From c25b5fe6a38034d44d131d77e9329d3dd965698a Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 25 Jun 2025 21:08:57 -0700 Subject: [PATCH 01/15] wip web interface --- .gitignore | 5 +- web/.npmrc | 1 + web/.prettierignore | 4 + web/.prettierrc | 15 + web/Dockerfile | 18 + web/README.md | 38 + web/eslint.config.js | 33 + web/package-lock.json | 4362 ++++++++++++++++++++++++++++++++++ web/package.json | 38 + web/src/app.d.ts | 13 + web/src/app.html | 12 + web/src/lib/Logo.svelte | 111 + web/src/lib/Mutations.svelte | 82 + web/src/lib/Sequence.svelte | 84 + web/src/lib/argsort.js | 7 + web/src/lib/flower.json | 51 + web/src/lib/index.ts | 1 + web/src/lib/normalize.ts | 6 + web/src/lib/tokenize.ts | 35 + web/src/lib/vocab.json | 35 + web/src/routes/+page.js | 18 + web/src/routes/+page.svelte | 281 +++ web/static/favicon.png | Bin 0 -> 1571 bytes web/svelte.config.js | 13 + web/tsconfig.json | 19 + web/vite.config.ts | 6 + 26 files changed, 5287 insertions(+), 1 deletion(-) create mode 100644 web/.npmrc create mode 100644 web/.prettierignore create mode 100644 web/.prettierrc create mode 100644 web/Dockerfile create mode 100644 web/README.md create mode 100644 web/eslint.config.js create mode 100644 web/package-lock.json create mode 100644 web/package.json create mode 100644 web/src/app.d.ts create mode 100644 web/src/app.html create mode 100644 web/src/lib/Logo.svelte create mode 100644 web/src/lib/Mutations.svelte create mode 100644 web/src/lib/Sequence.svelte create mode 100644 web/src/lib/argsort.js create mode 100644 web/src/lib/flower.json create mode 100644 web/src/lib/index.ts create mode 100644 web/src/lib/normalize.ts create mode 100644 web/src/lib/tokenize.ts create mode 100644 web/src/lib/vocab.json create mode 100644 web/src/routes/+page.js create mode 100644 web/src/routes/+page.svelte create mode 100644 web/static/favicon.png create mode 100644 web/svelte.config.js create mode 100644 web/tsconfig.json create mode 100644 web/vite.config.ts diff --git a/.gitignore b/.gitignore index 95a61586..18794762 100644 --- a/.gitignore +++ b/.gitignore @@ -43,4 +43,7 @@ lightning_logs .env dev -*.ckpt \ No newline at end of file +*.ckpt +web/build +web/node_modules +web/.svelte-kit diff --git a/web/.npmrc b/web/.npmrc new file mode 100644 index 00000000..b6f27f13 --- /dev/null +++ b/web/.npmrc @@ -0,0 +1 @@ +engine-strict=true diff --git a/web/.prettierignore b/web/.prettierignore new file mode 100644 index 00000000..ab78a95d --- /dev/null +++ b/web/.prettierignore @@ -0,0 +1,4 @@ +# Package Managers +package-lock.json +pnpm-lock.yaml +yarn.lock diff --git a/web/.prettierrc b/web/.prettierrc new file mode 100644 index 00000000..c84b786f --- /dev/null +++ b/web/.prettierrc @@ -0,0 +1,15 @@ +{ + "useTabs": false, + "singleQuote": true, + "trailingComma": "none", + "printWidth": 100, + "plugins": ["prettier-plugin-svelte"], + "overrides": [ + { + "files": "*.svelte", + "options": { + "parser": "svelte" + } + } + ] +} diff --git a/web/Dockerfile b/web/Dockerfile new file mode 100644 index 00000000..bed6e126 --- /dev/null +++ b/web/Dockerfile @@ -0,0 +1,18 @@ +FROM node:18-alpine AS builder +WORKDIR /app +COPY package*.json . +RUN npm ci +COPY . . +RUN npm run build +RUN npm prune --production + +FROM node:18-alpine +WORKDIR /app +COPY --from=builder /app/build build +COPY --from=builder /app/node_modules node_modules/ +COPY package.json . +EXPOSE 80 +ENV NODE_ENV=proudction \ + PORT=80 + +CMD ["node", "/app/build/index.js"] diff --git a/web/README.md b/web/README.md new file mode 100644 index 00000000..abd6f219 --- /dev/null +++ b/web/README.md @@ -0,0 +1,38 @@ +# create-svelte + +Everything you need to build a Svelte project, powered by [`create-svelte`](https://github.com/sveltejs/kit/tree/main/packages/create-svelte). + +## Creating a project + +If you're seeing this, you've probably already done this step. Congrats! + +```bash +# create a new project in the current directory +npx sv create + +# create a new project in my-app +npx sv create my-app +``` + +## Developing + +Once you've created a project and installed dependencies with `npm install` (or `pnpm install` or `yarn`), start a development server: + +```bash +npm run dev + +# or start the server and open the app in a new browser tab +npm run dev -- --open +``` + +## Building + +To create a production version of your app: + +```bash +npm run build +``` + +You can preview the production build with `npm run preview`. + +> To deploy your app, you may need to install an [adapter](https://svelte.dev/docs/kit/adapters) for your target environment. diff --git a/web/eslint.config.js b/web/eslint.config.js new file mode 100644 index 00000000..841d4763 --- /dev/null +++ b/web/eslint.config.js @@ -0,0 +1,33 @@ +import prettier from 'eslint-config-prettier'; +import js from '@eslint/js'; +import svelte from 'eslint-plugin-svelte'; +import globals from 'globals'; +import ts from 'typescript-eslint'; + +export default ts.config( + js.configs.recommended, + ...ts.configs.recommended, + ...svelte.configs['flat/recommended'], + prettier, + ...svelte.configs['flat/prettier'], + { + languageOptions: { + globals: { + ...globals.browser, + ...globals.node + } + } + }, + { + files: ['**/*.svelte'], + + languageOptions: { + parserOptions: { + parser: ts.parser + } + } + }, + { + ignores: ['build/', '.svelte-kit/', 'dist/'] + } +); diff --git a/web/package-lock.json b/web/package-lock.json new file mode 100644 index 00000000..1b60d504 --- /dev/null +++ b/web/package-lock.json @@ -0,0 +1,4362 @@ +{ + "name": "svelte5", + "version": "0.0.1", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "svelte5", + "version": "0.0.1", + "dependencies": { + "@types/d3": "^7.4.3", + "@types/opentype.js": "^1.3.8", + "d3": "^7.9.0", + "opentype.js": "^1.3.4" + }, + "devDependencies": { + "@sveltejs/adapter-auto": 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build", + "preview": "vite preview", + "check": "svelte-kit sync && svelte-check --tsconfig ./tsconfig.json", + "check:watch": "svelte-kit sync && svelte-check --tsconfig ./tsconfig.json --watch", + "format": "prettier --write .", + "lint": "prettier --check . && eslint ." + }, + "devDependencies": { + "@sveltejs/adapter-auto": "^3.0.0", + "@sveltejs/adapter-node": "^5.2.9", + "@sveltejs/kit": "^2.0.0", + "@sveltejs/vite-plugin-svelte": "^4.0.0", + "@types/eslint": "^9.6.0", + "eslint": "^9.7.0", + "eslint-config-prettier": "^9.1.0", + "eslint-plugin-svelte": "^2.36.0", + "globals": "^15.0.0", + "prettier": "^3.3.2", + "prettier-plugin-svelte": "^3.2.6", + "svelte": "^5.0.0", + "svelte-check": "^4.0.0", + "typescript": "^5.0.0", + "typescript-eslint": "^8.0.0", + "vite": "^5.0.3" + }, + "dependencies": { + "@types/d3": "^7.4.3", + "@types/opentype.js": "^1.3.8", + "d3": "^7.9.0", + "opentype.js": "^1.3.4" + } +} diff --git a/web/src/app.d.ts b/web/src/app.d.ts new file mode 100644 index 00000000..520c4217 --- /dev/null +++ b/web/src/app.d.ts @@ -0,0 +1,13 @@ +// See https://svelte.dev/docs/kit/types#app.d.ts +// for information about these interfaces +declare global { + namespace App { + // interface Error {} + // interface Locals {} + // interface PageData {} + // interface PageState {} + // interface Platform {} + } +} + +export {}; diff --git a/web/src/app.html b/web/src/app.html new file mode 100644 index 00000000..84ffad16 --- /dev/null +++ b/web/src/app.html @@ -0,0 +1,12 @@ + + + + + + + %sveltekit.head% + + +
%sveltekit.body%
+ + diff --git a/web/src/lib/Logo.svelte b/web/src/lib/Logo.svelte new file mode 100644 index 00000000..cb9b1de9 --- /dev/null +++ b/web/src/lib/Logo.svelte @@ -0,0 +1,111 @@ + + + + + + + bits + + {#each probs.keys() as i} + + {#each alphabet as c, j} + + + + + + + {/each} + + {/each} + + + diff --git a/web/src/lib/Mutations.svelte b/web/src/lib/Mutations.svelte new file mode 100644 index 00000000..c971dfe1 --- /dev/null +++ b/web/src/lib/Mutations.svelte @@ -0,0 +1,82 @@ + + + + + + {#each mutated_sequence as c, i} + + + + + + {/each} + + + diff --git a/web/src/lib/Sequence.svelte b/web/src/lib/Sequence.svelte new file mode 100644 index 00000000..6e59f925 --- /dev/null +++ b/web/src/lib/Sequence.svelte @@ -0,0 +1,84 @@ + + + + + + + {#each Array.from({ length: 101 }) as _, i} + + {/each} + + + + prob + + + + + + + {#each sequence as c, i} + + + + + + {/each} + + + diff --git a/web/src/lib/argsort.js b/web/src/lib/argsort.js new file mode 100644 index 00000000..e3d58f30 --- /dev/null +++ b/web/src/lib/argsort.js @@ -0,0 +1,7 @@ +function argsort(x, compareFn = (a, b) => a - b) { + return Array.from(x.entries()) + .sort(([, a], [, b]) => compareFn(a, b)) + .map(([i]) => i); +} + +export default argsort; diff --git a/web/src/lib/flower.json b/web/src/lib/flower.json new file mode 100644 index 00000000..23789594 --- /dev/null +++ b/web/src/lib/flower.json @@ -0,0 +1,51 @@ +{ + "name": "flower", + "alphabet": [ + "A", + "C", + "D", + "E", + "F", + "G", + "H", + "I", + "K", + "L", + "M", + "N", + "P", + "Q", + "R", + "S", + "T", + "V", + "W", + "Y", + "B", + "Z", + "X", + "*" + ], + "colors": { + "A": "#b18a51", + "C": "#ff5701", + "D": "#01a578", + "E": "#2da0a1", + "F": "#fa559d", + "G": "#b1c23c", + "H": "#0194f9", + "I": "#f27663", + "K": "#7fc3d7", + "L": "#df6e75", + "M": "#fe9daf", + "N": "#0bcec6", + "P": "#4fa32a", + "Q": "#7295ae", + "R": "#83bff1", + "S": "#b4bd9b", + "T": "#d2b576", + "V": "#fd997b", + "W": "#ff2ded", + "Y": "#c96ecf" + } +} diff --git a/web/src/lib/index.ts b/web/src/lib/index.ts new file mode 100644 index 00000000..856f2b6c --- /dev/null +++ b/web/src/lib/index.ts @@ -0,0 +1 @@ +// place files you want to import through the `$lib` alias in this folder. diff --git a/web/src/lib/normalize.ts b/web/src/lib/normalize.ts new file mode 100644 index 00000000..2dbf1165 --- /dev/null +++ b/web/src/lib/normalize.ts @@ -0,0 +1,6 @@ +function normalize(v: number[]) { + let norm = v.reduce((a, b) => a + b, 0); + return v.map((a) => a / norm); +} + +export default normalize; diff --git a/web/src/lib/tokenize.ts b/web/src/lib/tokenize.ts new file mode 100644 index 00000000..76884175 --- /dev/null +++ b/web/src/lib/tokenize.ts @@ -0,0 +1,35 @@ +import defaultVocabData from '$lib/vocab.json'; + +const defaultVocab: Map = new Map(Object.entries(defaultVocabData)); + +function tokenize(input: string, vocab: Map = defaultVocab) { + const tokens = []; + let i = 0; + + // Sort vocab keys by length in descending order once, outside the loop + const sortedKeys = Array.from(vocab.keys()).sort((a, b) => b.length - a.length); + + while (i < input.length) { + let matched = false; + + // Iterate over the sorted vocab keys + for (const key of sortedKeys) { + if (input.startsWith(key, i)) { + tokens.push(vocab.get(key)); + i += key.length; + matched = true; + break; + } + } + + // If no match is found, use + if (!matched) { + tokens.push(vocab.get('')); + i++; + } + } + + return tokens; +} + +export default tokenize; diff --git a/web/src/lib/vocab.json b/web/src/lib/vocab.json new file mode 100644 index 00000000..d807f5be --- /dev/null +++ b/web/src/lib/vocab.json @@ -0,0 +1,35 @@ +{ + "": 0, + "": 1, + "": 2, + "": 3, + "L": 4, + "A": 5, + "G": 6, + "V": 7, + "S": 8, + "E": 9, + "R": 10, + "T": 11, + "I": 12, + "D": 13, + "P": 14, + "K": 15, + "Q": 16, + "N": 17, + "F": 18, + "Y": 19, + "M": 20, + "H": 21, + "W": 22, + "C": 23, + "X": 24, + "B": 25, + "U": 26, + "Z": 27, + "O": 28, + ".": 29, + "-": 30, + "": 31, + "": 32 +} diff --git a/web/src/routes/+page.js b/web/src/routes/+page.js new file mode 100644 index 00000000..a995cffa --- /dev/null +++ b/web/src/routes/+page.js @@ -0,0 +1,18 @@ +/** @type {import('./$types').PageLoad} */ +import opentype from 'opentype.js'; + +// curl -L 'https://fonts.googleapis.com/css?family=Roboto%20Mono:400' +async function load_font(fetch) { + // const url = 'https://fonts.gstatic.com/s/roboto/v32/KFOmCnqEu92Fr1Mu4mxP.ttf'; // roboto 400 + // const url = 'https://fonts.gstatic.com/s/robotomono/v23/L0xuDF4xlVMF-BfR8bXMIhJHg45mwgGEFl0_3vq_ROW9.ttf'; // roboto mono 400 + const url = 'https://fonts.gstatic.com/s/spacemono/v13/i7dPIFZifjKcF5UAWdDRYEF8QA.ttf'; // space mono 400 + const response = await fetch(url); + const buffer = await response.arrayBuffer(); + const font = opentype.parse(buffer); + return font; +} + +export async function load({ fetch }) { + const font = await load_font(fetch); + return { font }; +} diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte new file mode 100644 index 00000000..0b8428b7 --- /dev/null +++ b/web/src/routes/+page.svelte @@ -0,0 +1,281 @@ + + +
+
+

Lobster Live

+
+ +
+
+
+ + +
+ +
+ + +
+ + {#await inference_result then { naturalness }} +
+
Naturalness
+
{naturalness.toFixed(2)}
+
+ {/await} +
+
+
+ +
+ {'0123456789'.repeat(sequence.length / 10 + 1).slice(0, sequence.length)} +
+ {#await inference_result then { probs, wt_probs }} + + + + {/await} +
+
+
+
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"accelerate", ] +web = [ + "fastapi>=0.115.14", + "uvicorn>=0.34.3", +] [tool.setuptools.packages.find] where = ["src"] diff --git a/uv.lock b/uv.lock index bcde49f3..c05a7d82 100644 --- a/uv.lock +++ b/uv.lock @@ -702,6 +702,20 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/7b/8f/c4d9bafc34ad7ad5d8dc16dd1347ee0e507a52c3adb6bfa8887e1c6a26ba/executing-2.2.0-py2.py3-none-any.whl", hash = "sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa", size = 26702, upload-time = "2025-01-22T15:41:25.929Z" }, ] +[[package]] +name = "fastapi" +version = "0.115.14" +source = { registry = "https://pypi.python.org/simple" } +dependencies = [ + { name = "pydantic", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, + { name = "starlette", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, + { name = "typing-extensions", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/ca/53/8c38a874844a8b0fa10dd8adf3836ac154082cf88d3f22b544e9ceea0a15/fastapi-0.115.14.tar.gz", hash = "sha256:b1de15cdc1c499a4da47914db35d0e4ef8f1ce62b624e94e0e5824421df99739", size = 296263, upload-time = "2025-06-26T15:29:08.21Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/53/50/b1222562c6d270fea83e9c9075b8e8600b8479150a18e4516a6138b980d1/fastapi-0.115.14-py3-none-any.whl", hash = "sha256:6c0c8bf9420bd58f565e585036d971872472b4f7d3f6c73b698e10cffdefb3ca", size = 95514, upload-time = "2025-06-26T15:29:06.49Z" }, +] + [[package]] name = "fastmcp" version = "2.10.1" @@ -1206,6 +1220,7 @@ flash = [ { name = "rotary-embedding-torch", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, ] mcp = [ + { name = "fastapi", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, { name = "fastmcp", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, { name = "mcp", extra = ["cli"], marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, { name = "pydantic", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, @@ -1219,6 +1234,10 @@ trl = [ { name = "accelerate", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, { name = "trl", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, ] +web = [ + { name = "fastapi", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, + { name = "uvicorn", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, +] [package.dev-dependencies] dev = [ @@ -1241,6 +1260,8 @@ requires-dist = [ { name = "dotenv", specifier = ">=0.9.9" }, { name = "edlib" }, { name = "einops" }, + { name = "fastapi", marker = "extra == 'mcp'", specifier = ">=0.115.14" }, + { name = "fastapi", marker = "extra == 'web'", specifier = ">=0.115.14" }, { name = "fastmcp", marker = "extra == 'mcp'", specifier = ">=0.2.0" }, { name = "flash-attn", marker = "sys_platform == 'linux' and extra == 'flash'", specifier = ">=2.8.0.post2" }, { name = "hydra-core" }, @@ -1272,9 +1293,10 @@ requires-dist = [ { name = "transformers", specifier = ">=4.24.0" }, { name = "trl", marker = "extra == 'trl'" }, { name = "universal-pathlib" }, + { name = "uvicorn", marker = "extra == 'web'", specifier = ">=0.34.3" }, { name = "wandb" }, ] -provides-extras = ["mgm", "flash", "mcp", "trl"] +provides-extras = ["flash", "mcp", "mgm", "trl", "web"] [package.metadata.requires-dev] dev = [ @@ -2907,15 +2929,14 @@ wheels = [ [[package]] name = "starlette" -version = "0.47.1" +version = "0.46.2" source = { registry = "https://pypi.python.org/simple" } dependencies = [ { name = "anyio", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, - { name = "typing-extensions", marker = "sys_platform == 'darwin' or sys_platform == 'linux'" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/0a/69/662169fdb92fb96ec3eaee218cf540a629d629c86d7993d9651226a6789b/starlette-0.47.1.tar.gz", hash = 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"2025-04-13T13:56:16.21Z" }, ] [[package]] From 8c012ca82c67212c467ea18b9f058f9aeb65fc46 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 12:09:10 -0700 Subject: [PATCH 03/15] wip server --- src/lobster/server/__init__.py | 1 + src/lobster/server/_app.py | 72 ++++++++++++++++++++++++++++++++++ src/lobster/server/_esm.py | 68 ++++++++++++++++++++++++++++++++ src/lobster/server/_server.py | 33 ---------------- src/lobster/server/_ume.py | 56 ++++++++++++++++++++++++++ src/lobster/server/_utils.py | 17 ++++++++ 6 files changed, 214 insertions(+), 33 deletions(-) create mode 100644 src/lobster/server/_app.py create mode 100644 src/lobster/server/_esm.py delete mode 100644 src/lobster/server/_server.py create mode 100644 src/lobster/server/_ume.py create mode 100644 src/lobster/server/_utils.py diff --git a/src/lobster/server/__init__.py b/src/lobster/server/__init__.py index e69de29b..4fbb8ee6 100644 --- a/src/lobster/server/__init__.py +++ b/src/lobster/server/__init__.py @@ -0,0 +1 @@ +from ._app import app diff --git a/src/lobster/server/_app.py b/src/lobster/server/_app.py new file mode 100644 index 00000000..cbae4bf7 --- /dev/null +++ b/src/lobster/server/_app.py @@ -0,0 +1,72 @@ +import os +from typing import Literal + +from fastmcp import FastMCP +from fastapi import FastAPI +from fastapi.middleware.cors import CORSMiddleware +from starlette.applications import Starlette +from starlette.routing import Mount +from pydantic import BaseModel, Field + +from ._esm import get_esm_cached, esm_aa_naturalness + +DEFAULT_LOBSTER_ALLOW_ORIGINS = "http://localhost" + +ALLOW_ORIGINS = os.getenv("LOBSTER_ALLOW_ORIGINS", DEFAULT_LOBSTER_ALLOW_ORIGINS).split(",") + + +class NaturalnessInput(BaseModel): + sequence: str + model_name: Literal[ + "facebook/esm2_t6_8M_UR50D", + "facebook/esm2_t30_150M_UR50D", + "facebook/esm2_t33_650M_UR50D", + ] = Field(default="facebook/esm2_t6_8M_UR50D") + + +class NaturalnessOutput(BaseModel): + logp: list[list[float]] + wt_logp: list[float] + naturalness: float + encoded: list[float] + + +fastapi_app = FastAPI() + + +@fastapi_app.post("/naturalness") +def naturalness(input: NaturalnessInput) -> NaturalnessOutput: + L = len(input.sequence) + if not L > 0: + return { + "logp": [], + "wt_logp": [], + "naturalness": None, + "encoded": [], + } + + model, tokenizer = get_esm_cached(input.model_name) + + out = esm_aa_naturalness(sequence=input.sequence, model=model, tokenizer=tokenizer, batch_size=64) + + return out + + +mcp = FastMCP.from_fastapi(app=fastapi_app) +mcp_app = mcp.http_app(path="/mcp") + +app = Starlette( + routes=[ + Mount("/mcp-server", app=mcp_app), + Mount("/api", app=fastapi_app), + ], + lifespan=mcp_app.lifespan, +) + +app.add_middleware( + CORSMiddleware, + allow_origins=ALLOW_ORIGINS, + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) diff --git a/src/lobster/server/_esm.py b/src/lobster/server/_esm.py new file mode 100644 index 00000000..f88e8fa4 --- /dev/null +++ b/src/lobster/server/_esm.py @@ -0,0 +1,68 @@ +import functools +from typing import Literal + +import einops +import torch +from transformers import EsmForMaskedLM, EsmTokenizer +from beignet.constants import STANDARD_RESIDUES + +from ._utils import single_position_masked_sequences, batched + + +@functools.cache +def get_esm_cached( + mlm_model_name: Literal[ + "facebook/esm2_t6_8M_UR50D", + "facebook/esm2_t30_150M_UR50D", + "facebook/esm2_t33_650M_UR50D", + ] = "facebook/esm2_t6_8M_UR50D", +): + assert mlm_model_name in { + "facebook/esm2_t6_8M_UR50D", + "facebook/esm2_t30_150M_UR50D", + "facebook/esm2_t33_650M_UR50D", + } + device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu") + tokenizer = EsmTokenizer.from_pretrained(mlm_model_name, clean_up_tokenization_spaces=False) + model = EsmForMaskedLM.from_pretrained(mlm_model_name) + model.to(device) + model.eval() + + return model, tokenizer + + +def esm_aa_naturalness(sequence: str, model, tokenizer, batch_size: int = 16) -> dict: + L = len(sequence) + vocab = tokenizer.get_vocab() + + assert set(sequence) <= set(STANDARD_RESIDUES) + + vocab_id_to_aa_id = {vocab[aa]: i for i, aa in enumerate(sorted(STANDARD_RESIDUES))} + amino_acid_vocab_ids = list(vocab_id_to_aa_id.keys()) + + encoded = tokenizer(sequence, return_tensors="pt") + encoded_aa_id = torch.as_tensor( + [vocab_id_to_aa_id[x] for x in encoded["input_ids"].squeeze(0)[1:-1].cpu().tolist()], device=model.device + ) + + masked_sequences = single_position_masked_sequences(sequence) + + with torch.inference_mode(): + logits = torch.cat( + [model(**tokenizer(input, return_tensors="pt")).logits for input in batched(masked_sequences, batch_size)], + dim=0, + ) + logits = torch.diagonal(logits[:, 1:-1, :], dim1=0, dim2=1) + logits = einops.rearrange(logits, "token length -> length token", length=L) + + logits = logits[:, torch.as_tensor(amino_acid_vocab_ids, device=model.device)] + logp = torch.nn.functional.log_softmax(logits, dim=-1) + wt_logp = logp[torch.arange(L), encoded_aa_id] + naturalness = torch.exp(wt_logp.mean()).item() + + return { + "logp": logp.cpu().tolist(), + "wt_logp": wt_logp.cpu().tolist(), + "naturalness": naturalness, + "encoded": encoded_aa_id.cpu().tolist(), + } diff --git a/src/lobster/server/_server.py b/src/lobster/server/_server.py deleted file mode 100644 index 91661a91..00000000 --- a/src/lobster/server/_server.py +++ /dev/null @@ -1,33 +0,0 @@ -from mcp.server.fastmcp import FastMCP - -from lobster.model import UME - - -class UMEServer: - def __init__(self, model: UME): - """Initialize the UME MCP server with a model. - - Args: - model: A UME model instance to use for embeddings - """ - self.model = model - self.server = FastMCP() - self._register_tools() - - def _register_tools(self): - """Register the embedding tool with the MCP server.""" - - @self.server.tool(description="Embed sequences into a latent space") - def embed_sequences(sequences, modality, aggregate=True): - return self.model.embed_sequences(sequences, modality, aggregate=aggregate) - - # Store the tool function as an instance method - self.embed_sequences = embed_sequences - - def get_server(self): - """Get the FastMCP server instance. - - Returns: - FastMCP: The configured MCP server instance - """ - return self.server diff --git a/src/lobster/server/_ume.py b/src/lobster/server/_ume.py new file mode 100644 index 00000000..b3296737 --- /dev/null +++ b/src/lobster/server/_ume.py @@ -0,0 +1,56 @@ +import functools + +import einops +import torch +from beignet.constants import STANDARD_RESIDUES + +from lobster.model import UME + +from ._utils import single_position_masked_sequences, batched + + +@functools.cache +def get_ume_cached(): + device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu") + + ume = UME.from_pretrained("ume-mini-base-12M") + ume.to(device) + ume.eval() + + return ume + + +def ume_aa_naturalness(sequence: str, model, batch_size: int = 16) -> dict: + L = len(sequence) + tokenizer = model.get_tokenizer("amino_acid") + vocab = tokenizer.get_vocab() + + assert set(sequence) <= set(STANDARD_RESIDUES) + + vocab_id_to_aa_id = {vocab[aa]: i for i, aa in enumerate(sorted(STANDARD_RESIDUES))} + amino_acid_vocab_ids = list(vocab_id_to_aa_id.keys()) + + encoded = tokenizer(sequence, return_tensors="pt") + encoded_aa_id = torch.as_tensor( + [vocab_id_to_aa_id[x] for x in encoded["input_ids"].squeeze(0)[1:-1].cpu().tolist()], device=model.device + ) + + masked_sequences = single_position_masked_sequences(sequence) + + with torch.inference_mode(): + logits = torch.cat( + [ + model.model.decoder(model.embed(tokenizer(input, return_tensors="pt"), aggregate=False)) + for input in batched(masked_sequences, batch_size) + ], + dim=0, + ) + logits = torch.diagonal(logits[:, 1:-1, :], dim1=0, dim2=1) + logits = einops.rearrange(logits, "token length -> length token", length=L) + + logits = logits[:, torch.as_tensor(amino_acid_vocab_ids, device=model.device)] + logp = torch.nn.functional.log_softmax(logits, dim=-1) + wt_logp = logp[torch.arange(L), encoded_aa_id] + naturalness = torch.exp(wt_logp.mean()).item() + + return {"logp": logp, "wt_logp": wt_logp, "naturalness": naturalness, "encoded": encoded_aa_id.cpu().tolist()} diff --git a/src/lobster/server/_utils.py b/src/lobster/server/_utils.py new file mode 100644 index 00000000..ed211c28 --- /dev/null +++ b/src/lobster/server/_utils.py @@ -0,0 +1,17 @@ +import itertools + +def single_position_masked_sequences(input: str, mask: str = "") -> list[str]: + return [str.join("", [aa if j != i else mask for j, aa in enumerate(input)]) for i in range(len(input))] + +# python < 3.12 compat +def batched(iterable, n, *, strict=False): + # batched('ABCDEFG', 3) → ABC DEF G + if n < 1: + raise ValueError("n must be at least one") + iterator = iter(iterable) + while batch := tuple(itertools.islice(iterator, n)): + if strict and len(batch) != n: + raise ValueError("batched(): incomplete batch") + yield batch + + From 6d570b858a4e5278af3b76c7fb00d950e353fdb2 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 13:27:18 -0700 Subject: [PATCH 04/15] adjust frontent --- web/src/lib/vocab.json | 35 ----------------------------------- web/src/routes/+page.svelte | 15 +++++++-------- 2 files changed, 7 insertions(+), 43 deletions(-) delete mode 100644 web/src/lib/vocab.json diff --git a/web/src/lib/vocab.json b/web/src/lib/vocab.json deleted file mode 100644 index d807f5be..00000000 --- a/web/src/lib/vocab.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "": 0, - "": 1, - "": 2, - "": 3, - "L": 4, - "A": 5, - "G": 6, - "V": 7, - "S": 8, - "E": 9, - "R": 10, - "T": 11, - "I": 12, - "D": 13, - "P": 14, - "K": 15, - "Q": 16, - "N": 17, - "F": 18, - "Y": 19, - "M": 20, - "H": 21, - "W": 22, - "C": 23, - "X": 24, - "B": 25, - "U": 26, - "Z": 27, - "O": 28, - ".": 29, - "-": 30, - "": 31, - "": 32 -} diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index 0b8428b7..3cff07ec 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -4,7 +4,6 @@ import Mutations from '$lib/Mutations.svelte'; import { PUBLIC_INFERENCE_SERVER } from '$env/static/public'; import normalize from '$lib/normalize.ts'; - import defaultVocabData from '$lib/vocab.json'; let sequence = $state( 'DIQMTQSPSSLSASVGDRVTITCQASQDIGISLSWYQQKPGKAPKLLIYNANNLADGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQHNSAPYTFGQGTKLEIKR' @@ -16,14 +15,12 @@ let selectedModel = $state(models[1]); let threshold = $state(1); - const defaultVocab: Map = new Map(Object.entries(defaultVocabData)); const alphabet = [...'ACDEFGHIKLMNPQRSTVWY']; - const alphabet_vocab_indices = alphabet.map((c) => defaultVocab.get(c)); let inference_result = $derived.by(async () => { - let inference_data = { sequence: sequence, mlm_model_name: `facebook/${selectedModel}` }; + let inference_data = { sequence: sequence, model_name: `facebook/${selectedModel}` }; - let url = new URL('./mlm_probabilities', PUBLIC_INFERENCE_SERVER); + let url = new URL('./naturalness', PUBLIC_INFERENCE_SERVER); const response = await fetch(url, { method: 'POST', @@ -34,11 +31,13 @@ }); const data = await response.json(); - const { logprobs, wt_logprobs, naturalness } = data; + const { logp, wt_logp, naturalness } = data; - const probs = logprobs.map((v) => normalize(alphabet_vocab_indices.map((i) => Math.exp(v[i])))); + //const probs = logp.map((v) => normalize(alphabet_vocab_indices.map((i) => Math.exp(v[i])))); - const wt_probs = wt_logprobs.map((p) => Math.exp(p)); + const probs = logp.map((v) => v.map((p) => Math.exp(p))); + + const wt_probs = wt_logp.map((p) => Math.exp(p)); return { probs, wt_probs, naturalness }; }); From 3add5047563d502df64a58f88ae119a6cd5e2e59 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 13:27:29 -0700 Subject: [PATCH 05/15] fix middleware --- src/lobster/server/_app.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/lobster/server/_app.py b/src/lobster/server/_app.py index cbae4bf7..8ca3a0df 100644 --- a/src/lobster/server/_app.py +++ b/src/lobster/server/_app.py @@ -33,6 +33,14 @@ class NaturalnessOutput(BaseModel): fastapi_app = FastAPI() +fastapi_app.add_middleware( + CORSMiddleware, + allow_origins=ALLOW_ORIGINS, + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + @fastapi_app.post("/naturalness") def naturalness(input: NaturalnessInput) -> NaturalnessOutput: @@ -62,11 +70,3 @@ def naturalness(input: NaturalnessInput) -> NaturalnessOutput: ], lifespan=mcp_app.lifespan, ) - -app.add_middleware( - CORSMiddleware, - allow_origins=ALLOW_ORIGINS, - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) From 2f5571933e297d696cf4902170a8f15deb6eda80 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 17:04:47 -0700 Subject: [PATCH 06/15] wip bundle web interface --- hatch_build.py | 65 +++++++++++++++++++ pyproject.toml | 35 +++++----- ...ying_file_42688fa5f3a65e2caa822dec544d5694 | 1 + src/lobster/server/__init__.py | 3 +- src/lobster/server/_app.py | 40 +++++++----- src/lobster/server/_mcp.py | 9 +++ src/lobster/server/_utils.py | 25 +++++++ web/package-lock.json | 11 ++++ web/package.json | 1 + web/src/routes/+layout.js | 1 + web/src/routes/+page.svelte | 8 +-- web/svelte.config.js | 2 +- 12 files changed, 159 insertions(+), 42 deletions(-) create mode 100644 hatch_build.py create mode 100644 share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694 create mode 100644 src/lobster/server/_mcp.py create mode 100644 web/src/routes/+layout.js diff --git a/hatch_build.py b/hatch_build.py new file mode 100644 index 00000000..998b2f19 --- /dev/null +++ b/hatch_build.py @@ -0,0 +1,65 @@ +import os +import shutil +import subprocess +import sys +from pathlib import Path + +from hatchling.builders.hooks.plugin.interface import BuildHookInterface + + +class CustomHook(BuildHookInterface): + """ + A custom build hook for lobster that builds the UI in share/lobster + """ + + def initialize(self, version, build_data): + # https://hatch.pypa.io/1.1/plugins/build-hook/#hatchling.builders.hooks.plugin.interface.BuildHookInterface + + # Hatchling intends for us to mutate the input build_data communicate + # that 'share/tiled/ui' contains build artifacts that should be included + # in the distribution. + + # Set this irrespective of whether the build happens below. It may have + # already been done manually by the user. This simply allow-lists the + # files, however they were put there. + artifact_path = "share/lobster/ui" # must be relative + build_data["artifacts"].append(artifact_path) + + if os.getenv("LOBSTER_BUILD_SKIP_UI"): + print( + "Will skip building the lobster web UI because LOBSTER_BUILD_SKIP_UI is set", + file=sys.stderr, + ) + return + npm_path = shutil.which("npm") + if npm_path is None: + print( + "Will skip building the lobster web UI because 'npm' executable is not found", + file=sys.stderr, + ) + return + print( + f"Building lobster web UI using {npm_path!r}. (Set LOBSTER_BUILD_SKIP_UI=1 to skip.)", + file=sys.stderr, + ) + try: + subprocess.check_call([npm_path, "install"], cwd="web") + subprocess.check_call( + [ + npm_path, + "run", + "build", + ], + cwd="web", + ) + if Path(artifact_path).exists(): + shutil.rmtree(artifact_path) + shutil.copytree("web/build", artifact_path) + except Exception: + print( + f"There was an error while building the lobster web UI using {npm_path!r}. " + "If you do not need the web UI, you can LOBSTER_BUILD_SKIP_UI=1 to skip it; " + "the Python aspects will work fine without it.", + file=sys.stderr, + ) + raise diff --git a/pyproject.toml b/pyproject.toml index 1ef213f1..482381cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,8 +40,8 @@ dependencies = [ ] [build-system] -requires = ["setuptools >= 65", "setuptools_scm[toml]>=6.2"] -build-backend = 'setuptools.build_meta' +requires = ["hatchling", "hatch-vcs"] +build-backend = "hatchling.build" [project.scripts] lobster_train = "lobster.cmdline:train" @@ -52,7 +52,8 @@ lobster_intervene_multiproperty = "lobster.cmdline:intervene_multiproperty" lobster_perplexity = "lobster.cmdline:perplexity" lobster_eval_embed = "lobster.cmdline:eval_embed" lobster_eval = "lobster.cmdline:evaluate" -lobster_mcp_server = "lobster.mcp.inference_server:main" +lobster_mcp_server = "lobster.server:run_mcp_server" +lobster_web = "lobster.server:serve" lobster_mcp_setup = "lobster.mcp.setup:main" [project.optional-dependencies] @@ -84,20 +85,6 @@ web = [ "uvicorn>=0.34.3", ] -[tool.setuptools.packages.find] -where = ["src"] - -[tool.setuptools.package-data] -lobster = ["*.txt", "*.json", "*.yaml"] -"lobster.assets" = ["**/*.txt", "**/*.json", "**/*.yaml"] -"lobster.hydra_config" = [ "**/*.yaml"] - -[tool.setuptools_scm] -search_parent_directories = true -version_scheme = "no-guess-dev" -fallback_version = "0.0.0" -local_scheme = "no-local-version" # see https://github.com/pypa/setuptools-scm/issues/455 - [tool.ruff] line-length = 120 exclude = [ @@ -163,3 +150,17 @@ dev = [ [[tool.uv.index]] url = "https://pypi.python.org/simple" + +[tool.hatch] +version.source = "vcs" +version.fallback-version = "0.0.0" + +# Defining this (empty) section invokes hatch_build.py +[tool.hatch.build.hooks.custom] + +[tool.hatch.build.targets.wheel] +packages = ["src/lobster"] + +[tool.hatch.build.targets.wheel.shared-data] +"share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694" = "share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694" +"share/lobster/ui" = "share/lobster/ui" diff --git a/share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694 b/share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694 new file mode 100644 index 00000000..e7118c3f --- /dev/null +++ b/share/lobster/.identifying_file_42688fa5f3a65e2caa822dec544d5694 @@ -0,0 +1 @@ +this file is used to identify share/lobster diff --git a/src/lobster/server/__init__.py b/src/lobster/server/__init__.py index 4fbb8ee6..97d6fb36 100644 --- a/src/lobster/server/__init__.py +++ b/src/lobster/server/__init__.py @@ -1 +1,2 @@ -from ._app import app +from ._app import app, serve +from ._mcp import run_mcp_server diff --git a/src/lobster/server/_app.py b/src/lobster/server/_app.py index 8ca3a0df..204e1734 100644 --- a/src/lobster/server/_app.py +++ b/src/lobster/server/_app.py @@ -1,16 +1,16 @@ import os from typing import Literal +from pathlib import Path -from fastmcp import FastMCP from fastapi import FastAPI from fastapi.middleware.cors import CORSMiddleware -from starlette.applications import Starlette -from starlette.routing import Mount +from fastapi.staticfiles import StaticFiles from pydantic import BaseModel, Field from ._esm import get_esm_cached, esm_aa_naturalness +from ._utils import SHARE_LOBSTER_PATH -DEFAULT_LOBSTER_ALLOW_ORIGINS = "http://localhost" +DEFAULT_LOBSTER_ALLOW_ORIGINS = "*" ALLOW_ORIGINS = os.getenv("LOBSTER_ALLOW_ORIGINS", DEFAULT_LOBSTER_ALLOW_ORIGINS).split(",") @@ -31,18 +31,24 @@ class NaturalnessOutput(BaseModel): encoded: list[float] -fastapi_app = FastAPI() +app = FastAPI() -fastapi_app.add_middleware( +app.mount( + "/ui", + StaticFiles(directory=Path(SHARE_LOBSTER_PATH, "ui")), + name="ui", +) + +app.add_middleware( CORSMiddleware, - allow_origins=ALLOW_ORIGINS, + allow_origins=["*"], allow_credentials=True, allow_methods=["*"], allow_headers=["*"], ) -@fastapi_app.post("/naturalness") +@app.post("/naturalness") def naturalness(input: NaturalnessInput) -> NaturalnessOutput: L = len(input.sequence) if not L > 0: @@ -60,13 +66,13 @@ def naturalness(input: NaturalnessInput) -> NaturalnessOutput: return out -mcp = FastMCP.from_fastapi(app=fastapi_app) -mcp_app = mcp.http_app(path="/mcp") +def serve(): + import uvicorn -app = Starlette( - routes=[ - Mount("/mcp-server", app=mcp_app), - Mount("/api", app=fastapi_app), - ], - lifespan=mcp_app.lifespan, -) + host = "localhost" + port = 8000 + + url = f"http://{host}:{port}/ui/index.html" + print(f"visit {url}") + + uvicorn.run(app, host=host, port=port) diff --git a/src/lobster/server/_mcp.py b/src/lobster/server/_mcp.py new file mode 100644 index 00000000..db2bf494 --- /dev/null +++ b/src/lobster/server/_mcp.py @@ -0,0 +1,9 @@ +from fastmcp import FastMCP + +from lobster.server import app + +mcp = FastMCP.from_fastapi(app=app) + + +def run_mcp_server(): + mcp.run() diff --git a/src/lobster/server/_utils.py b/src/lobster/server/_utils.py index ed211c28..3bff2ede 100644 --- a/src/lobster/server/_utils.py +++ b/src/lobster/server/_utils.py @@ -1,8 +1,10 @@ import itertools + def single_position_masked_sequences(input: str, mask: str = "") -> list[str]: return [str.join("", [aa if j != i else mask for j, aa in enumerate(input)]) for i in range(len(input))] + # python < 3.12 compat def batched(iterable, n, *, strict=False): # batched('ABCDEFG', 3) → ABC DEF G @@ -15,3 +17,26 @@ def batched(iterable, n, *, strict=False): yield batch +def get_share_path(): + import sys + from os.path import abspath, dirname, exists, join, split + + path = abspath(dirname(__file__)) + starting_points = [path] + if not path.startswith(sys.prefix): + starting_points.append(sys.prefix) + for path in starting_points: + # walk up, looking for prefix/share/tiled + while path != "/": + share_tiled = join(path, "share", "lobster") + if exists(join(share_tiled, ".identifying_file_42688fa5f3a65e2caa822dec544d5694")): + # We have the found the right directory, + # or one that is trying very hard to pretend to be! + return share_tiled + path, _ = split(path) + # Give up + return "" + + +# Package managers can just override this with the appropriate constant +SHARE_LOBSTER_PATH = get_share_path() diff --git a/web/package-lock.json b/web/package-lock.json index 1b60d504..9dca64a1 100644 --- a/web/package-lock.json +++ b/web/package-lock.json @@ -16,6 +16,7 @@ "devDependencies": { "@sveltejs/adapter-auto": "^3.0.0", "@sveltejs/adapter-node": "^5.2.9", + "@sveltejs/adapter-static": "^3.0.8", "@sveltejs/kit": "^2.0.0", "@sveltejs/vite-plugin-svelte": "^4.0.0", "@types/eslint": "^9.6.0", @@ -1183,6 +1184,16 @@ "@sveltejs/kit": "^2.4.0" } }, + "node_modules/@sveltejs/adapter-static": { + "version": "3.0.8", + "resolved": "https://registry.npmjs.org/@sveltejs/adapter-static/-/adapter-static-3.0.8.tgz", + "integrity": "sha512-YaDrquRpZwfcXbnlDsSrBQNCChVOT9MGuSg+dMAyfsAa1SmiAhrA5jUYUiIMC59G92kIbY/AaQOWcBdq+lh+zg==", + "dev": true, + "license": "MIT", + "peerDependencies": { + "@sveltejs/kit": "^2.0.0" + } + }, "node_modules/@sveltejs/kit": { "version": "2.22.0", "resolved": "https://registry.npmjs.org/@sveltejs/kit/-/kit-2.22.0.tgz", diff --git a/web/package.json b/web/package.json index de90cdad..240ba04a 100644 --- a/web/package.json +++ b/web/package.json @@ -14,6 +14,7 @@ "devDependencies": { "@sveltejs/adapter-auto": "^3.0.0", "@sveltejs/adapter-node": "^5.2.9", + "@sveltejs/adapter-static": "^3.0.8", "@sveltejs/kit": "^2.0.0", "@sveltejs/vite-plugin-svelte": "^4.0.0", "@types/eslint": "^9.6.0", diff --git a/web/src/routes/+layout.js b/web/src/routes/+layout.js new file mode 100644 index 00000000..189f71e2 --- /dev/null +++ b/web/src/routes/+layout.js @@ -0,0 +1 @@ +export const prerender = true; diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index 3cff07ec..c805de07 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -2,7 +2,6 @@ import Logo from '$lib/Logo.svelte'; import Sequence from '$lib/Sequence.svelte'; import Mutations from '$lib/Mutations.svelte'; - import { PUBLIC_INFERENCE_SERVER } from '$env/static/public'; import normalize from '$lib/normalize.ts'; let sequence = $state( @@ -20,9 +19,8 @@ let inference_result = $derived.by(async () => { let inference_data = { sequence: sequence, model_name: `facebook/${selectedModel}` }; - let url = new URL('./naturalness', PUBLIC_INFERENCE_SERVER); - - const response = await fetch(url, { + // FIXME here we assume we are serving frontend and backend together + const response = await fetch('../naturalness', { method: 'POST', headers: { 'Content-Type': 'application/json' @@ -33,8 +31,6 @@ const { logp, wt_logp, naturalness } = data; - //const probs = logp.map((v) => normalize(alphabet_vocab_indices.map((i) => Math.exp(v[i])))); - const probs = logp.map((v) => v.map((p) => Math.exp(p))); const wt_probs = wt_logp.map((p) => Math.exp(p)); diff --git a/web/svelte.config.js b/web/svelte.config.js index 1e76cee2..acba1a1d 100644 --- a/web/svelte.config.js +++ b/web/svelte.config.js @@ -1,4 +1,4 @@ -import adapter from '@sveltejs/adapter-node'; +import adapter from '@sveltejs/adapter-static'; import { vitePreprocess } from '@sveltejs/vite-plugin-svelte'; /** @type {import('@sveltejs/kit').Config} */ From 292029deef49507830f37734de31db1032b15db3 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 17:07:44 -0700 Subject: [PATCH 07/15] no-local-version --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 482381cd..2d6985bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -155,6 +155,9 @@ url = "https://pypi.python.org/simple" version.source = "vcs" version.fallback-version = "0.0.0" +[tool.hatch.version.raw-options] +local_scheme = "no-local-version" + # Defining this (empty) section invokes hatch_build.py [tool.hatch.build.hooks.custom] From dec9f6bd125e8333b52db2ffc3ab47c62de3fafa Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 20:57:26 -0700 Subject: [PATCH 08/15] fix device placement --- src/lobster/server/_esm.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/lobster/server/_esm.py b/src/lobster/server/_esm.py index f88e8fa4..81dc3644 100644 --- a/src/lobster/server/_esm.py +++ b/src/lobster/server/_esm.py @@ -34,6 +34,7 @@ def get_esm_cached( def esm_aa_naturalness(sequence: str, model, tokenizer, batch_size: int = 16) -> dict: L = len(sequence) vocab = tokenizer.get_vocab() + device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu") assert set(sequence) <= set(STANDARD_RESIDUES) @@ -49,7 +50,10 @@ def esm_aa_naturalness(sequence: str, model, tokenizer, batch_size: int = 16) -> with torch.inference_mode(): logits = torch.cat( - [model(**tokenizer(input, return_tensors="pt")).logits for input in batched(masked_sequences, batch_size)], + [ + model(**{k: v.to(device) for k, v in tokenizer(input, return_tensors="pt").items()}).logits + for input in batched(masked_sequences, batch_size) + ], dim=0, ) logits = torch.diagonal(logits[:, 1:-1, :], dim1=0, dim2=1) From f3671ad9508c0b09377d4d6d62655d67117c5c0d Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 21:13:05 -0700 Subject: [PATCH 09/15] wip separate mcp from web --- .gitignore | 2 ++ pyproject.toml | 2 +- src/lobster/mcp/__init__.py | 18 +----------------- src/lobster/{server => mcp}/_mcp.py | 2 +- src/lobster/server/__init__.py | 1 - src/lobster/server/_app.py | 29 +++++++++++++++-------------- 6 files changed, 20 insertions(+), 34 deletions(-) rename src/lobster/{server => mcp}/_mcp.py (83%) diff --git a/.gitignore b/.gitignore index 18794762..79b342be 100644 --- a/.gitignore +++ b/.gitignore @@ -47,3 +47,5 @@ dev web/build web/node_modules web/.svelte-kit + +share/lobster/ui diff --git a/pyproject.toml b/pyproject.toml index 2d6985bf..8a0565ce 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -52,8 +52,8 @@ lobster_intervene_multiproperty = "lobster.cmdline:intervene_multiproperty" lobster_perplexity = "lobster.cmdline:perplexity" lobster_eval_embed = "lobster.cmdline:eval_embed" lobster_eval = "lobster.cmdline:evaluate" -lobster_mcp_server = "lobster.server:run_mcp_server" lobster_web = "lobster.server:serve" +lobster_mcp_server = "lobster.mcp:serve" lobster_mcp_setup = "lobster.mcp.setup:main" [project.optional-dependencies] diff --git a/src/lobster/mcp/__init__.py b/src/lobster/mcp/__init__.py index 83f1aa46..e57855f7 100644 --- a/src/lobster/mcp/__init__.py +++ b/src/lobster/mcp/__init__.py @@ -1,17 +1 @@ -""" -Lobster MCP (Model Context Protocol) Integration - -This module provides MCP servers that expose Lobster's pretrained models -for sequence representation, concept analysis, and interventions. - -Available when the 'mcp' extra is installed: - uv sync --extra mcp -""" - -try: - from .inference_server import LobsterInferenceServer - - __all__ = ["LobsterInferenceServer"] -except ImportError: - # MCP dependencies not installed - __all__ = [] +from ._mcp import serve diff --git a/src/lobster/server/_mcp.py b/src/lobster/mcp/_mcp.py similarity index 83% rename from src/lobster/server/_mcp.py rename to src/lobster/mcp/_mcp.py index db2bf494..81258fce 100644 --- a/src/lobster/server/_mcp.py +++ b/src/lobster/mcp/_mcp.py @@ -5,5 +5,5 @@ mcp = FastMCP.from_fastapi(app=app) -def run_mcp_server(): +def serve(): mcp.run() diff --git a/src/lobster/server/__init__.py b/src/lobster/server/__init__.py index 97d6fb36..66055580 100644 --- a/src/lobster/server/__init__.py +++ b/src/lobster/server/__init__.py @@ -1,2 +1 @@ from ._app import app, serve -from ._mcp import run_mcp_server diff --git a/src/lobster/server/_app.py b/src/lobster/server/_app.py index 204e1734..fabc85a6 100644 --- a/src/lobster/server/_app.py +++ b/src/lobster/server/_app.py @@ -33,20 +33,6 @@ class NaturalnessOutput(BaseModel): app = FastAPI() -app.mount( - "/ui", - StaticFiles(directory=Path(SHARE_LOBSTER_PATH, "ui")), - name="ui", -) - -app.add_middleware( - CORSMiddleware, - allow_origins=["*"], - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) - @app.post("/naturalness") def naturalness(input: NaturalnessInput) -> NaturalnessOutput: @@ -66,6 +52,21 @@ def naturalness(input: NaturalnessInput) -> NaturalnessOutput: return out +app.mount( + "/", + StaticFiles(directory=Path(SHARE_LOBSTER_PATH, "ui"), html=True), + name="ui", +) + +app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=True, + allow_methods=["*"], + allow_headers=["*"], +) + + def serve(): import uvicorn From ec0db18c5da2fe7794570d0b0aee69d6667d8db5 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 21:26:46 -0700 Subject: [PATCH 10/15] don't change mcp for now --- pyproject.toml | 2 +- src/lobster/mcp/__init__.py | 3 +- src/lobster/mcp/_server.py | 31 +++++++++++++++++++ .../{server => mcp}/test__ume_server.py | 2 +- 4 files changed, 35 insertions(+), 3 deletions(-) create mode 100644 src/lobster/mcp/_server.py rename tests/lobster/{server => mcp}/test__ume_server.py (98%) diff --git a/pyproject.toml b/pyproject.toml index 8a0565ce..5a0d2ddb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ lobster_perplexity = "lobster.cmdline:perplexity" lobster_eval_embed = "lobster.cmdline:eval_embed" lobster_eval = "lobster.cmdline:evaluate" lobster_web = "lobster.server:serve" -lobster_mcp_server = "lobster.mcp:serve" +lobster_mcp_server = "lobster.mcp.inference_server:main" lobster_mcp_setup = "lobster.mcp.setup:main" [project.optional-dependencies] diff --git a/src/lobster/mcp/__init__.py b/src/lobster/mcp/__init__.py index e57855f7..94f9bea0 100644 --- a/src/lobster/mcp/__init__.py +++ b/src/lobster/mcp/__init__.py @@ -1 +1,2 @@ -from ._mcp import serve +# TODO +# from ._mcp import serve diff --git a/src/lobster/mcp/_server.py b/src/lobster/mcp/_server.py new file mode 100644 index 00000000..3a7465f9 --- /dev/null +++ b/src/lobster/mcp/_server.py @@ -0,0 +1,31 @@ +from mcp.server.fastmcp import FastMCP + +from lobster.model import UME + + +class UMEServer: + def __init__(self, model: UME): + """Initialize the UME MCP server with a model. + Args: + model: A UME model instance to use for embeddings + """ + self.model = model + self.server = FastMCP() + self._register_tools() + + def _register_tools(self): + """Register the embedding tool with the MCP server.""" + + @self.server.tool(description="Embed sequences into a latent space") + def embed_sequences(sequences, modality, aggregate=True): + return self.model.embed_sequences(sequences, modality, aggregate=aggregate) + + # Store the tool function as an instance method + self.embed_sequences = embed_sequences + + def get_server(self): + """Get the FastMCP server instance. + Returns: + FastMCP: The configured MCP server instance + """ + return self.server diff --git a/tests/lobster/server/test__ume_server.py b/tests/lobster/mcp/test__ume_server.py similarity index 98% rename from tests/lobster/server/test__ume_server.py rename to tests/lobster/mcp/test__ume_server.py index f4aa05e7..b27e7f6f 100644 --- a/tests/lobster/server/test__ume_server.py +++ b/tests/lobster/mcp/test__ume_server.py @@ -4,7 +4,7 @@ import torch from lobster.model import UME -from lobster.server._server import UMEServer +from lobster.mcp._server import UMEServer @pytest.fixture From 0c2a055a7d069c818a27b126ea354dd37234652a Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Wed, 2 Jul 2025 21:34:28 -0700 Subject: [PATCH 11/15] don't print wrong url --- src/lobster/server/_app.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/lobster/server/_app.py b/src/lobster/server/_app.py index fabc85a6..1b86d04d 100644 --- a/src/lobster/server/_app.py +++ b/src/lobster/server/_app.py @@ -73,7 +73,4 @@ def serve(): host = "localhost" port = 8000 - url = f"http://{host}:{port}/ui/index.html" - print(f"visit {url}") - uvicorn.run(app, host=host, port=port) From 63c254e526985ba9919ff1f4050c67e4d9f42725 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Jul 2025 10:43:07 -0700 Subject: [PATCH 12/15] wip styling --- web/src/routes/+page.svelte | 480 +++++++++++++++++++++++++----------- 1 file changed, 332 insertions(+), 148 deletions(-) diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index c805de07..f688b50f 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -41,55 +41,86 @@
-

Lobster Live

+
+

🦞 Lobster Web

+

Protein Sequence Analysis & Visualization

+
-
- - -
+
+

Configuration

+ +
+ + +
-
- - +
+ + +
{#await inference_result then { naturalness }} -
-
Naturalness
-
{naturalness.toFixed(2)}
+
+

Analysis

+
+
Naturalness Score
+
{naturalness.toFixed(2)}
+
{/await}
+
- -
- {'0123456789'.repeat(sequence.length / 10 + 1).slice(0, sequence.length)} +
+ + +
+ +
+ {#await inference_result then { probs, wt_probs }} +
+

Sequence Logo

+ +
+ +
+

Sequence Visualization

+ +
+ +
+

Mutation Analysis

+ +
+ {/await}
- {#await inference_result then { probs, wt_probs }} - - - - {/await}
@@ -100,177 +131,330 @@ margin: 0; height: 100%; width: 100%; - } - - h1 { - margin: 0; - margin-left: 1em; - text-align: left; + font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif; + background: linear-gradient(135deg, #f5f7fa 0%, #c3cfe2 100%); } .app-container { display: flex; flex-direction: column; - height: 100vh; + min-height: 100vh; width: 100%; border: none; } .header { width: 100%; - background-color: #001f3f; - color: #fff; - padding: 20px 0; + background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); + color: white; + padding: 0; + box-shadow: 0 4px 20px rgba(0, 0, 0, 0.1); + position: relative; + overflow: hidden; + flex-shrink: 0; + } + + .header::before { + content: ''; + position: absolute; + top: 0; + left: 0; + right: 0; + bottom: 0; + background: url('data:image/svg+xml,'); + pointer-events: none; + } + + .header-content { + position: relative; + z-index: 1; + padding: 2rem; text-align: center; } + .header h1 { + margin: 0; + font-size: 2.5rem; + font-weight: 700; + letter-spacing: -0.025em; + text-shadow: 0 2px 4px rgba(0, 0, 0, 0.1); + } + + .subtitle { + margin: 0.5rem 0 0 0; + font-size: 1.1rem; + opacity: 0.9; + font-weight: 400; + } + .content-wrapper { display: flex; flex-grow: 1; width: 100%; + min-height: 0; } .sidebar { - width: 300px; - background-color: #f4f4f4; - padding: 20px; + width: 320px; + background: white; + padding: 2rem; margin: 0; display: flex; flex-direction: column; - align-items: center; - box-sizing: border-box; + gap: 2rem; + box-shadow: 4px 0 20px rgba(0, 0, 0, 0.08); + position: relative; } - .model-select-label { - margin-bottom: 10px; - font-weight: bold; - font-size: 1em; + .sidebar-section { + display: flex; + flex-direction: column; + gap: 1.5rem; } - .model-selection-container { - background-color: #ffffff; - border: 1px solid #e0e0e0; - border-radius: 10px; - box-shadow: 0px 4px 8px rgba(0, 0, 0, 0.1); - padding: 15px; - margin-bottom: 20px; - width: 90%; + + .sidebar-section h3 { + margin: 0; + font-size: 1.3rem; + font-weight: 600; + color: #2d3748; + border-bottom: 2px solid #e2e8f0; + padding-bottom: 0.5rem; } - .model-selection-container label { - font-size: 1.1em; + .control-group { + display: flex; + flex-direction: column; + gap: 0.75rem; + } + + .control-label { + font-size: 0.95rem; font-weight: 600; - color: #333; - margin-bottom: 10px; - display: block; + color: #4a5568; + margin: 0; } - .model-selection-container select { + .modern-select { + padding: 0.75rem; + font-size: 1rem; + border: 2px solid #e2e8f0; + border-radius: 8px; + background: white; + transition: all 0.2s ease; + cursor: pointer; + } + + .modern-select:hover { + border-color: #cbd5e0; + } + + .modern-select:focus { + outline: none; + border-color: #667eea; + box-shadow: 0 0 0 3px rgba(102, 126, 234, 0.1); + } + + .modern-slider { + -webkit-appearance: none; + appearance: none; width: 100%; - padding: 10px; - font-size: 1em; - border: 1px solid #ccc; - border-radius: 5px; - margin-top: 5px; - } - - .threshold-selection-container { - background-color: #ffffff; - border: 1px solid #e0e0e0; - border-radius: 10px; - box-shadow: 0px 4px 8px rgba(0, 0, 0, 0.1); - padding: 15px; - margin-bottom: 20px; - max-width: 220px; - width: 90%; - } - - .threshold-selection-container label { - font-size: 1.1em; - font-weight: 600; - color: #333; - margin-bottom: 10px; - display: block; + height: 8px; + border-radius: 4px; + background: #e2e8f0; + outline: none; + transition: all 0.2s ease; } - .threshold-selection-container input { - padding: 10px; - font-size: 1em; - border: 1px solid #ccc; - border-radius: 5px; - margin-top: 5px; + .modern-slider::-webkit-slider-thumb { + -webkit-appearance: none; + appearance: none; + width: 20px; + height: 20px; + border-radius: 50%; + background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); + cursor: pointer; + box-shadow: 0 2px 8px rgba(0, 0, 0, 0.2); + transition: all 0.2s ease; } - .model-select { - margin-bottom: 15px; - padding: 5px; - font-size: 1em; - border-radius: 5px; - border: 1px solid #ccc; - width: 80%; + .modern-slider::-webkit-slider-thumb:hover { + transform: scale(1.1); + box-shadow: 0 4px 12px rgba(0, 0, 0, 0.3); + } + + .modern-slider::-moz-range-thumb { + width: 20px; + height: 20px; + border-radius: 50%; + background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); + cursor: pointer; + border: none; + box-shadow: 0 2px 8px rgba(0, 0, 0, 0.2); + } + + .metric-card { + background: linear-gradient(135deg, #f8fafc 0%, #e2e8f0 100%); + border: 1px solid #e2e8f0; + border-radius: 12px; + padding: 1.5rem; + text-align: center; + box-shadow: 0 4px 12px rgba(0, 0, 0, 0.05); + } + + .metric-label { + font-size: 0.9rem; + font-weight: 500; + color: #64748b; + margin-bottom: 0.5rem; + text-transform: uppercase; + letter-spacing: 0.05em; + } + + .metric-value { + font-size: 2rem; + font-weight: 700; + color: #1e293b; + background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); + -webkit-background-clip: text; + -webkit-text-fill-color: transparent; + background-clip: text; } .main-content { flex-grow: 1; display: flex; - align-items: center; + align-items: flex-start; justify-content: center; + padding: 2rem; + overflow-y: auto; + min-height: 0; } .container { display: flex; flex-direction: column; - align-items: center; - justify-content: center; - padding: 20px; - box-sizing: border-box; + gap: 2rem; + width: 100%; + max-width: 1500px; + } + + .input-section { + display: flex; + flex-direction: column; + gap: 0.75rem; + } + + .input-label { + font-size: 1.1rem; + font-weight: 600; + color: #2d3748; + margin: 0; } .sequence-input { - margin-bottom: 0px; - padding: 0px; - font-size: 1.2em; - width: 1000px; - max-width: 1000px; - border: 2px solid #ccc; - border-radius: 5px; - font-family: monospace; + padding: 1rem; + font-size: 1.1rem; + width: 100%; + max-width: 1200px; + border: 2px solid #e2e8f0; + border-radius: 8px; + font-family: 'SF Mono', 'Monaco', 'Cascadia Code', 'Roboto Mono', monospace; + background: white; + transition: all 0.2s ease; + box-shadow: 0 2px 8px rgba(0, 0, 0, 0.05); + } + + .sequence-input:focus { + outline: none; + border-color: #667eea; + box-shadow: 0 0 0 3px rgba(102, 126, 234, 0.1), 0 4px 12px rgba(0, 0, 0, 0.1); } .character-guide { - margin-bottom: 20px; - padding: 0px; - font-size: 1.2em; - width: 1000px; - max-width: 1000px; - border: 2px solid #ccc; - border-radius: 5px; - font-family: monospace; - color: grey; - } - - .naturalness-container { - background-color: #ffffff; - border: 1px solid #e0e0e0; - border-radius: 10px; - box-shadow: 0px 4px 8px rgba(0, 0, 0, 0.1); - padding: 15px; - margin-top: 20px; - width: 90%; - max-width: 220px; - text-align: center; + padding: 0.5rem 1rem; + font-size: 0.9rem; + width: 100%; + max-width: 1200px; + background: #f8fafc; + border: 1px solid #e2e8f0; + border-radius: 6px; + font-family: 'SF Mono', 'Monaco', 'Cascadia Code', 'Roboto Mono', monospace; + color: #64748b; + letter-spacing: 0.05em; } - .naturalness-label { - font-size: 1.1em; + .visualization-section { + display: flex; + flex-direction: column; + gap: 2rem; + } + + .viz-card { + background: white; + border: 1px solid #e2e8f0; + border-radius: 12px; + padding: 2rem; + box-shadow: 0 4px 20px rgba(0, 0, 0, 0.08); + transition: all 0.2s ease; + } + + .viz-card:hover { + box-shadow: 0 8px 30px rgba(0, 0, 0, 0.12); + transform: translateY(-2px); + } + + .viz-card h3 { + margin: 0 0 1.5rem 0; + font-size: 1.3rem; font-weight: 600; - color: #333; - margin-bottom: 10px; - display: block; + color: #2d3748; + border-bottom: 2px solid #e2e8f0; + padding-bottom: 0.75rem; + } + + /* Responsive adjustments */ + @media (max-width: 1024px) { + .content-wrapper { + flex-direction: column; + } + + .sidebar { + width: 100%; + flex-direction: row; + gap: 2rem; + padding: 1.5rem; + } + + .sidebar-section { + flex: 1; + min-width: 0; + } } - .naturalness-value { - font-size: 1.3em; - font-weight: bold; - color: #001f3f; + @media (max-width: 768px) { + .header-content { + padding: 1.5rem; + } + + .header h1 { + font-size: 2rem; + } + + .subtitle { + font-size: 1rem; + } + + .sidebar { + flex-direction: column; + gap: 1.5rem; + } + + .main-content { + padding: 1rem; + } + + .sequence-input { + font-size: 1rem; + } } From 247a23e1cd1a3d1cbf86dae5ddb4debc22053a8e Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Jul 2025 16:55:56 -0700 Subject: [PATCH 13/15] wip styling * explicit submit button to run inference * don't overflow outside of cards --- web/src/routes/+page.svelte | 230 ++++++++++++++++++++++++++++++------ 1 file changed, 192 insertions(+), 38 deletions(-) diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index f688b50f..82514f75 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -2,7 +2,7 @@ import Logo from '$lib/Logo.svelte'; import Sequence from '$lib/Sequence.svelte'; import Mutations from '$lib/Mutations.svelte'; - import normalize from '$lib/normalize.ts'; + import normalize from '$lib/normalize'; let sequence = $state( 'DIQMTQSPSSLSASVGDRVTITCQASQDIGISLSWYQQKPGKAPKLLIYNANNLADGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQHNSAPYTFGQGTKLEIKR' @@ -13,30 +13,41 @@ let selectedModel = $state(models[1]); let threshold = $state(1); + let isLoading = $state(false); + let inference_result = $state(null); const alphabet = [...'ACDEFGHIKLMNPQRSTVWY']; - let inference_result = $derived.by(async () => { - let inference_data = { sequence: sequence, model_name: `facebook/${selectedModel}` }; - - // FIXME here we assume we are serving frontend and backend together - const response = await fetch('../naturalness', { - method: 'POST', - headers: { - 'Content-Type': 'application/json' - }, - body: JSON.stringify(inference_data) - }); - const data = await response.json(); - - const { logp, wt_logp, naturalness } = data; - - const probs = logp.map((v) => v.map((p) => Math.exp(p))); - - const wt_probs = wt_logp.map((p) => Math.exp(p)); - - return { probs, wt_probs, naturalness }; - }); + async function runInference() { + if (!sequence.trim()) return; + + isLoading = true; + try { + let inference_data = { sequence: sequence, model_name: `facebook/${selectedModel}` }; + + // FIXME here we assume we are serving frontend and backend together + const response = await fetch('../naturalness', { + method: 'POST', + headers: { + 'Content-Type': 'application/json' + }, + body: JSON.stringify(inference_data) + }); + const data = await response.json(); + + const { logp, wt_logp, naturalness } = data; + + const probs = logp.map((v: any) => v.map((p: any) => Math.exp(p))); + + const wt_probs = wt_logp.map((p: any) => Math.exp(p)); + + inference_result = { probs, wt_probs, naturalness }; + } catch (error) { + console.error('Inference failed:', error); + } finally { + isLoading = false; + } + }
@@ -80,46 +91,75 @@
- {#await inference_result then { naturalness }} + {#if inference_result}

Analysis

Naturalness Score
-
{naturalness.toFixed(2)}
+
{inference_result.naturalness.toFixed(2)}
- {/await} + {/if}
- +
+ + +
- {#await inference_result then { probs, wt_probs }} + {#if inference_result}

Sequence Logo

- +
+ +

Sequence Visualization

- +
+ +

Mutation Analysis

- +
+ +
- {/await} + {:else if isLoading} +
+
+ +

Analyzing sequence...

+
+
+ {:else} +
+
+

Enter a protein sequence and click "Analyze Sequence" to see visualization

+
+
+ {/if}
@@ -335,7 +375,7 @@ flex-direction: column; gap: 2rem; width: 100%; - max-width: 1500px; + max-width: 1200px; } .input-section { @@ -351,17 +391,26 @@ margin: 0; } + .textarea-container { + position: relative; + width: 100%; + max-width: 1200px; + } + .sequence-input { padding: 1rem; + padding-right: 120px; /* Make room for button */ font-size: 1.1rem; width: 100%; - max-width: 1200px; border: 2px solid #e2e8f0; border-radius: 8px; font-family: 'SF Mono', 'Monaco', 'Cascadia Code', 'Roboto Mono', monospace; background: white; transition: all 0.2s ease; box-shadow: 0 2px 8px rgba(0, 0, 0, 0.05); + resize: vertical; + min-height: 120px; + box-sizing: border-box; } .sequence-input:focus { @@ -370,6 +419,65 @@ box-shadow: 0 0 0 3px rgba(102, 126, 234, 0.1), 0 4px 12px rgba(0, 0, 0, 0.1); } + .submit-button { + position: absolute; + top: 1rem; + right: 1rem; + padding: 0.5rem 1rem; + font-size: 0.9rem; + font-weight: 600; + color: white; + background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); + border: none; + border-radius: 6px; + cursor: pointer; + transition: all 0.2s ease; + box-shadow: 0 2px 8px rgba(102, 126, 234, 0.3); + white-space: nowrap; + z-index: 1; + } + + .submit-button:hover:not(:disabled) { + transform: translateY(-1px); + box-shadow: 0 4px 12px rgba(102, 126, 234, 0.4); + } + + .submit-button:disabled { + opacity: 0.6; + cursor: not-allowed; + transform: none; + } + + .loading-message, .empty-message { + display: flex; + flex-direction: column; + align-items: center; + justify-content: center; + padding: 3rem; + text-align: center; + } + + .loading-message p, .empty-message p { + margin: 0; + color: #64748b; + font-size: 1.1rem; + } + + .loading-spinner { + width: 40px; + height: 40px; + border: 4px solid #e2e8f0; + border-top: 4px solid #667eea; + border-radius: 50%; + animation: spin 1s linear infinite; + margin-bottom: 1rem; + } + + @keyframes spin { + 0% { transform: rotate(0deg); } + 100% { transform: rotate(360deg); } + } + .character-guide { padding: 0.5rem 1rem; font-size: 0.9rem; @@ -412,6 +520,44 @@ padding-bottom: 0.75rem; } + .viz-container { + width: 100%; + overflow-x: auto; + overflow-y: hidden; + border-radius: 8px; + background: #fafafa; + padding: 1rem; + min-height: 120px; + /* Allow content to scroll horizontally when needed */ + scrollbar-width: thin; + scrollbar-color: #cbd5e0 #f7fafc; + } + + .viz-container::-webkit-scrollbar { + height: 8px; + } + + .viz-container::-webkit-scrollbar-track { + background: #f7fafc; + border-radius: 4px; + } + + .viz-container::-webkit-scrollbar-thumb { + background: #cbd5e0; + border-radius: 4px; + } + + .viz-container::-webkit-scrollbar-thumb:hover { + background: #a0aec0; + } + + .viz-container :global(svg) { + height: auto; + display: block; + min-width: 800px; /* Ensure minimum readable size */ + /* SVG will maintain its natural width for scrolling */ + } + /* Responsive adjustments */ @media (max-width: 1024px) { .content-wrapper { @@ -456,5 +602,13 @@ .sequence-input { font-size: 1rem; } + + .viz-container { + padding: 0.5rem; + } + + .viz-card { + padding: 1rem; + } } From 17c994ffe4150c67d0aa37fbdb39e64087d58398 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Jul 2025 16:58:11 -0700 Subject: [PATCH 14/15] lobster live --- web/src/routes/+page.svelte | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index 82514f75..78122d91 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -53,7 +53,7 @@
-

🦞 Lobster Web

+

🦞 Lobster Live 🦞

Protein Sequence Analysis & Visualization

From cbb1e7f53b1dcbffbf7b4c251ef4543e27dc3c42 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Jul 2025 16:58:55 -0700 Subject: [PATCH 15/15] prettier --- web/src/routes/+page.svelte | 78 ++++++++++++++++++++++++------------- 1 file changed, 50 insertions(+), 28 deletions(-) diff --git a/web/src/routes/+page.svelte b/web/src/routes/+page.svelte index 78122d91..a48e0b84 100644 --- a/web/src/routes/+page.svelte +++ b/web/src/routes/+page.svelte @@ -20,7 +20,7 @@ async function runInference() { if (!sequence.trim()) return; - + isLoading = true; try { let inference_data = { sequence: sequence, model_name: `facebook/${selectedModel}` }; @@ -62,7 +62,7 @@

Configuration

- +
-
- +
{#if inference_result}
@@ -132,18 +132,31 @@
- +

Sequence Visualization

- +
- +

Mutation Analysis

- +
{:else if isLoading} @@ -171,7 +184,8 @@ margin: 0; height: 100%; width: 100%; - font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif; + font-family: + -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, sans-serif; background: linear-gradient(135deg, #f5f7fa 0%, #c3cfe2 100%); } @@ -416,7 +430,9 @@ .sequence-input:focus { outline: none; border-color: #667eea; - box-shadow: 0 0 0 3px rgba(102, 126, 234, 0.1), 0 4px 12px rgba(0, 0, 0, 0.1); + box-shadow: + 0 0 0 3px rgba(102, 126, 234, 0.1), + 0 4px 12px rgba(0, 0, 0, 0.1); } .submit-button { @@ -448,7 +464,8 @@ transform: none; } - .loading-message, .empty-message { + .loading-message, + .empty-message { display: flex; flex-direction: column; align-items: center; @@ -457,7 +474,8 @@ text-align: center; } - .loading-message p, .empty-message p { + .loading-message p, + .empty-message p { margin: 0; color: #64748b; font-size: 1.1rem; @@ -474,8 +492,12 @@ } @keyframes spin { - 0% { transform: rotate(0deg); } - 100% { transform: rotate(360deg); } + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(360deg); + } } .character-guide { @@ -563,14 +585,14 @@ .content-wrapper { flex-direction: column; } - + .sidebar { width: 100%; flex-direction: row; gap: 2rem; padding: 1.5rem; } - + .sidebar-section { flex: 1; min-width: 0; @@ -581,32 +603,32 @@ .header-content { padding: 1.5rem; } - + .header h1 { font-size: 2rem; } - + .subtitle { font-size: 1rem; } - + .sidebar { flex-direction: column; gap: 1.5rem; } - + .main-content { padding: 1rem; } - + .sequence-input { font-size: 1rem; } - + .viz-container { padding: 0.5rem; } - + .viz-card { padding: 1rem; }