color-sidebar-primary: var(--sidebar-primary);
+  --color-sidebar-primary-foreground: var(--sidebar-primary-foreground);
+  --color-sidebar-accent: var(--sidebar-accent);
+  --color-sidebar-accent-foreground: var(--sidebar-accent-foreground);
+  --color-sidebar-border: var(--sidebar-border);
+  --color-sidebar-ring: var(--sidebar-ring);
+}
+
+:root {
+  --radius: 0.3rem;
+  --background: oklch(1 0 0);
+  --foreground: oklch(0.141 0.005 285.823);
+  --card: oklch(1 0 0);
+  --card-foreground: oklch(0.141 0.005 285.823);
+  --popover: oklch(1 0 0);
+  --popover-foreground: oklch(0.141 0.005 285.823);
+  --primary: oklch(0.623 0.214 259.815);
+  --primary-foreground: oklch(0.97 0.014 254.604);
+  --secondary: oklch(0.967 0.001 286.375);
+  --secondary-foreground: oklch(0.21 0.006 285.885);
+  --muted: oklch(0.967 0.001 286.375);
+  --muted-foreground: oklch(0.552 0.016 285.938);
+  --accent: oklch(0.967 0.001 286.375);
+  --accent-foreground: oklch(0.21 0.006 285.885);
+  --destructive: oklch(0.577 0.245 27.325);
+  --border: oklch(0.92 0.004 286.32);
+  --input: oklch(0.92 0.004 286.32);
+  --ring: oklch(0.623 0.214 259.815);
+  --chart-1: oklch(0.646 0.222 41.116);
+  --chart-2: oklch(0.6 0.118 184.704);
+  --chart-3: oklch(0.398 0.07 227.392);
+  --chart-4: oklch(0.828 0.189 84.429);
+  --chart-5: oklch(0.769 0.188 70.08);
+  --sidebar: oklch(0.985 0 0);
+  --sidebar-foreground: oklch(0.141 0.005 285.823);
+  --sidebar-primary: oklch(0.623 0.214 259.815);
+  --sidebar-primary-foreground: oklch(0.97 0.014 254.604);
+  --sidebar-accent: oklch(0.967 0.001 286.375);
+  --sidebar-accent-foreground: oklch(0.21 0.006 285.885);
+  --sidebar-border: oklch(0.92 0.004 286.32);
+  --sidebar-ring: oklch(0.623 0.214 259.815);
+}
+
+.dark {
+  --background: oklch(0.141 0.005 285.823);
+  --foreground: oklch(0.985 0 0);
+  --card: oklch(0.21 0.006 285.885);
+  --card-foreground: oklch(0.985 0 0);
+  --popover: oklch(0.21 0.006 285.885);
+  --popover-foreground: oklch(0.985 0 0);
+  --primary: oklch(0.546 0.245 262.881);
+  --primary-foreground: oklch(0.379 0.146 265.522);
+  --secondary: oklch(0.274 0.006 286.033);
+  --secondary-foreground: oklch(0.985 0 0);
+  --muted: oklch(0.274 0.006 286.033);
+  --muted-foreground: oklch(0.705 0.015 286.067);
+  --accent: oklch(0.274 0.006 286.033);
+  --accent-foreground: oklch(0.985 0 0);
+  --destructive: oklch(0.704 0.191 22.216);
+  --border: oklch(1 0 0 / 10%);
+  --input: oklch(1 0 0 / 15%);
+  --ring: oklch(0.488 0.243 264.376);
+  --chart-1: oklch(0.488 0.243 264.376);
+  --chart-2: oklch(0.696 0.17 162.48);
+  --chart-3: oklch(0.769 0.188 70.08);
+  --chart-4: oklch(0.627 0.265 303.9);
+  --chart-5: oklch(0.645 0.246 16.439);
+  --sidebar: oklch(0.21 0.006 285.885);
+  --sidebar-foreground: oklch(0.985 0 0);
+  --sidebar-primary: oklch(0.546 0.245 262.881);
+  --sidebar-primary-foreground: oklch(0.379 0.146 265.522);
+  --sidebar-accent: oklch(0.274 0.006 286.033);
+  --sidebar-accent-foreground: oklch(0.985 0 0);
+  --sidebar-border: oklch(1 0 0 / 10%);
+  --sidebar-ring: oklch(0.488 0.243 264.376);
+}
+
+@layer base {
+  * {
+    @apply border-border outline-ring/50;
+  }
+  body {
+    @apply bg-background text-foreground;
+  }
+}

xspect/xspect-web/src/lib/utils.ts

@@ -0,0 +1,6 @@
+import { clsx, type ClassValue } from "clsx"
+import { twMerge } from "tailwind-merge"
+
+export function cn(...inputs: ClassValue[]) {
+  return twMerge(clsx(inputs))
+}

xspect/xspect-web/src/main.tsx

@@ -0,0 +1,10 @@
+import { StrictMode } from 'react'
+import { createRoot } from 'react-dom/client'
+import './index.css'
+import App from './App.tsx'
+
+createRoot(document.getElementById('root')!).render(
+  <StrictMode>
+    <App />
+  </StrictMode>,
+)

xspect/xspect-web/src/types.tsx

@@ -0,0 +1,34 @@
+export interface Models {
+  [key: string]: string[];
+}
+
+export interface ModelTableEntry {
+  "model_type": "Species" | "Genus" | "Family" | "Order" | "Class" | "Phylum" | "Kingdom";
+  "name": string;
+}
+
+export interface ModelMetadata {
+  model_slug: string;
+  model_display_name: string;
+  model_type: string;
+  author: string;
+  author_email: string;
+  k: number;
+  display_names: { [key: string]: string };
+  fpr: number;
+  num_hashes?: number;
+  kernel?: Partial<string>;
+  C?: Partial<number>;
+  training_accessions: { [key: string]: string[] } | string[];
+  svm_accessions: { [key: string]: string[] };
+}
+
+export interface ClassificationResult {
+  input_source: string;
+  model_slug: string;
+  sparse_sampling_step: number;
+  hits: { [subsequence: string]: { [label: string]: number } };
+  scores: { [subsequence: string]: { [label: string]: number } };
+  num_kmers: { [subsequence: string]: number };
+  prediction: string;
+}

xspect/xspect-web/src/utils.tsx

@@ -0,0 +1,6 @@
+import { ClassValue, clsx } from 'clsx'
+import { twMerge } from 'tailwind-merge'
+
+export const cn = (...inputs: ClassValue[]) => {
+  return twMerge(clsx(inputs))
+}

xspect/xspect-web/src/vite-env.d.ts

@@ -0,0 +1 @@
+/// <reference types="vite/client" />

xspect/xspect-web/tsconfig.app.json

@@ -0,0 +1,32 @@
+{
+  "compilerOptions": {
+    "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.app.tsbuildinfo",
+    "target": "ES2020",
+    "useDefineForClassFields": true,
+    "lib": ["ES2020", "DOM", "DOM.Iterable"],
+    "module": "ESNext",
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "isolatedModules": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+    "jsx": "react-jsx",
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noFallthroughCasesInSwitch": true,
+    "noUncheckedSideEffectImports": true
+  },
+  "include": ["src"],
+  "baseUrl": ".",
+    "paths": {
+      "@/*": [
+        "./src/*"
+      ]
+    }
+}

xspect/xspect-web/tsconfig.json

@@ -0,0 +1,13 @@
+{
+  "files": [],
+  "references": [
+    { "path": "./tsconfig.app.json" },
+    { "path": "./tsconfig.node.json" }
+  ],
+  "compilerOptions": {
+    "baseUrl": ".",
+    "paths": {
+      "@/*": ["./src/*"]
+    }
+  }
+}

xspect/xspect-web/tsconfig.node.json

@@ -0,0 +1,24 @@
+{
+  "compilerOptions": {
+    "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo",
+    "target": "ES2022",
+    "lib": ["ES2023"],
+    "module": "ESNext",
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "isolatedModules": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noFallthroughCasesInSwitch": true,
+    "noUncheckedSideEffectImports": true
+  },
+  "include": ["vite.config.ts"]
+}

xspect/xspect-web/vite.config.ts

@@ -0,0 +1,24 @@
+import { defineConfig } from 'vite'
+import path from "path"
+import tailwindcss from "@tailwindcss/vite"
+import react from '@vitejs/plugin-react'
+
+// https://vite.dev/config/
+export default defineConfig({
+  plugins: [react(), tailwindcss()],
+  resolve: {
+    alias: {
+      "@": path.resolve(__dirname, "./src"),
+    },
+  },
+  base: "/xspect-web",
+  server: {
+    proxy: {
+      '/api': {
+        target: 'http://localhost:8000/api',
+        changeOrigin: true,
+        rewrite: (path) => path.replace(/^\/api/, ''),
+      },
+    },
+  },
+})

{xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: XspecT
-Version: 0.4.0
+Version: 0.5.0
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         
@@ -46,14 +46,13 @@ Requires-Dist: fastapi
 Requires-Dist: uvicorn
 Requires-Dist: python-multipart
 Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: furo; extra == "docs"
-Requires-Dist: myst-parser; extra == "docs"
-Requires-Dist: sphinx-copybutton; extra == "docs"
-Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+Requires-Dist: mkdocs-include-markdown-plugin; extra == "docs"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-retry; extra == "test"
+Requires-Dist: httpx; extra == "test"
 Dynamic: license-file
 
 # XspecT - Acinetobacter Species Assignment Tool
@@ -78,7 +77,7 @@ To install XspecT, please download the lastest 64 bit Python version and install
 ```
 pip install xspect
 ```
-Please note that Windows and Alpine Linux is currently not supported.
+Please note that Windows and Alpine Linux are currently not supported.
 
 ## Usage
 ### Get the models
@@ -106,5 +105,5 @@ For further instructions on how to use the command line interface, please refer
 ```
 xspect --help
 ```
-[documentation]: https://bionf.github.io/XspecT2/cli.html
+[documentation]: https://bionf.github.io/XspecT2/cli/index.html
 <!-- end quickstart -->

xspect-0.5.0.dist-info/RECORD

@@ -0,0 +1,85 @@
+xspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xspect/classify.py,sha256=e0soOihf9KuVFuZ7VXs0EZKYzOFsM4-4IpOsYJtOORg,1148
+xspect/definitions.py,sha256=fVn_li_s2hriOSGJ69o_H8H-vkw1znvkryhBj7WMnF4,1219
+xspect/download_models.py,sha256=y1wFJZa1xOJfvUP78zKkRs46O-WqKBL90vmo5AYUio0,853
+xspect/file_io.py,sha256=-3xm7IfOlmWJHxfrKPX5Qqit10zqsBUVt5Z7z1No2AI,5669
+xspect/filter_sequences.py,sha256=UeIPmn5MquT-vVGFYna-IZRmDzaStI-d2wExYA7M7u0,1839
+xspect/main.py,sha256=_-H6xFB3Z_rATblunTF1YhjxP6V_k8nPrnLcwAR3dcw,11913
+xspect/model_management.py,sha256=UbmAr3YOZ4oy_9iVvApCLstYHGkcmneHEC_yftRIqCI,3010
+xspect/ncbi.py,sha256=PDoVraZ8ntZIqBESLS27ZcxzgW5nqFc8ipvrHpIKb38,10100
+xspect/train.py,sha256=dnmLIhDrHTKbXzLjcF1VZAdsDDmnpv_6qqk-st4E9V8,11053
+xspect/web.py,sha256=M4fQUbmCnkpmdJeL-j-FD8r115EctWtWQZttuZWEsL8,5115
+xspect/mlst_feature/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xspect/mlst_feature/mlst_helper.py,sha256=Ff0kUdu-80969ZyYL6qUJNwEqf9eq72CC8zUyuoDElk,8114
+xspect/mlst_feature/pub_mlst_handler.py,sha256=Ez5YHKfhsLsKdHf1aNMfz7JJVVV_DpA27mah9fgNeJc,5919
+xspect/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+xspect/models/probabilistic_filter_mlst_model.py,sha256=v9yriJX_i8-SRzU8W8RvDPrBvlR_ONSMVypZWGAJpv8,16164
+xspect/models/probabilistic_filter_model.py,sha256=K2gWpte2BCb03msgY-x18NVRMv1xHpDVWQWhbf4vWU4,10068
+xspect/models/probabilistic_filter_svm_model.py,sha256=xXimcv3iWnG1JiFyrk6UqkP9hFIxWGDdb__fRdQYwro,6245
+xspect/models/probabilistic_single_filter_model.py,sha256=yxWnCt4IP-3ZRLP4pRA3f2VTHc0_4g17PDCyOFayDDg,4090
+xspect/models/result.py,sha256=ELWiDlQPlxNG7ceLpth60Z_Hb1ZdopDJ3vgHBPgSRm8,3989
+xspect/xspect-web/.gitignore,sha256=_nGOe6uxTzy60tl_CIibnOUhXtP-DkOyuM-_s7m4ROg,253
+xspect/xspect-web/README.md,sha256=Fa5cCk66ohbqD_AAVgnXUZLhuzshnLxhlUFhxyscScc,1942
+xspect/xspect-web/components.json,sha256=5emhfq5JRW9J8Zga-1N5jAcj4B-r8VREXnH7Z6tZGNk,425
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{xspect-0.4.0.dist-info → xspect-0.5.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.0.0)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any