pybiolib 1.2.1007__tar.gz → 1.2.1018__tar.gz

{pybiolib-1.2.1007 → pybiolib-1.2.1018}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.1007
+Version: 1.2.1018
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.1007 → pybiolib-1.2.1018}/biolib/_internal/add_copilot_prompts.py

@@ -2,10 +2,10 @@ import os
 import shutil
 import sys
 
-from biolib._internal import llm_instructions
+from biolib._internal.templates import templates
 
 
-def add_copilot_prompts(force: bool, style: bool = True, silent: bool = False) -> None:
+def add_copilot_prompts(force: bool, silent: bool = False) -> None:
     current_working_directory = os.getcwd()
     config_file_path = f'{current_working_directory}/.biolib/config.yml'
     if not os.path.exists(config_file_path):
@@ -14,7 +14,7 @@ Error: Current directory has not been initialized as a BioLib application.
        Please run the \"biolib init\" command first"""
         print(err_string, file=sys.stderr)
         exit(1)
-    source_path = os.path.join(os.path.dirname(llm_instructions.__file__), '.github')
+    source_path = os.path.join(templates.copilot_template(), '.github')
     destination_path = os.path.join(current_working_directory, '.github')
 
     conflicting_files = []
@@ -23,8 +23,6 @@ Error: Current directory has not been initialized as a BioLib application.
         relative_dir = os.path.relpath(root, source_path)
         destination_dir = os.path.join(destination_path, relative_dir)
         for filename in filenames:
-            if 'style' in filename and not style:
-                continue
             source_file = os.path.join(root, filename)
             destination_file = os.path.join(destination_dir, filename)
             if os.path.exists(destination_file) and not force:

pybiolib-1.2.1018/biolib/_internal/add_gui_files.py

@@ -0,0 +1,59 @@
+import os
+import shutil
+import sys
+
+from biolib._internal.templates import templates
+
+
+def add_gui_files(force=False, silent=False) -> None:
+    cwd = os.getcwd()
+    template_dir = templates.gui_template()
+
+    root_files = ['package.json', 'Dockerfile', 'index.html', 'vite.config.mts', '.yarnrc.yml']
+
+    conflicting_files = []
+
+    # Copy root_files to init_template root and rest to subdirectory
+    for root, _, filenames in os.walk(template_dir):
+        relative_dir = os.path.relpath(root, template_dir)
+
+        for filename in filenames:
+            if filename in root_files:
+                destination_dir = cwd
+            else:
+                if relative_dir == '.':
+                    destination_dir = os.path.join(cwd, 'gui')
+                else:
+                    destination_dir = os.path.join(cwd, 'gui', relative_dir)
+
+            source_file = os.path.join(root, filename)
+            destination_file = os.path.join(destination_dir, filename)
+
+            if filename == 'Dockerfile':
+                force = True
+
+            if os.path.exists(destination_file) and not force:
+                with open(source_file, 'rb') as fsrc, open(destination_file, 'rb') as fdest:
+                    if fsrc.read() != fdest.read():
+                        conflicting_files.append(os.path.relpath(destination_file, cwd))
+            else:
+                os.makedirs(destination_dir, exist_ok=True)
+                shutil.copy2(source_file, destination_file)
+
+    gitignore_path = os.path.join(cwd, '.gitignore')
+    with open(gitignore_path, 'a') as gitignore_file:
+        gitignore_file.write('\n# gui\n')
+        gitignore_file.write('.yarn\n')
+        gitignore_file.write('dist\n')
+        gitignore_file.write('yarn.lock\n')
+        gitignore_file.write('tsconfig.tsbuildinfo\n')
+        gitignore_file.write('node_modules\n')
+
+    if conflicting_files:
+        print('The following files were not overwritten. Use --force to override them:', file=sys.stderr)
+        for conflicting_file in list(set(conflicting_files)):
+            print(f'  {conflicting_file}', file=sys.stderr)
+        exit(1)
+
+    if not silent:
+        print('gui files added to project root and gui/ subdirectory')

{pybiolib-1.2.1007/biolib/_internal/llm_instructions → pybiolib-1.2.1018/biolib/_internal/templates/copilot_template}/.github/instructions/style-react-ts.instructions.md

@@ -20,3 +20,5 @@ Apply the [general coding guidelines](./style-general.instructions.md) to all co
 - Follow the React hooks rules (no conditional hooks)
 - Prefer one component per file
 - Use Tailwindcss for styling
+- Extract props in components with object destructuring like `const { prop1, prop2 } = props;`
+- Instantiate functional components with props like `export default function MyComponent(props: IProps) { ... }`.

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/.yarnrc.yml

@@ -0,0 +1 @@
+nodeLinker: node-modules

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/App.tsx

@@ -0,0 +1,17 @@
+export default function App() {
+  return (
+    <div className="min-h-screen bg-gray-100 flex items-center justify-center">
+      <div className="text-center">
+        <h1 className="text-4xl font-bold mb-4">
+          Hello, BioLib!
+        </h1>
+        <p className="text-lg mb-2">
+          You have successfully set up your BioLib GUI application.
+        </p>
+        <p className="italic">
+          This is a simple React template with Tailwind CSS styling.
+        </p>
+      </div>
+    </div>
+  );
+}

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/Dockerfile

@@ -0,0 +1,26 @@
+FROM node:24.4.1-alpine3.21 AS gui_builder
+
+WORKDIR /home/biolib/
+
+RUN corepack enable
+COPY .yarnrc.yml .
+COPY package.json .
+COPY index.html .
+COPY vite.config.mts .
+RUN yarn install
+
+COPY gui gui
+RUN yarn build
+
+FROM python:3.13.5-slim
+WORKDIR /home/biolib/
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY run.sh .
+COPY run.py .
+
+RUN mkdir output
+
+COPY --from=gui_builder /home/biolib/dist/index.html gui.html

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/index.css

@@ -0,0 +1,5 @@
+@import "tailwindcss";
+
+* {
+  font-family: "Noto Sans", sans-serif;
+}

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/index.html

@@ -0,0 +1,13 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <link href="gui/index.css" rel="stylesheet">
+    <title>BIOLIB_REPLACE_APP_NAME</title>
+  </head>
+  <body style="overflow: hidden; background: white">
+    <div id="root"></div>
+    <script type="module" src="gui/index.tsx"></script>
+  </body>
+</html>

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/index.tsx

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

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/package.json

@@ -0,0 +1,26 @@
+{
+  "name": "biolib_replace_app_name",
+  "version": "0.1.0",
+  "private": true,
+  "type": "module",
+  "scripts": {
+    "dev": "vite",
+    "build": "tsc --noEmit -p gui/tsconfig.json && vite build",
+    "preview": "vite preview"
+  },
+  "dependencies": {
+    "react": "18.3.1",
+    "react-dom": "18.3.1"
+  },
+  "devDependencies": {
+    "@tailwindcss/vite": "4.0.14",
+    "@types/react": "18.3.3",
+    "@types/react-dom": "18.3.0",
+    "@vitejs/plugin-react": "4.2.1",
+    "tailwindcss": "4.0.14",
+    "typescript": "5.2.2",
+    "vite": "5.3.4",
+    "vite-plugin-singlefile": "2.0.2"
+  },
+  "packageManager": "yarn@4.6.0"
+}

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/tsconfig.json

@@ -0,0 +1,24 @@
+{
+  "compilerOptions": {
+    "composite": true,
+    "target": "ES2020",
+    "lib": ["ES2020", "DOM", "DOM.Iterable"],
+    "module": "ESNext",
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "verbatimModuleSyntax": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+    "jsx": "react-jsx",
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noFallthroughCasesInSwitch": true
+  },
+  "include": ["."]
+}

pybiolib-1.2.1018/biolib/_internal/templates/gui_template/vite.config.mts

@@ -0,0 +1,8 @@
+import { defineConfig } from "vite";
+import react from "@vitejs/plugin-react";
+import tailwindcss from "@tailwindcss/vite";
+import { viteSingleFile } from "vite-plugin-singlefile";
+
+export default defineConfig({
+  plugins: [react(), tailwindcss(), viteSingleFile()],
+});

pybiolib-1.2.1018/biolib/_internal/templates/templates.py

@@ -0,0 +1,13 @@
+import os
+
+
+def init_template() -> str:
+    return os.path.join(os.path.dirname(__file__), 'init_template')
+
+
+def copilot_template() -> str:
+    return os.path.join(os.path.dirname(__file__), 'copilot_template')
+
+
+def gui_template() -> str:
+    return os.path.join(os.path.dirname(__file__), 'gui_template')

{pybiolib-1.2.1007 → pybiolib-1.2.1018}/biolib/cli/init.py

@@ -6,6 +6,7 @@ import click
 
 from biolib import utils  # Import like this to let BASE_URL_IS_PUBLIC_BIOLIB be set correctly
 from biolib._internal.add_copilot_prompts import add_copilot_prompts
+from biolib._internal.add_gui_files import add_gui_files
 from biolib._internal.string_utils import normalize_for_docker_tag
 from biolib._internal.templates import templates
 from biolib.utils import BIOLIB_PACKAGE_VERSION
@@ -23,24 +24,27 @@ def init() -> None:
             'Remember to set the app URI in the .biolib/config.yml file later, '
             'and docker image name in the .biolib/config.yml and .github/workflows/biolib.yml files.'
         )
-    copilot_enabled_input = input('Do you want to include Copilot instructions and prompts? [y/N]: ')
-    include_copilot_enabled = copilot_enabled_input.lower() == 'y'
-
-    include_copilot_style = True  # Default to True if copilot is enabled
-    if include_copilot_enabled:
-        copilot_style_input = input('Do you want to include Copilot style prompts? [Y/n]: ')
-        include_copilot_style = copilot_style_input.lower() != 'n'
-
-    template_dir = templates.init_template()
+    advanced_setup_input = input('Do you want to set up advanced features like Copilot and GUI? [y/N]: ')
+    advanced_setup = advanced_setup_input.lower() == 'y'
+    include_copilot = False
+    include_gui = False
+    if advanced_setup:
+        copilot_enabled_input = input('Do you want to include Copilot instructions and prompts? [y/N]: ')
+        include_copilot = copilot_enabled_input.lower() == 'y'
+        include_gui_input = input('Do you want to include GUI setup? [y/N]: ')
+        include_gui = include_gui_input.lower() == 'y'
+
+    init_template_dir = templates.init_template()
     conflicting_files = []
     files_to_overwrite = set()
 
     try:
         # First pass: check for conflicts
-        for root, dirs, filenames in os.walk(template_dir):
+        for root, dirs, filenames in os.walk(init_template_dir):
             dirs[:] = [d for d in dirs if '__pycache__' not in d]
-            relative_dir = os.path.relpath(root, template_dir)
+            relative_dir = os.path.relpath(root, init_template_dir)
             destination_dir = cwd if relative_dir == '.' else os.path.join(cwd, relative_dir)
+
             for filename in filenames:
                 source_file = os.path.join(root, filename)
                 destination_file = os.path.join(destination_dir, filename)
@@ -61,18 +65,22 @@ def init() -> None:
                     files_to_overwrite.add(conflicting_file)
 
         replace_app_uri = app_uri if app_uri else 'PUT_APP_URI_HERE'
+        replace_app_name = app_name if app_name else 'biolib-app'
 
         # Second pass: copy files (only if no conflicts)
-        for root, dirs, filenames in os.walk(template_dir):
+        for root, dirs, filenames in os.walk(init_template_dir):
             dirs[:] = [d for d in dirs if '__pycache__' not in d]
-            relative_dir = os.path.relpath(root, template_dir)
+            relative_dir = os.path.relpath(root, init_template_dir)
             destination_dir = os.path.join(cwd, relative_dir)
+
             os.makedirs(destination_dir, exist_ok=True)
 
             for filename in filenames:
                 if utils.BASE_URL_IS_PUBLIC_BIOLIB and filename == 'biolib.yml':
                     continue
 
+                relative_file_path = os.path.join(relative_dir, filename) if relative_dir != '.' else filename
+
                 source_file = os.path.join(root, filename)
                 destination_file = os.path.join(destination_dir, filename)
                 relative_file_path = os.path.relpath(destination_file, cwd)
@@ -88,6 +96,7 @@ def init() -> None:
                             'BIOLIB_REPLACE_DOCKER_TAG',
                             docker_tag if docker_tag else 'PUT_DOCKER_TAG_HERE',
                         )
+                        new_content = new_content.replace('BIOLIB_REPLACE_APP_NAME', replace_app_name)
 
                         with open(destination_file, 'w') as f:
                             f.write(new_content)
@@ -99,8 +108,11 @@ def init() -> None:
             with open(readme_path, 'w') as readme_file:
                 readme_file.write(f'# {app_name}\n')
 
-        if include_copilot_enabled:
-            add_copilot_prompts(force=False, style=include_copilot_style, silent=True)
+        if include_copilot:
+            add_copilot_prompts(force=False, silent=True)
+
+        if include_gui:
+            add_gui_files(force=False, silent=True)
 
     except KeyboardInterrupt:
         print('\nInit command cancelled.', file=sys.stderr)

{pybiolib-1.2.1007 → pybiolib-1.2.1018}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.1007"
+version = "1.2.1018"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"

pybiolib-1.2.1007/biolib/_internal/templates/templates.py

@@ -1,5 +0,0 @@
-import os
-
-
-def init_template():
-    return os.path.join(os.path.dirname(__file__), 'init_template')