File structure + python package

.github/workflows/ci.yml

@@ -44,6 +44,7 @@ jobs:
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install .[dev]
         pip install -r requirements.txt
 
     - name: Install Node.js dependencies
@@ -158,6 +159,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install .[dev]
         pip install -r requirements.txt
         npm ci
 

.gitignore

@@ -27,3 +27,12 @@ venv/
 
 docs/_build
 
+# python 
+__pycache__
+*.py[cod]
+*.pyo
+*.pyd
+.Python
+*.egg
+*.egg-info
+*_version.py

Dockerfile

@@ -23,6 +23,9 @@ WORKDIR /app
 COPY requirements.txt .
 RUN pip install --no-cache-dir -r requirements.txt
 
+# Install python core package
+RUN pip install .
+
 # Install gunicorn for production WSGI server
 RUN pip install gunicorn
 

README.md

@@ -37,7 +37,8 @@ python -m venv venv
 source venv/bin/activate        # macOS/Linux
 venv\Scripts\activate           # Windows
 
-pip install -r requirements.txt
+pip install -r requirements.txt  # install the web app requirements (eg. Flask)
+pip install -e .[dev]  # install the python module containing pathsim utils
 ```
 # Running Application
 You can run both frontend and backend at once

package.json

@@ -8,7 +8,7 @@
     "build": "vite build",
     "lint": "eslint .",
     "preview": "vite preview",
-    "start:backend": "python -m src.backend",
+    "start:backend": "python src/backend.py",
     "start:both": "concurrently \"npm run dev\" \"npm run start:backend\""
   },
   "dependencies": {

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel", "setuptools-scm[toml] >= 7.0.5"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "fuel-cycle-sim"
+version = "0.1.0"
+description = "A Python package for fuel cycle simulation with pathsim integration"
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Your Name", email = "your.email@example.com"}
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "pathsim>=0.7.0",
+    "matplotlib>=3.7.0",
+    "numpy>=1.24.0",
+    "plotly>=6.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest"
+]
+
+
+[project.urls]
+Homepage = "https://github.com/yourusername/fuel-cycle-sim"
+Documentation = "https://fuel-cycle-sim.readthedocs.io/"
+Repository = "https://github.com/yourusername/fuel-cycle-sim.git"
+Issues = "https://github.com/yourusername/fuel-cycle-sim/issues"
+
+[tool.setuptools]
+packages = ["fuel_cycle_sim"]
+package-dir = {"fuel_cycle_sim" = "src/python"}
+
+[tool.setuptools_scm]
+write_to = "src/python/_version.py"
+
+[tool.setuptools.package-data]
+fuel_cycle_sim = ["templates/*"]

requirements.txt

@@ -1,15 +1,7 @@
-blinker==1.9.0
-click==8.2.1
-Flask==3.1.1
-flask-cors==6.0.1
-itsdangerous==2.2.0
-Jinja2==3.1.6
-MarkupSafe==3.0.2
-Werkzeug==3.1.3
-pathsim==0.7.0
-matplotlib==3.7.0
-numpy==1.24.0
-plotly~=6.0
-pytest
+# Web application dependencies (not needed for core package)
+Flask>=3.1.1
+flask-cors>=6.0.1
+
+# Development dependencies
 sphinx>=4.0.0
-docutils>=0.17.0
+docutils>=0.17.0

src/App.jsx

@@ -11,17 +11,16 @@
   useEdgesState,
 } from '@xyflow/react';
 import '@xyflow/react/dist/style.css';
-import './App.css';
+import './styles/App.css';
 import Plot from 'react-plotly.js';
 import { getApiEndpoint } from './config.js';
-import Sidebar from './Sidebar';
-import NodeSidebar from './NodeSidebar';
-import { DnDProvider, useDnD } from './DnDContext.jsx';
-import ContextMenu from './ContextMenu.jsx';
-import EventsTab from './EventsTab.jsx';
-import GlobalVariablesTab from './GlobalVariablesTab.jsx';
-import { isValidPythonIdentifier } from './utils.js';
-import { makeEdge } from './CustomEdge';
+import Sidebar from './components/Sidebar';
+import NodeSidebar from './components/NodeSidebar';
+import { DnDProvider, useDnD } from './components/DnDContext.jsx';
+import ContextMenu from './components/ContextMenu.jsx';
+import EventsTab from './components/EventsTab.jsx';
+import GlobalVariablesTab from './components/GlobalVariablesTab.jsx';
+import { makeEdge } from './components/CustomEdge';
 import { nodeTypes } from './nodeConfig.js';
 
 // * Declaring variables *
@@ -59,7 +58,7 @@
   }, []);
 
   const onDragStart = (event, nodeType) => {
     setType(nodeType);
     event.dataTransfer.setData('text/plain', nodeType);
     event.dataTransfer.effectAllowed = 'move';
   };
@@ -216,7 +215,7 @@
       setNodes((nds) => [...nds, newNode]);
       setNodeCounter((count) => count + 1);
     },
     [screenToFlowPosition, type, nodeCounter, fetchDefaultValues, setDefaultValues, setNodes, setNodeCounter],
   );
 
   // Function to save a graph to computer with "Save As" dialog
@@ -898,7 +897,7 @@
     return () => {
       document.removeEventListener('keydown', handleKeyDown);
     };
   }, [selectedEdge, selectedNode, copiedNode, duplicateNode, setCopyFeedback]);
 
   return (
     <div style={{ width: '100vw', height: '100vh', display: 'flex', flexDirection: 'column' }}>

src/backend.py

@@ -11,8 +11,8 @@
 import io
 from contextlib import redirect_stdout, redirect_stderr
 
-from .convert_to_python import convert_graph_to_python
-from .pathsim_utils import make_pathsim_model, map_str_to_object
+from fuel_cycle_sim.convert_to_python import convert_graph_to_python
+from fuel_cycle_sim.pathsim_utils import make_pathsim_model, map_str_to_object
 from pathsim.blocks import Scope, Spectrum
 
 # Sphinx imports for docstring processing

src/GlobalVariablesTab.jsx → src/components/GlobalVariablesTab.jsx

@@ -1,8 +1,8 @@
-import { isValidPythonIdentifier } from './utils.js';
+import { isValidPythonIdentifier } from '../utils.js';
 
 
 import PythonCodeEditor from './PythonCodeEditor';
-import './PythonCodeEditor.css';
+import '../styles/PythonCodeEditor.css';
 
 export const IdeWithAutocomplete = ({ pythonCode, setPythonCode }) => {
   const handleCodeExecution = (result) => {

src/NodeSidebar.jsx → src/components/NodeSidebar.jsx

@@ -1,4 +1,4 @@
-import { isValidPythonIdentifier } from './utils.js';
+import { isValidPythonIdentifier } from '../utils.js';
 
 const makeVarName = (node) => {
   // Create a base variable name from the node label

src/PythonCodeEditor.jsx → src/components/PythonCodeEditor.jsx

@@ -2,7 +2,7 @@ import { useState, useCallback } from 'react';
 import CodeMirror from '@uiw/react-codemirror';
 import { vscodeDark } from '@uiw/codemirror-theme-vscode';
 import { python } from '@codemirror/lang-python';
-import { getApiEndpoint } from './config.js';
+import { getApiEndpoint } from '../config.js';
 
 
 const PythonCodeEditor = ({ 

src/Sidebar.jsx → src/components/Sidebar.jsx

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import { useDnD } from './DnDContext';
-import { nodeCategories, getNodeDisplayName } from './nodeConfig.js';
+import { nodeCategories, getNodeDisplayName } from '../nodeConfig.js';
 
 export default () => {
   const [_, setType] = useDnD();
   const [expandedCategories, setExpandedCategories] = useState({
     'Sources': true,

src/main.jsx

@@ -1,6 +1,6 @@
 import { StrictMode } from 'react'
 import { createRoot } from 'react-dom/client'
-import './index.css'
+import './styles/index.css'
 import { App } from './App.jsx'
 
 createRoot(document.getElementById('root')).render(

src/nodeConfig.js

@@ -1,18 +1,18 @@
 // Node type definitions and categorization
-import { ProcessNode, ProcessNodeHorizontal } from './ProcessNode';
-import DelayNode from './DelayNode';
-import SourceNode from './ConstantNode';
-import { AmplifierNode, AmplifierNodeReverse } from './AmplifierNode';
-import IntegratorNode from './IntegratorNode';
-import AdderNode from './AdderNode';
-import ScopeNode from './ScopeNode';
-import StepSourceNode from './StepSourceNode';
-import {createFunctionNode} from './FunctionNode';
-import DefaultNode from './DefaultNode';
-import MultiplierNode from './MultiplierNode';
-import { Splitter2Node, Splitter3Node } from './Splitters';
-import BubblerNode from './BubblerNode';
-import WallNode from './WallNode';
+import { ProcessNode, ProcessNodeHorizontal } from './components/nodes/ProcessNode';
+import DelayNode from './components/nodes/DelayNode';
+import SourceNode from './components/nodes/ConstantNode';
+import { AmplifierNode, AmplifierNodeReverse } from './components/nodes/AmplifierNode';
+import IntegratorNode from './components/nodes/IntegratorNode';
+import AdderNode from './components/nodes/AdderNode';
+import ScopeNode from './components/nodes/ScopeNode';
+import StepSourceNode from './components/nodes/StepSourceNode';
+import {createFunctionNode} from './components/nodes/FunctionNode';
+import DefaultNode from './components/nodes/DefaultNode';
+import MultiplierNode from './components/nodes/MultiplierNode';
+import { Splitter2Node, Splitter3Node } from './components/nodes/Splitters';
+import BubblerNode from './components/nodes/BubblerNode';
+import WallNode from './components/nodes/WallNode';
 
 // Node types mapping
 export const nodeTypes = {

src/python/__init__.py

@@ -0,0 +1,23 @@
+"""
+Fuel Cycle Simulation Package
+
+A Python package for fuel cycle simulation with pathsim integration.
+"""
+
+from importlib import metadata
+
+try:
+    __version__ = metadata.version("fuel_cycle_sim")
+except Exception:
+    __version__ = "unknown"
+
+# Import main functions for easy access
+from .pathsim_utils import make_pathsim_model, map_str_to_object
+from .convert_to_python import convert_graph_to_python
+
+# Define what gets exported when someone does "from python import *"
+__all__ = [
+    "make_pathsim_model",
+    "map_str_to_object",
+    "convert_graph_to_python",
+]

src/templates/template_with_macros.py → src/python/templates/template_with_macros.py

@@ -2,7 +2,7 @@
 from pathsim import Simulation, Connection
 import numpy as np
 import matplotlib.pyplot as plt
-import src
+import fuel_cycle_sim
 {# Import macros #}
 {% from 'block_macros.py' import create_block, create_integrator_block, create_bubbler_block, create_connections, create_event -%}
 

test/test_backend.py

@@ -1,5 +1,11 @@
-from src.pathsim_utils import auto_block_construction, make_connections
-from src.custom_pathsim_blocks import Process, Splitter2, Splitter3, Bubbler, Integrator
+from fuel_cycle_sim.pathsim_utils import auto_block_construction, make_connections
+from fuel_cycle_sim.custom_pathsim_blocks import (
+    Process,
+    Splitter2,
+    Splitter3,
+    Bubbler,
+    Integrator,
+)
 
 import pathsim.blocks
 

test/test_convert_python.py

@@ -1,4 +1,4 @@
-from src.convert_to_python import convert_graph_to_python
+from fuel_cycle_sim import convert_graph_to_python
 import json
 import pytest
 from pathlib import Path

test/test_custom_blocks.py

@@ -1,6 +1,6 @@
 import pathsim.blocks
 from pathsim import Simulation, Connection
-from src.custom_pathsim_blocks import Bubbler
+from fuel_cycle_sim.custom_pathsim_blocks import Bubbler
 
 
 def test_bubbler():

test/test_events.py

@@ -1,5 +1,5 @@
 import pytest
-from src.pathsim_utils import make_events
+from fuel_cycle_sim.pathsim_utils import make_events
 
 
 events_data = [

test/test_examples.py

@@ -1,4 +1,4 @@
-from src.pathsim_utils import make_pathsim_model
+from fuel_cycle_sim.pathsim_utils import make_pathsim_model
 import json
 
 import pytest