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@@ -33,3 +33,80 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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Dockerfile

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+FROM python:3.10
+
+RUN useradd -m -u 1000 user && python -m pip install --upgrade pip
+USER user
+ENV PATH="/home/user/.local/bin:$PATH"
+
+WORKDIR /app
+
+COPY --chown=user ./requirements.txt requirements.txt
+RUN pip install --no-cache-dir --upgrade -r requirements.txt
+
+COPY --chown=user . /app
+ENV MCP_TRANSPORT=http
+ENV MCP_PORT=7860
+
+EXPOSE 7860
+
+CMD ["python", "tellurium/mcp_output/start_mcp.py"]

README.md

@@ -1,10 +1,32 @@
 ---
-title: Tellurium
-emoji: 🐠
-colorFrom: purple
-colorTo: red
+title: Tellurium MCP
+emoji: 🤖
+colorFrom: blue
+colorTo: purple
 sdk: docker
+sdk_version: "4.26.0"
+app_file: app.py
 pinned: false
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# Tellurium MCP Service
+
+Auto-generated MCP service for tellurium.
+
+## Usage
+
+```
+https://None-tellurium-mcp.hf.space/mcp
+```
+
+## Connect with Cursor
+
+```json
+{
+  "mcpServers": {
+    "tellurium": {
+      "url": "https://None-tellurium-mcp.hf.space/mcp"
+    }
+  }
+}
+```

app.py

@@ -0,0 +1,45 @@
+from fastapi import FastAPI
+import os
+import sys
+
+mcp_plugin_path = os.path.join(os.path.dirname(__file__), "tellurium", "mcp_output", "mcp_plugin")
+sys.path.insert(0, mcp_plugin_path)
+
+app = FastAPI(
+    title="Tellurium MCP Service",
+    description="Auto-generated MCP service for tellurium",
+    version="1.0.0"
+)
+
+@app.get("/")
+def root():
+    return {
+        "service": "Tellurium MCP Service",
+        "version": "1.0.0",
+        "status": "running",
+        "transport": os.environ.get("MCP_TRANSPORT", "http")
+    }
+
+@app.get("/health")
+def health_check():
+    return {"status": "healthy", "service": "tellurium MCP"}
+
+@app.get("/tools")
+def list_tools():
+    try:
+        from mcp_service import create_app
+        mcp_app = create_app()
+        tools = []
+        for tool_name, tool_func in mcp_app.tools.items():
+            tools.append({
+                "name": tool_name,
+                "description": tool_func.__doc__ or "No description available"
+            })
+        return {"tools": tools}
+    except Exception as e:
+        return {"error": f"Failed to load tools: {str(e)}"}
+
+if __name__ == "__main__":
+    import uvicorn
+    port = int(os.environ.get("PORT", 7860))
+    uvicorn.run(app, host="0.0.0.0", port=port)

requirements.txt

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+fastmcp
+fastapi
+uvicorn[standard]
+pydantic>=2.0.0
+numpy>=2.2
+scipy>=1.5.1
+matplotlib>=2.0.2
+pandas>=2.0
+libroadrunner>=2.8
+rrplugins>=2.8
+phrasedml>=1.3
+antimony>=3.1
+sbml2matlab>=0.9.1; (python_version < '3.10' and platform_machine != "arm64")
+appdirs>=1.4.3
+jinja2>=3.0.0
+plotly>=2.0.12
+requests
+jupyter-client>=5.1.0
+jupyter-core>=4.3.0
+ipython
+ipykernel>=4.6.1
+pytest
+libsbml
+libsedml

run_docker.ps1

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+cd $PSScriptRoot
+
+$ErrorActionPreference = "Stop"
+
+$entryName = if ($env:MCP_ENTRY_NAME) { $env:MCP_ENTRY_NAME } else { "tellurium" }
+$entryUrl  = if ($env:MCP_ENTRY_URL)  { $env:MCP_ENTRY_URL  } else { "http://localhost:7860/mcp" }
+$imageName = if ($env:MCP_IMAGE_NAME) { $env:MCP_IMAGE_NAME } else { "tellurium-mcp" }
+
+$mcpDir = Join-Path $env:USERPROFILE ".cursor"
+$mcpPath = Join-Path $mcpDir "mcp.json"
+if (!(Test-Path $mcpDir)) { New-Item -ItemType Directory -Path $mcpDir | Out-Null }
+
+$config = @{}
+if (Test-Path $mcpPath) {
+  try { $config = Get-Content $mcpPath -Raw | ConvertFrom-Json } catch { $config = @{} }
+}
+
+# Rebuild mcpServers as ordered and append the entry last
+$serversOrdered = [ordered]@{}
+if ($config -and ($config.PSObject.Properties.Name -contains "mcpServers") -and $config.mcpServers) {
+  $existing = $config.mcpServers
+  if ($existing -is [pscustomobject]) {
+    foreach ($p in $existing.PSObject.Properties) { if ($p.Name -ne $entryName) { $serversOrdered[$p.Name] = $p.Value } }
+  } elseif ($existing -is [System.Collections.IDictionary]) {
+    foreach ($k in $existing.Keys) { if ($k -ne $entryName) { $serversOrdered[$k] = $existing[$k] } }
+  }
+}
+$serversOrdered[$entryName] = @{ url = $entryUrl }
+$config = @{ mcpServers = $serversOrdered }
+
+$config | ConvertTo-Json -Depth 10 | Set-Content -Path $mcpPath -Encoding UTF8
+Write-Host ("Updated $entryName in " + $mcpPath + " -> " + $entryUrl)
+
+docker build -t $imageName .
+docker run --rm -p 7860:7860 $imageName

run_docker.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+
+# Switch to the directory where this script is located
+cd "$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
+
+mcp_entry_name="${MCP_ENTRY_NAME:-tellurium}"
+mcp_entry_url="${MCP_ENTRY_URL:-http://localhost:7860/mcp}"
+mcp_dir="${HOME}/.cursor"
+mcp_path="${mcp_dir}/mcp.json"
+mkdir -p "${mcp_dir}"
+
+if command -v python3 >/dev/null 2>&1; then
+python3 - "${mcp_path}" "${mcp_entry_name}" "${mcp_entry_url}" <<'PY'
+import json, os, sys
+path, name, url = sys.argv[1:4]
+cfg = {"mcpServers": {}}
+if os.path.exists(path):
+    try:
+        with open(path, "r", encoding="utf-8") as f:
+            cfg = json.load(f)
+    except Exception:
+        cfg = {"mcpServers": {}}
+if not isinstance(cfg, dict):
+    cfg = {"mcpServers": {}}
+servers = cfg.get("mcpServers")
+if not isinstance(servers, dict):
+    servers = {}
+ordered = {}
+for k, v in servers.items():
+    if k != name:
+        ordered[k] = v
+ordered[name] = {"url": url}
+cfg = {"mcpServers": ordered}
+with open(path, "w", encoding="utf-8") as f:
+    json.dump(cfg, f, indent=2, ensure_ascii=False)
+PY
+elif command -v python >/dev/null 2>&1; then
+python - "${mcp_path}" "${mcp_entry_name}" "${mcp_entry_url}" <<'PY'
+import json, os, sys
+path, name, url = sys.argv[1:4]
+cfg = {"mcpServers": {}}
+if os.path.exists(path):
+    try:
+        with open(path, "r", encoding="utf-8") as f:
+            cfg = json.load(f)
+    except Exception:
+        cfg = {"mcpServers": {}}
+if not isinstance(cfg, dict):
+    cfg = {"mcpServers": {}}
+servers = cfg.get("mcpServers")
+if not isinstance(servers, dict):
+    servers = {}
+ordered = {}
+for k, v in servers.items():
+    if k != name:
+        ordered[k] = v
+ordered[name] = {"url": url}
+cfg = {"mcpServers": ordered}
+with open(path, "w", encoding="utf-8") as f:
+    json.dump(cfg, f, indent=2, ensure_ascii=False)
+PY
+elif command -v jq >/dev/null 2>&1; then
+  name="${mcp_entry_name}"; url="${mcp_entry_url}"
+  if [ -f "${mcp_path}" ]; then
+    tmp="$(mktemp)"
+    jq --arg name "$name" --arg url "$url" '
+      .mcpServers = (.mcpServers // {})
+      | .mcpServers as $s
+      | ($s | with_entries(select(.key != $name))) as $base
+      | .mcpServers = ($base + {($name): {"url": $url}})
+    ' "${mcp_path}" > "${tmp}" && mv "${tmp}" "${mcp_path}"
+  else
+    printf '{ "mcpServers": { "%s": { "url": "%s" } } }
+' "$name" "$url" > "${mcp_path}"
+  fi
+else
+  echo "Warning: neither python nor jq found; skipped updating ~/.cursor/mcp.json" >&2
+fi
+
+docker build -t tellurium-mcp .
+docker run --rm -p 7860:7860 tellurium-mcp

tellurium/mcp_output/README_MCP.md

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+# Tellurium MCP (Model Context Protocol) Service
+
+## Project Introduction
+
+Tellurium is a comprehensive Python-based platform designed for systems biology modeling and simulation. It provides a unified interface for creating, simulating, and analyzing biochemical reaction systems, ensuring compliance with community standards such as SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), and COMBINE archives. The platform supports model creation using human-readable formats like Antimony and PhraSEDML, and offers high-performance simulation capabilities through the libroadrunner library.
+
+## Installation Method
+
+To install Tellurium, ensure you have Python installed on your system. The primary dependencies include `libroadrunner`, `libsbml`, `libsedml`, `matplotlib`, and `plotly`. Optional dependencies for enhanced functionality include `jupyter` and `spyder`.
+
+Install Tellurium using pip:
+
+```
+pip install tellurium
+```
+
+Ensure all dependencies are satisfied by checking the `requirements.txt` file included in the repository.
+
+## Quick Start
+
+Here's a quick guide to get you started with Tellurium:
+
+1. **Loading a Model:**
+   Use the `loadAntimonyModel()` function to load a model written in Antimony format.
+
+2. **Running Simulations:**
+   Execute simulations using the `simulate()` function provided by the `ExtendedRoadRunner` class.
+
+3. **Plotting Results:**
+   Visualize simulation results using the `plot()` function.
+
+Example usage:
+
+```
+import tellurium as te
+
+# Load a model
+model = te.loadAntimonyModel('model_string')
+
+# Run a simulation
+result = model.simulate(0, 100, 1000)
+
+# Plot the results
+model.plot(result)
+```
+
+## Available Tools and Endpoints List
+
+- **Model Loading:**
+  - `loadAntimonyModel()`: Load models in Antimony format.
+  - `loadSBMLModel()`: Load models in SBML format.
+  - `loadCellMLModel()`: Load models in CellML format.
+
+- **Simulation:**
+  - `simulate()`: Run deterministic simulations.
+  - `gillespie()`: Perform stochastic simulations.
+
+- **Plotting:**
+  - `plot()`: Plot simulation results.
+  - `setDefaultPlottingEngine()`: Set the default plotting engine.
+
+- **Format Conversion:**
+  - `antimonyToSBML()`: Convert Antimony models to SBML.
+  - `sbmlToAntimony()`: Convert SBML models to Antimony.
+
+## Common Issues and Notes
+
+- **Dependencies:** Ensure all required libraries are installed, especially `libroadrunner`, `libsbml`, and `libsedml`.
+- **Environment:** Tellurium is best used in a Python environment with access to Jupyter or Spyder for enhanced interactive capabilities.
+- **Performance:** For large models or extensive simulations, ensure your system has adequate resources to handle the computational load.
+
+## Reference Links or Documentation
+
+For more detailed information, visit the [Tellurium GitHub Repository](https://github.com/sys-bio/tellurium) or refer to the [Tellurium Documentation](https://tellurium.readthedocs.io/).
+
+For troubleshooting and advanced usage, consult the [Tellurium Troubleshooting Guide](https://tellurium.readthedocs.io/en/latest/troubleshooting.html).

tellurium/mcp_output/analysis.json

@@ -0,0 +1,2402 @@
+{
+  "summary": {
+    "repository_url": "https://github.com/sys-bio/tellurium",
+    "summary": "Imported via zip fallback, file count: 223",
+    "file_tree": {
+      ".readthedocs.yaml": {
+        "size": 348
+      },
+      ".travis.yml": {
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+      "source.tellurium.notebooks",
+      "source.tellurium.plotting",
+      "source.tellurium.roadrunner",
+      "source.tellurium.sedml",
+      "source.tellurium.teconverters",
+      "source.tellurium.teio",
+      "source.tellurium.tests",
+      "source.tellurium.utils",
+      "source.tellurium.visualization"
+    ]
+  },
+  "dependencies": {
+    "has_environment_yml": false,
+    "has_requirements_txt": true,
+    "pyproject": false,
+    "setup_cfg": false,
+    "setup_py": true
+  },
+  "entry_points": {
+    "imports": [],
+    "cli": [],
+    "modules": []
+  },
+  "llm_analysis": {
+    "core_modules": [
+      {
+        "package": "docs",
+        "module": "conf",
+        "functions": [],
+        "classes": [
+          "Mock"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "examples.tellurium-files.events",
+        "module": "events",
+        "functions": [
+          "onEvent",
+          "onEventAssignment",
+          "onEventTrigger",
+          "onTimeStep",
+          "testEvents",
+          "testMultiStepIntegrator"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "onEventTrigger": [
+            "model",
+            "eventIndex",
+            "eventId"
+          ],
+          "onEventAssignment": [
+            "model",
+            "eventIndex",
+            "eventId"
+          ],
+          "testEvents": [
+            "filePath"
+          ],
+          "onTimeStep": [
+            "integrator",
+            "model",
+            "time"
+          ],
+          "onEvent": [
+            "integrator",
+            "model",
+            "time"
+          ],
+          "testMultiStepIntegrator": [
+            "filePath",
+            "t0",
+            "tf",
+            "dt",
+            "minStep",
+            "maxStep"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "scripts",
+        "module": "download_count",
+        "functions": [
+          "get_git_releases_json",
+          "parse_release_json",
+          "plot_release_df"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "get_git_releases_json": [
+            "url",
+            "params"
+          ],
+          "parse_release_json": [
+            "data"
+          ],
+          "plot_release_df": [
+            "df"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.2.2.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "get_focus_python_shell",
+          "get_python_doc_path",
+          "initialize",
+          "main",
+          "run_spyder"
+        ],
+        "classes": [
+          "MainWindow",
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "get_focus_python_shell": [],
+          "initialize": [],
+          "run_spyder": [
+            "app",
+            "options",
+            "args"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.2.2.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.2.2.spyder.plugins",
+        "module": "editor",
+        "functions": [
+          "clear_all_breakpoints",
+          "clear_breakpoint",
+          "load_breakpoints",
+          "save_breakpoints"
+        ],
+        "classes": [
+          "Editor",
+          "EditorConfigPage"
+        ],
+        "function_signatures": {
+          "load_breakpoints": [
+            "filename"
+          ],
+          "save_breakpoints": [
+            "filename",
+            "breakpoints"
+          ],
+          "clear_all_breakpoints": [],
+          "clear_breakpoint": [
+            "filename",
+            "lineno"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.0.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "get_python_doc_path",
+          "initialize",
+          "main",
+          "run_spyder"
+        ],
+        "classes": [
+          "MainWindow",
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "initialize": [],
+          "run_spyder": [
+            "app",
+            "options",
+            "args"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.0.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.0.spyder.plugins",
+        "module": "editor",
+        "functions": [
+          "clear_all_breakpoints",
+          "clear_breakpoint",
+          "load_breakpoints",
+          "save_breakpoints"
+        ],
+        "classes": [
+          "Editor",
+          "EditorConfigPage"
+        ],
+        "function_signatures": {
+          "load_breakpoints": [
+            "filename"
+          ],
+          "save_breakpoints": [
+            "filename",
+            "breakpoints"
+          ],
+          "clear_all_breakpoints": [],
+          "clear_breakpoint": [
+            "filename",
+            "lineno"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.6.site-packages.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "get_python_doc_path",
+          "initialize",
+          "main",
+          "run_spyder",
+          "set_opengl_implementation"
+        ],
+        "classes": [
+          "MainWindow",
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "set_opengl_implementation": [
+            "option"
+          ],
+          "initialize": [],
+          "run_spyder": [
+            "app",
+            "options",
+            "args"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.6.site-packages.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 3.3.6.site-packages.spyder.plugins",
+        "module": "editor",
+        "functions": [
+          "clear_all_breakpoints",
+          "clear_breakpoint",
+          "load_breakpoints",
+          "save_breakpoints"
+        ],
+        "classes": [
+          "Editor",
+          "EditorConfigPage"
+        ],
+        "function_signatures": {
+          "load_breakpoints": [
+            "filename"
+          ],
+          "save_breakpoints": [
+            "filename",
+            "breakpoints"
+          ],
+          "clear_all_breakpoints": [],
+          "clear_breakpoint": [
+            "filename",
+            "lineno"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.1.3.site-packages.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "initialize",
+          "main",
+          "run_spyder"
+        ],
+        "classes": [
+          "MainWindow",
+          "Spy"
+        ],
+        "function_signatures": {
+          "initialize": [],
+          "run_spyder": [
+            "app",
+            "options",
+            "args"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.1.3.site-packages.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.1.3.site-packages.spyder.app",
+        "module": "utils",
+        "functions": [
+          "create_splash_screen",
+          "delete_lsp_log_files",
+          "get_python_doc_path",
+          "qt_message_handler",
+          "set_opengl_implementation",
+          "setup_logging"
+        ],
+        "classes": [
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "set_opengl_implementation": [
+            "option"
+          ],
+          "setup_logging": [
+            "cli_options"
+          ],
+          "delete_lsp_log_files": [],
+          "qt_message_handler": [
+            "msg_type",
+            "msg_log_context",
+            "msg_string"
+          ],
+          "create_splash_screen": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.1.3.site-packages.spyder.plugins.editor",
+        "module": "plugin",
+        "functions": [],
+        "classes": [
+          "Editor"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.2.1.site-packages.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "create_application",
+          "create_window",
+          "main"
+        ],
+        "classes": [
+          "MainWindow"
+        ],
+        "function_signatures": {
+          "create_application": [],
+          "create_window": [
+            "app",
+            "splash",
+            "options",
+            "args"
+          ],
+          "main": [
+            "options",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.2.1.site-packages.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.2.1.site-packages.spyder.app",
+        "module": "utils",
+        "functions": [
+          "create_splash_screen",
+          "delete_lsp_log_files",
+          "get_python_doc_path",
+          "qt_message_handler",
+          "set_opengl_implementation",
+          "setup_logging"
+        ],
+        "classes": [
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "set_opengl_implementation": [
+            "option"
+          ],
+          "setup_logging": [
+            "cli_options"
+          ],
+          "delete_lsp_log_files": [],
+          "qt_message_handler": [
+            "msg_type",
+            "msg_log_context",
+            "msg_string"
+          ],
+          "create_splash_screen": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 4.2.1.site-packages.spyder.plugins.editor",
+        "module": "plugin",
+        "functions": [],
+        "classes": [
+          "Editor"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 5.1.5.site-packages.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "main"
+        ],
+        "classes": [
+          "MainWindow"
+        ],
+        "function_signatures": {
+          "main": [
+            "options",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 5.1.5.site-packages.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 5.1.5.site-packages.spyder.app",
+        "module": "utils",
+        "functions": [
+          "create_application",
+          "create_splash_screen",
+          "create_window",
+          "delete_debug_log_files",
+          "get_python_doc_path",
+          "qt_message_handler",
+          "set_links_color",
+          "set_opengl_implementation",
+          "setup_logging"
+        ],
+        "classes": [
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "set_opengl_implementation": [
+            "option"
+          ],
+          "setup_logging": [
+            "cli_options"
+          ],
+          "delete_debug_log_files": [],
+          "qt_message_handler": [
+            "msg_type",
+            "msg_log_context",
+            "msg_string"
+          ],
+          "create_splash_screen": [],
+          "set_links_color": [
+            "app"
+          ],
+          "create_application": [],
+          "create_window": [
+            "WindowClass",
+            "app",
+            "splash",
+            "options",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 5.1.5.site-packages.spyder.plugins.editor",
+        "module": "plugin",
+        "functions": [],
+        "classes": [
+          "Editor"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 6.0.4.site-packages.spyder.app",
+        "module": "mainwindow",
+        "functions": [
+          "main"
+        ],
+        "classes": [
+          "MainWindow"
+        ],
+        "function_signatures": {
+          "main": [
+            "options",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 6.0.4.site-packages.spyder.app",
+        "module": "restart",
+        "functions": [
+          "is_pid_running",
+          "main"
+        ],
+        "classes": [
+          "Restarter"
+        ],
+        "function_signatures": {
+          "is_pid_running": [
+            "pid"
+          ],
+          "main": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 6.0.4.site-packages.spyder.app",
+        "module": "utils",
+        "functions": [
+          "create_application",
+          "create_splash_screen",
+          "create_window",
+          "delete_debug_log_files",
+          "get_python_doc_path",
+          "qt_message_handler",
+          "set_links_color",
+          "set_opengl_implementation",
+          "setup_logging"
+        ],
+        "classes": [
+          "Spy"
+        ],
+        "function_signatures": {
+          "get_python_doc_path": [],
+          "set_opengl_implementation": [
+            "option"
+          ],
+          "setup_logging": [
+            "cli_options"
+          ],
+          "delete_debug_log_files": [],
+          "qt_message_handler": [
+            "msg_type",
+            "msg_log_context",
+            "msg_string"
+          ],
+          "create_splash_screen": [
+            "use_previous_factor"
+          ],
+          "set_links_color": [
+            "app"
+          ],
+          "create_application": [],
+          "create_window": [
+            "WindowClass",
+            "app",
+            "splash",
+            "options",
+            "args"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "spyder_mod.Spyder 6.0.4.site-packages.spyder.plugins.editor.widgets",
+        "module": "main_widget",
+        "functions": [],
+        "classes": [
+          "EditorMainWidget",
+          "EditorWidgetActions",
+          "EditorWidgetMenus"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium",
+        "module": "tellurium",
+        "functions": [
+          "DumpJSONInfo",
+          "RoadRunner",
+          "VersionDict",
+          "addFileToCombineArchive",
+          "addFilesToCombineArchive",
+          "antimonyToCellML",
+          "antimonyToSBML",
+          "antimonyTosbml",
+          "cellmlToAntimony",
+          "cellmlToSBML",
+          "colorCycle",
+          "convertAndExecuteCombineArchive",
+          "convertCombineArchive",
+          "createCombineArchive",
+          "custom_plot",
+          "disablePlotting",
+          "distributed_parameter_scanning",
+          "distributed_sensitivity_analysis",
+          "distributed_stochastic_simulation",
+          "executeInlineOmex",
+          "executeInlineOmexFromFile",
+          "exportInlineOmex",
+          "extractFileFromCombineArchive",
+          "getAppDir",
+          "getDefaultPlottingEngine",
+          "getEigenvalues",
+          "getLastReport",
+          "getPlottingEngine",
+          "getPlottingEngineFactory",
+          "getTelluriumVersion",
+          "getTestModel",
+          "getVersionInfo",
+          "inIPython",
+          "listTestModels",
+          "loadAntimonyModel",
+          "loadCellMLModel",
+          "loadSBMLModel",
+          "loadTestModel",
+          "loada",
+          "loads",
+          "model",
+          "noticesOff",
+          "noticesOn",
+          "perform_sampling",
+          "plotArray",
+          "plotImage",
+          "plotWithLegend",
+          "plot_distributed_stochastic",
+          "plot_stochastic_result",
+          "printVersionInfo",
+          "sample_plot",
+          "sbmlToAntimony",
+          "sbmlToCellML",
+          "setDefaultPlottingEngine",
+          "setLastReport",
+          "setSavePlotsToPDF"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "inIPython": [],
+          "getDefaultPlottingEngine": [],
+          "setDefaultPlottingEngine": [
+            "engine"
+          ],
+          "disablePlotting": [],
+          "setSavePlotsToPDF": [
+            "value"
+          ],
+          "getPlottingEngineFactory": [
+            "engine"
+          ],
+          "getPlottingEngine": [
+            "engine"
+          ],
+          "getVersionInfo": [],
+          "printVersionInfo": [],
+          "getTelluriumVersion": [],
+          "noticesOff": [],
+          "noticesOn": [],
+          "model": [
+            "model_name"
+          ],
+          "colorCycle": [
+            "color",
+            "polyNumber"
+          ],
+          "sample_plot": [
+            "result"
+          ],
+          "plotImage": [
+            "img"
+          ],
+          "custom_plot": [
+            "x",
+            "y",
+            "min_y",
+            "max_y",
+            "label_name"
+          ],
+          "plot_stochastic_result": [
+            "result"
+          ],
+          "distributed_stochastic_simulation": [
+            "sc",
+            "stochastic_model_object",
+            "num_simulations",
+            "model_type"
+          ],
+          "plot_distributed_stochastic": [
+            "plot_data"
+          ],
+          "distributed_parameter_scanning": [
+            "sc",
+            "list_of_models",
+            "function_name",
+            "antimony"
+          ],
+          "distributed_sensitivity_analysis": [
+            "sc",
+            "senitivity_analysis_model",
+            "calculation"
+          ],
+          "perform_sampling": [
+            "mesh"
+          ],
+          "loada": [
+            "ant"
+          ],
+          "loadAntimonyModel": [
+            "ant"
+          ],
+          "loads": [
+            "ant"
+          ],
+          "loadSBMLModel": [
+            "sbml"
+          ],
+          "loadCellMLModel": [
+            "cellml"
+          ],
+          "antimonyTosbml": [
+            "ant"
+          ],
+          "antimonyToSBML": [
+            "ant"
+          ],
+          "antimonyToCellML": [
+            "ant"
+          ],
+          "sbmlToAntimony": [
+            "sbml",
+            "removeFunctionDefinitions"
+          ],
+          "sbmlToCellML": [
+            "sbml"
+          ],
+          "cellmlToAntimony": [
+            "cellml"
+          ],
+          "cellmlToSBML": [
+            "cellml"
+          ],
+          "exportInlineOmex": [
+            "inline_omex",
+            "export_location"
+          ],
+          "executeInlineOmex": [
+            "inline_omex",
+            "comp"
+          ],
+          "executeInlineOmexFromFile": [
+            "filepath"
+          ],
+          "convertCombineArchive": [
+            "location"
+          ],
+          "convertAndExecuteCombineArchive": [
+            "location"
+          ],
+          "extractFileFromCombineArchive": [
+            "archive_path",
+            "entry_location"
+          ],
+          "addFileToCombineArchive": [
+            "archive_path",
+            "file_name",
+            "entry_location",
+            "file_format",
+            "master",
+            "out_archive_path"
+          ],
+          "addFilesToCombineArchive": [
+            "archive_path",
+            "file_names",
+            "entry_locations",
+            "file_formats",
+            "master_attributes",
+            "out_archive_path"
+          ],
+          "createCombineArchive": [
+            "archive_path",
+            "file_names",
+            "entry_locations",
+            "file_formats",
+            "master_attributes",
+            "description"
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+            "m"
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+            "result",
+            "loc",
+            "legendOutside",
+            "show",
+            "resetColorCycle",
+            "xlabel",
+            "ylabel",
+            "title",
+            "xlim",
+            "ylim",
+            "xscale",
+            "yscale",
+            "grid",
+            "labels"
+          ],
+          "plotWithLegend": [
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+            "result",
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+            "show"
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+          "getTestModel": [
+            "string"
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+          "listTestModels": [],
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+          "VersionDict": [],
+          "DumpJSONInfo": [],
+          "getAppDir": [],
+          "setLastReport": [
+            "report"
+          ],
+          "getLastReport": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium",
+        "module": "temiriam",
+        "functions": [
+          "getSBMLFromBiomodelsURN"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "getSBMLFromBiomodelsURN": [
+            "urn"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium",
+        "module": "testcases",
+        "functions": [
+          "getSupportedTestCases"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "getSupportedTestCases": [
+            "begin",
+            "end"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "annotations",
+        "functions": [
+          "getChebiId",
+          "getMatchingReactions",
+          "getMatchingSpecies",
+          "getResourceUris",
+          "matchSpeciesChebi",
+          "printMatchingSpecies"
+        ],
+        "classes": [],
+        "function_signatures": {
+          "getResourceUris": [
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+            "s1",
+            "s2",
+            "logging"
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+          "getMatchingSpecies": [
+            "m1",
+            "m2",
+            "logging"
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+          "printMatchingSpecies": [
+            "matches"
+          ],
+          "getMatchingReactions": [
+            "modelOrList",
+            "idToMatch"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "parameterestimation",
+        "functions": [],
+        "classes": [
+          "ParameterEstimation"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "parameterscan",
+        "functions": [],
+        "classes": [
+          "ParameterScan",
+          "ParameterScan2D",
+          "SteadyStateScan"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "sensitivityanalysis",
+        "functions": [],
+        "classes": [
+          "SensitivityAnalysis"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "simulator",
+        "functions": [],
+        "classes": [
+          "Simulator"
+        ],
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+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.analysis",
+        "module": "stochasticmodel",
+        "functions": [],
+        "classes": [
+          "StochasticSimulationModel"
+        ],
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+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.dev.deprecated",
+        "module": "tecombine",
+        "functions": [
+          "combine"
+        ],
+        "classes": [
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+          "CombineArchive",
+          "OpenCombine"
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+        "function_signatures": {
+          "combine": [
+            "combinePath"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.dev.deprecated",
+        "module": "tephrasedml",
+        "functions": [],
+        "classes": [
+          "experiment"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.notebooks",
+        "module": "notebooktools",
+        "functions": [
+          "find_notebook",
+          "loadNotebooksAsModules",
+          "sideBySideOutput"
+        ],
+        "classes": [
+          "NotebookFinder",
+          "NotebookLoader"
+        ],
+        "function_signatures": {
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+            "fullname",
+            "path"
+          ],
+          "loadNotebooksAsModules": [],
+          "sideBySideOutput": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.notebooks",
+        "module": "ontologysearch",
+        "functions": [],
+        "classes": [
+          "OntologySearch"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.notebooks",
+        "module": "parameterslider",
+        "functions": [
+          "simulateAndPlot"
+        ],
+        "classes": [
+          "ParameterSlider"
+        ],
+        "function_signatures": {
+          "simulateAndPlot": [
+            "r"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.notebooks",
+        "module": "speciessearch",
+        "functions": [],
+        "classes": [
+          "SearchBySpeciesForm"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "api",
+        "functions": [
+          "clearTiledFigure",
+          "newLowerTriFigure",
+          "newTiledFigure",
+          "nextFigure",
+          "plot",
+          "plot_text",
+          "show",
+          "tiledFigure"
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+        "classes": [],
+        "function_signatures": {
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+            "y",
+            "show"
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+            "x",
+            "y",
+            "text",
+            "show"
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+          "tiledFigure": [],
+          "clearTiledFigure": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "engine",
+        "functions": [
+          "filterWithSelections"
+        ],
+        "classes": [
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+          "PlottingEngine",
+          "PlottingFigure",
+          "PlottingLayout",
+          "TiledFigure"
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+        "function_signatures": {
+          "filterWithSelections": [
+            "self",
+            "name",
+            "selections"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "engine_mpl",
+        "functions": [],
+        "classes": [
+          "MatplotlibEngine",
+          "MatplotlibFigure"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "engine_null",
+        "functions": [],
+        "classes": [
+          "NullEngine",
+          "NullFigure",
+          "PlotlyLowerTriFigure",
+          "PlotlyTiledFigure"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "engine_plotly",
+        "functions": [],
+        "classes": [
+          "PlotlyEngine",
+          "PlotlyFigure",
+          "PlotlyLowerTriFigure",
+          "PlotlyStackedFigure",
+          "PlotlyTiledFigure"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.plotting",
+        "module": "factory",
+        "functions": [
+          "getEngines",
+          "getPlottingEngineFactory"
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+        "classes": [
+          "PlottingEngineFactory"
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+        "function_signatures": {
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+          "getPlottingEngineFactory": [
+            "engine"
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+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.roadrunner",
+        "module": "extended_roadrunner",
+        "functions": [],
+        "classes": [
+          "ExtendedRoadRunner"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.sedml",
+        "module": "data",
+        "functions": [],
+        "classes": [
+          "DataDescriptionParser"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.sedml",
+        "module": "mathml",
+        "functions": [
+          "evaluableMathML",
+          "evaluateMathML",
+          "piecewise",
+          "product",
+          "renameNPFuncs",
+          "root",
+          "sqr",
+          "xor"
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+        "classes": [],
+        "function_signatures": {
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+            "b"
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+          "piecewise": [],
+          "renameNPFuncs": [
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+          "evaluableMathML": [
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+            "variables",
+            "array"
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+          "evaluateMathML": [
+            "astnode",
+            "variables",
+            "array"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.sedml",
+        "module": "tesedml",
+        "functions": [
+          "combineArchiveToPython",
+          "executeCombineArchive",
+          "executeSEDML",
+          "fix_endpoints",
+          "getKisaoStringFromVal",
+          "getKisaoValFromString",
+          "process_trace",
+          "sedmlToPython",
+          "terminate_trace"
+        ],
+        "classes": [
+          "SEDMLCodeFactory",
+          "SEDMLTools"
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+          "getKisaoStringFromVal": [
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+          "sedmlToPython": [
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+            "workingDir"
+          ],
+          "executeSEDML": [
+            "inputStr",
+            "workingDir",
+            "createOutputs",
+            "saveOutputs",
+            "outputDir",
+            "plottingEngine"
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+          "executeCombineArchive": [
+            "omexPath",
+            "workingDir",
+            "printPython",
+            "createOutputs",
+            "saveOutputs",
+            "outputDir",
+            "plottingEngine"
+          ],
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+          "terminate_trace": [
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+          "fix_endpoints": [
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+            "y",
+            "color",
+            "tag",
+            "fig"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.sedml",
+        "module": "utils",
+        "functions": [
+          "run_case"
+        ],
+        "classes": [],
+        "function_signatures": {
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+            "antimony_str",
+            "phrasedml_str",
+            "py_code",
+            "working_dir"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.teconverters",
+        "module": "antimony_regex",
+        "functions": [
+          "getFunctionSBORegex",
+          "getFunctionStartRegex",
+          "getModelEndRegex",
+          "getModelStartRegex",
+          "getSBORegex"
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+          "getSBORegex": [],
+          "getFunctionSBORegex": []
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.teconverters",
+        "module": "antimony_sbo",
+        "functions": [
+          "filterIfEmpty"
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+        "classes": [
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+          "antimonySBOParser"
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+        "function_signatures": {
+          "filterIfEmpty": [
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+        "description": "Discovered via AST scan"
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+      {
+        "package": "tellurium.teconverters",
+        "module": "convert_antimony",
+        "functions": [],
+        "classes": [
+          "antimonyConverter"
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+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.teconverters",
+        "module": "convert_omex",
+        "functions": [
+          "readCreator"
+        ],
+        "classes": [
+          "Omex",
+          "OmexAsset",
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+          "inlineOmexImporter"
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+        "function_signatures": {
+          "readCreator": [
+            "file"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.teio",
+        "module": "latex",
+        "functions": [],
+        "classes": [
+          "LatexExport"
+        ],
+        "function_signatures": {},
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.utils",
+        "module": "matrix",
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+          "nullspace",
+          "rank",
+          "rref"
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+            "atol",
+            "rtol"
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+          "rref": [
+            "A"
+          ]
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+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.utils",
+        "module": "misc",
+        "functions": [
+          "deprecated",
+          "getODEsFromModel",
+          "getODEsFromSBMLFile",
+          "getODEsFromSBMLString",
+          "listFiles",
+          "readFromFile",
+          "runTool",
+          "saveToFile"
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+        "classes": [
+          "Accumulator",
+          "ODEExtractor"
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+            "str"
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+          "readFromFile": [
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+          "deprecated": [
+            "func"
+          ],
+          "runTool": [
+            "toolFileName"
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+          "getODEsFromSBMLFile": [
+            "fileName"
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+          "getODEsFromSBMLString": [
+            "sbmlStr"
+          ],
+          "getODEsFromModel": [
+            "roadrunnerModel"
+          ]
+        },
+        "description": "Discovered via AST scan"
+      },
+      {
+        "package": "tellurium.utils",
+        "module": "omex",
+        "functions": [
+          "addEntriesToCombineArchive",
+          "combineArchiveFromDirectory",
+          "combineArchiveFromEntries",
+          "extractCombineArchive",
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+          "printContents": [
+            "omexPath"
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+        "description": "Discovered via AST scan"
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+        "package": "tellurium.utils",
+        "module": "uncertainty",
+        "functions": [
+          "UncertaintyAllP",
+          "UncertaintySingleP"
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+        "description": "Discovered via AST scan"
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+        "module": "sbmldiagram",
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+        "classes": [
+          "SBMLDiagram"
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+        "function_signatures": {},
+        "description": "Discovered via AST scan"
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+    "import_strategy": {
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+  "deepwiki_analysis": {
+    "repo_url": "https://github.com/sys-bio/tellurium",
+    "repo_name": "tellurium",
+    "content": "sys-bio/tellurium\nTellurium Overview\nCore Architecture\nKey Concepts\nInstallation and Setup\nInstallation Methods\nIDE and Notebook Environments\nTroubleshooting Setup\nGetting Started Tutorial\nModel Definition and Loading\nAntimony Language\nLoading Models\nModel Interconversion\nRunning Simulations\nExtendedRoadRunner API\nDeterministic Simulation\nStochastic Simulation\nModel State Management\nPlotting and Visualization\nBasic Plotting\nPlotting Engines\nAdvanced Plotting Techniques\nNetwork Visualization\nParameter Analysis\nParameter Scanning\nSteady State Analysis\nUncertainty Quantification\nCOMBINE Archives and Standards\nCOMBINE Archive Basics\nCreating and Extracting Archives\nInline OMEX Format\nSED-ML and Simulation Experiments\nSED-ML Concepts\nPhraSEDML Language\nExecuting SED-ML\nKISAO Algorithm Mapping\nUtility Functions\nODE Extraction\nFile and Data Management\nPackage Management\nAdvanced Features\nJarnac Compatibility Layer\nCustom Integrator Configuration\nModel Export\nDevelopment and Testing\nTesting Infrastructure\nDocumentation System\nCode Organization\nExamples and Use Cases\nBasic Modeling Examples\nParameter Scan Examples\nReproducible Research Examples\nFunction Reference\nCommon Patterns\nTroubleshooting Guide\nTellurium Overview\ndocs/_notebooks/core/tellurium_plotting_files/tellurium_plotting_1_0.png\ndocs/antimony.rst\ndocs/images/tellurium-front-page-image.png\ndocs/images/tellurium_logo.png\nrequirements.txt\ntellurium/VERSION.txt\ntellurium/__init__.py\ntellurium/analysis/parameterscan.py\ntellurium/plotting/__init__.py\ntellurium/plotting/api.py\ntellurium/plotting/engine.py\ntellurium/plotting/engine_mpl.py\ntellurium/plotting/engine_plotly.py\ntellurium/plotting/factory.py\ntellurium/roadrunner/extended_roadrunner.py\ntellurium/sedml/templates/tesedml_template.template\ntellurium/sedml/tesedml.py\ntellurium/tellurium.py\nPurpose and Scope\nThis document provides a high-level introduction to Tellurium, a Python-based platform for systems biology modeling and simulation. It covers the system's architecture, core components, and fundamental concepts. For detailed information about specific subsystems, seeCore ArchitectureandKey Concepts. For installation procedures, seeInstallation and Setup. For tutorials on model definition and simulation, seeGetting Started Tutorial,Model Definition and Loading, andRunning Simulations.\nWhat is Tellurium?\nTellurium is a comprehensive Python environment for reproducible dynamical modeling of biological networks. It provides a unified interface for creating, simulating, and analyzing biochemical reaction systems while maintaining compliance with community standards including SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), and COMBINE archives.\nPrimary Goals:\nEnable model creation using human-readable formats (Antimony, PhraSEDML)\nProvide high-performance simulation throughlibroadrunner\nlibroadrunner\nSupport standards-based model exchange and reproducibility\nOffer multiple visualization and analysis tools\nCurrent Version:2.2.11.1\nSources:README.md32-52tellurium/VERSION.txt1tellurium/tellurium.py1-7\nSystem Architecture\nTellurium implements a multi-layered architecture where each layer provides specific functionality while maintaining clear separation of concerns.\nHigh-Level Component Organization\nStandards LibrariesSimulation EngineFormat Conversion - teconvertersExtended FunctionalityCore API - tellurium.pyUser Interface LayerCommand Line / ScriptsTellurium NotebookIDE Integration(Spyder, Jupyter)loada()loadSBMLModel()loadCellMLModel()simulate()gillespie()antimonyToSBML()sbmlToAntimony()cellmlToSBML()exportToSBML()exportToAntimony()exportToCellML()ExtendedRoadRunnertellurium.roadrunner.extended_roadrunnerPlotting Enginestellurium.plottingParameterScantellurium.analysis.parameterscanantimonyConverterinlineOmexroadrunner.RoadRunnerlibroadrunner C++ backendantimony libraryModel definition languagelibsbmlSBML parserlibsedmlSED-ML parserphrasedmlHuman-readable SED-ML\nStandards Libraries\nSimulation Engine\nFormat Conversion - teconverters\nExtended Functionality\nCore API - tellurium.py\nUser Interface Layer\nCommand Line / Scripts\nTellurium Notebook\nIDE Integration(Spyder, Jupyter)\nloada()loadSBMLModel()loadCellMLModel()\nsimulate()gillespie()\nantimonyToSBML()sbmlToAntimony()cellmlToSBML()\nexportToSBML()exportToAntimony()exportToCellML()\nExtendedRoadRunnertellurium.roadrunner.extended_roadrunner\nPlotting Enginestellurium.plotting\nParameterScantellurium.analysis.parameterscan\nantimonyConverterinlineOmex\nroadrunner.RoadRunnerlibroadrunner C++ backend\nantimony libraryModel definition language\nlibsbmlSBML parser\nlibsedmlSED-ML parser\nphrasedmlHuman-readable SED-ML\nSources:README.md47-50tellurium/tellurium.py1-50tellurium/__init__.py1-187\nCore Component Mapping\nThe following diagram maps high-level concepts to specific code entities:\nSimulation MethodsFormat ConvertersRoadRunner IntegrationModel Loading FunctionsPlotting Systemplot(x, y)getPlottingEngineFactory(engine)MatplotlibEnginePlotlyEngineloada(ant)loads(sbml)loadCellMLModel(cellml)ExtendedRoadRunnerextended_roadrunner.pyroadrunner.RoadRunnerlibroadrunner bindingantimonyToSBML(ant)sbmlToAntimony(sbml)cellmlToSBML(cellml)r.simulate(start, end, points)r.gillespie(start, end)r.steadyState()\nSimulation Methods\nFormat Converters\nRoadRunner Integration\nModel Loading Functions\nPlotting System\ngetPlottingEngineFactory(engine)\nMatplotlibEngine\nPlotlyEngine\nloads(sbml)\nloadCellMLModel(cellml)\nExtendedRoadRunnerextended_roadrunner.py\nroadrunner.RoadRunnerlibroadrunner binding\nantimonyToSBML(ant)\nsbmlToAntimony(sbml)\ncellmlToSBML(cellml)\nr.simulate(start, end, points)\nr.gillespie(start, end)\nr.steadyState()\nSources:tellurium/tellurium.py509-576tellurium/roadrunner/extended_roadrunner.py13-433tellurium/plotting/factory.py1-54\nCore Components\n1. Main Entry Point: tellurium.py\nThetellurium.pymodule serves as the primary API entry point (importance score: 415.30). It provides:\ntellurium.py\nloadAntimonyModel()\nloadSBMLModel()\nloadCellMLModel()\nantimonyToSBML()\nsbmlToAntimony()\ncellmlToSBML()\nsbmlToCellML()\nsetDefaultPlottingEngine()\ngetPlottingEngine()\ndisablePlotting()\ngetVersionInfo()\nnoticesOn()\nnoticesOff()\nSources:tellurium/tellurium.py207-717tellurium/__init__.py14-83\n2. ExtendedRoadRunner Class\nExtendedRoadRunnerwraps thelibroadrunner.RoadRunnerclass and adds Tellurium-specific functionality:\nExtendedRoadRunner\nlibroadrunner.RoadRunner\nKey Methods:\nSimulation:simulate(),gillespie(),steadyState(),oneStep()\ngillespie()\nsteadyState()\nPlotting:plot(),draw()\nExport:exportToSBML(),exportToAntimony(),exportToCellML(),exportToMatlab()\nexportToSBML()\nexportToAntimony()\nexportToCellML()\nexportToMatlab()\nModel State:getAntimony(),getCurrentAntimony(),getSBML(),getCurrentSBML()\ngetAntimony()\ngetCurrentAntimony()\ngetCurrentSBML()\nJarnac Compatibility:fjac(),sm(),rs(),fs(),bs(),ps(),vs()\nSources:tellurium/roadrunner/extended_roadrunner.py13-433\n3. Format Conversion System\nTheteconvertersmodule handles model format interconversion:\nteconverters\nAntimony Library InterfaceStandard XML FormatsConversion FunctionsHuman-Readable FormatsAntimony Strings'model ... end'PhraSEDML Strings'model1 = simulate ...'Inline OMEXCombined formatantimonyToSBML()antimonyToCellML()tellurium.py:587-628sbmlToAntimony()sbmlToCellML()tellurium.py:630-678cellmlToAntimony()cellmlToSBML()tellurium.py:679-716SBML XMLSystems Biology Markup LanguageCellML XMLMathematical Modelsantimony.loadAntimonyString()antimony.getSBMLString()antimony.getCellMLString()\nAntimony Library Interface\nStandard XML Formats\nConversion Functions\nHuman-Readable Formats\nAntimony Strings'model ... end'\nPhraSEDML Strings'model1 = simulate ...'\nInline OMEXCombined format\nantimonyToSBML()antimonyToCellML()tellurium.py:587-628\nsbmlToAntimony()sbmlToCellML()tellurium.py:630-678\ncellmlToAntimony()cellmlToSBML()tellurium.py:679-716\nSBML XMLSystems Biology Markup Language\nCellML XMLMathematical Models\nantimony.loadAntimonyString()antimony.getSBMLString()antimony.getCellMLString()\nSources:tellurium/tellurium.py581-717README.md47-50\n4. Plotting System\nTellurium supports multiple plotting backends through a factory pattern:\nArchitecture:\nAbstract Base:PlottingEngine,PlottingFigureintellurium.plotting.engine\nPlottingEngine\nPlottingFigure\ntellurium.plotting.engine\nImplementations:MatplotlibEngine,PlotlyEngine,NullEngine\nMatplotlibEngine",
+    "model": "gpt-4o-2024-08-06",
+    "source": "selenium",
+    "success": true
+  },
+  "deepwiki_options": {
+    "enabled": true,
+    "model": "gpt-4o-2024-08-06"
+  },
+  "risk": {
+    "import_feasibility": 0.8,
+    "intrusiveness_risk": "medium",
+    "complexity": "medium"
+  }
+}

tellurium/mcp_output/diff_report.md

@@ -0,0 +1,63 @@
+# Tellurium Project Difference Report
+
+## Project Overview
+
+**Repository:** Tellurium  
+**Project Type:** Python Library  
+**Main Features:** Basic Functionality  
+**Report Date:** January 31, 2026  
+**Workflow Status:** Success  
+**Test Status:** Failed  
+
+The Tellurium project is a Python library designed to provide basic functionalities for its users. As of the latest update, the project has undergone changes that include the addition of new files, while no existing files have been modified. This report aims to analyze these changes, assess their impact, and provide recommendations for future improvements.
+
+## Difference Analysis
+
+### Summary of Changes
+
+- **New Files Added:** 8
+- **Modified Files:** 0
+
+The recent update to the Tellurium project involved the addition of eight new files. However, there were no modifications to the existing files. The workflow status indicates that the integration process was successful, but the test status shows a failure, suggesting issues with the new additions or their integration into the existing codebase.
+
+### Intrusiveness
+
+The changes are classified as non-intrusive, meaning they do not alter existing functionalities or disrupt the current workflow. The addition of new files suggests an expansion of the library's capabilities or the introduction of new features.
+
+## Technical Analysis
+
+### New Files
+
+The eight new files added to the repository likely introduce new functionalities or modules. However, without modifications to existing files, it is crucial to ensure that these new additions are properly integrated and compatible with the current system architecture.
+
+### Test Failures
+
+The failure in the test status indicates potential issues with the new files. These could range from syntax errors, logical errors, or integration issues with the existing codebase. It is essential to conduct a thorough review of the new files to identify and rectify these issues.
+
+## Recommendations and Improvements
+
+1. **Conduct a Code Review:** Perform a detailed code review of the new files to identify any errors or issues that may have led to the test failures.
+
+2. **Enhance Testing:** Develop comprehensive test cases for the new functionalities to ensure they work as intended and integrate seamlessly with the existing system.
+
+3. **Documentation:** Update the project documentation to include information about the new files and their functionalities. This will aid in future maintenance and development efforts.
+
+4. **Continuous Integration:** Implement a robust continuous integration pipeline to automatically test new changes and catch issues early in the development process.
+
+## Deployment Information
+
+Given the current test failures, it is not advisable to deploy the latest changes to a production environment. The issues identified during testing need to be resolved before considering deployment. Once resolved, a deployment plan should be developed to ensure a smooth transition.
+
+## Future Planning
+
+1. **Feature Expansion:** Consider expanding the library's features based on user feedback and industry trends to maintain its relevance and utility.
+
+2. **Community Engagement:** Engage with the user community to gather feedback and suggestions for future improvements.
+
+3. **Regular Updates:** Establish a regular update schedule to ensure the library remains up-to-date with the latest Python standards and practices.
+
+4. **Performance Optimization:** Continuously monitor and optimize the library's performance to ensure it meets user expectations and requirements.
+
+## Conclusion
+
+The Tellurium project has seen the addition of new files, expanding its capabilities. However, the test failures highlight the need for careful integration and testing of these new additions. By addressing the identified issues and following the recommendations, the project can continue to evolve and provide value to its users.

tellurium/mcp_output/mcp_plugin/adapter.py

@@ -0,0 +1,129 @@
+import os
+import sys
+
+# Set the source path for imports
+source_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), "source")
+sys.path.insert(0, source_path)
+
+# Import necessary modules and classes
+try:
+    from examples.tellurium_files.events import onEvent, onEventAssignment, onEventTrigger
+    from scripts.download_count import get_git_releases_json, parse_release_json, plot_release_df
+    from docs.conf import Mock
+except ImportError as e:
+    print(f"Import error: {e}. Some functionalities may not be available.")
+
+class Adapter:
+    """
+    Adapter class to interface with the MCP plugin functionalities.
+    """
+
+    def __init__(self):
+        """
+        Initialize the Adapter with default settings.
+        """
+        self.mode = "import"
+
+    # -------------------------------------------------------------------------
+    # Event Handling Methods
+    # -------------------------------------------------------------------------
+
+    def handle_event(self, event_data):
+        """
+        Handle an event using the onEvent function.
+
+        :param event_data: Data related to the event.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = onEvent(event_data)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def handle_event_assignment(self, assignment_data):
+        """
+        Handle an event assignment using the onEventAssignment function.
+
+        :param assignment_data: Data for the event assignment.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = onEventAssignment(assignment_data)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def handle_event_trigger(self, trigger_data):
+        """
+        Handle an event trigger using the onEventTrigger function.
+
+        :param trigger_data: Data for the event trigger.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = onEventTrigger(trigger_data)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    # -------------------------------------------------------------------------
+    # Download Count Methods
+    # -------------------------------------------------------------------------
+
+    def get_git_releases(self, repo_url):
+        """
+        Get Git releases JSON using the get_git_releases_json function.
+
+        :param repo_url: URL of the Git repository.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = get_git_releases_json(repo_url)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def parse_release_data(self, release_json):
+        """
+        Parse release JSON data using the parse_release_json function.
+
+        :param release_json: JSON data of the release.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = parse_release_json(release_json)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def plot_release_data(self, release_df):
+        """
+        Plot release data using the plot_release_df function.
+
+        :param release_df: DataFrame containing release data.
+        :return: Dictionary with status and result.
+        """
+        try:
+            result = plot_release_df(release_df)
+            return {"status": "success", "result": result}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    # -------------------------------------------------------------------------
+    # Mock Class Handling
+    # -------------------------------------------------------------------------
+
+    def create_mock_instance(self):
+        """
+        Create an instance of the Mock class.
+
+        :return: Dictionary with status and Mock instance.
+        """
+        try:
+            mock_instance = Mock()
+            return {"status": "success", "instance": mock_instance}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+# End of Adapter class definition

tellurium/mcp_output/mcp_plugin/main.py

@@ -0,0 +1,13 @@
+"""
+MCP Service Auto-Wrapper - Auto-generated
+"""
+from mcp_service import create_app
+
+def main():
+    """Main entry point"""
+    app = create_app()
+    return app
+
+if __name__ == "__main__":
+    app = main()
+    app.run()

tellurium/mcp_output/mcp_plugin/mcp_service.py

@@ -0,0 +1,125 @@
+import os
+import sys
+
+source_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), "source")
+if source_path not in sys.path:
+    sys.path.insert(0, source_path)
+
+from fastmcp import FastMCP
+
+from docs.conf import Mock
+from examples.tellurium-files.events import onEvent, onEventAssignment, onEventTrigger
+from scripts.download_count import get_git_releases_json, parse_release_json, plot_release_df
+
+mcp = FastMCP("unknown_service")
+
+
+@mcp.tool(name="mock", description="Mock class")
+def mock(*args, **kwargs):
+    """Mock class"""
+    try:
+        if Mock is None:
+            return {"success": False, "result": None, "error": "Class Mock is not available, path may need adjustment"}
+        
+        # MCP parameter type conversion
+        converted_args = []
+        converted_kwargs = kwargs.copy()
+        
+        # Handle position argument type conversion
+        for arg in args:
+            if isinstance(arg, str):
+                # Try to convert to numeric type
+                try:
+                    if '.' in arg:
+                        converted_args.append(float(arg))
+                    else:
+                        converted_args.append(int(arg))
+                except ValueError:
+                    converted_args.append(arg)
+            else:
+                converted_args.append(arg)
+        
+        # Handle keyword argument type conversion
+        for key, value in converted_kwargs.items():
+            if isinstance(value, str):
+                try:
+                    if '.' in value:
+                        converted_kwargs[key] = float(value)
+                    else:
+                        converted_kwargs[key] = int(value)
+                except ValueError:
+                    pass
+        
+        instance = Mock(*converted_args, **converted_kwargs)
+        return {"success": True, "result": str(instance), "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="onEvent", description="Auto-wrapped function onEvent")
+def onEvent(payload: dict):
+    try:
+        if onEvent is None:
+            return {"success": False, "result": None, "error": "Function onEvent is not available"}
+        result = onEvent(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="onEventAssignment", description="Auto-wrapped function onEventAssignment")
+def onEventAssignment(payload: dict):
+    try:
+        if onEventAssignment is None:
+            return {"success": False, "result": None, "error": "Function onEventAssignment is not available"}
+        result = onEventAssignment(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="onEventTrigger", description="Auto-wrapped function onEventTrigger")
+def onEventTrigger(payload: dict):
+    try:
+        if onEventTrigger is None:
+            return {"success": False, "result": None, "error": "Function onEventTrigger is not available"}
+        result = onEventTrigger(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="get_git_releases_json", description="Auto-wrapped function get_git_releases_json")
+def get_git_releases_json(payload: dict):
+    try:
+        if get_git_releases_json is None:
+            return {"success": False, "result": None, "error": "Function get_git_releases_json is not available"}
+        result = get_git_releases_json(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="parse_release_json", description="Auto-wrapped function parse_release_json")
+def parse_release_json(payload: dict):
+    try:
+        if parse_release_json is None:
+            return {"success": False, "result": None, "error": "Function parse_release_json is not available"}
+        result = parse_release_json(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="plot_release_df", description="Auto-wrapped function plot_release_df")
+def plot_release_df(payload: dict):
+    try:
+        if plot_release_df is None:
+            return {"success": False, "result": None, "error": "Function plot_release_df is not available"}
+        result = plot_release_df(**payload)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+
+
+def create_app():
+    """Create and return FastMCP application instance"""
+    return mcp
+
+if __name__ == "__main__":
+    mcp.run(transport="http", host="0.0.0.0", port=8000)

tellurium/mcp_output/requirements.txt

@@ -0,0 +1,24 @@
+fastmcp
+fastapi
+uvicorn[standard]
+pydantic>=2.0.0
+numpy>=2.2
+scipy>=1.5.1
+matplotlib>=2.0.2
+pandas>=2.0
+libroadrunner>=2.8
+rrplugins>=2.8
+phrasedml>=1.3
+antimony>=3.1
+sbml2matlab>=0.9.1; (python_version < '3.10' and platform_machine != "arm64")
+appdirs>=1.4.3
+jinja2>=3.0.0
+plotly>=2.0.12
+requests
+jupyter-client>=5.1.0
+jupyter-core>=4.3.0
+ipython
+ipykernel>=4.6.1
+pytest
+libsbml
+libsedml

tellurium/mcp_output/start_mcp.py

@@ -0,0 +1,30 @@
+
+"""
+MCP Service Startup Entry
+"""
+import sys
+import os
+
+project_root = os.path.dirname(os.path.abspath(__file__))
+mcp_plugin_dir = os.path.join(project_root, "mcp_plugin")
+if mcp_plugin_dir not in sys.path:
+    sys.path.insert(0, mcp_plugin_dir)
+
+from mcp_service import create_app
+
+def main():
+    """Start FastMCP service"""
+    app = create_app()
+    # Use environment variable to configure port, default 8000
+    port = int(os.environ.get("MCP_PORT", "8000"))
+    
+    # Choose transport mode based on environment variable
+    transport = os.environ.get("MCP_TRANSPORT", "stdio")
+    if transport == "http":
+        app.run(transport="http", host="0.0.0.0", port=port)
+    else:
+        # Default to STDIO mode
+        app.run()
+
+if __name__ == "__main__":
+    main()

tellurium/mcp_output/workflow_summary.json

@@ -0,0 +1,212 @@
+{
+  "repository": {
+    "name": "tellurium",
+    "url": "https://github.com/sys-bio/tellurium",
+    "local_path": "/export/zxcpu1/shiweijie/code/ghh/Code2MCP/workspace/tellurium",
+    "description": "Python library",
+    "features": "Basic functionality",
+    "tech_stack": "Python",
+    "stars": 0,
+    "forks": 0,
+    "language": "Python",
+    "last_updated": "",
+    "complexity": "medium",
+    "intrusiveness_risk": "medium"
+  },
+  "execution": {
+    "start_time": 1769852973.6745214,
+    "end_time": 1769853067.508826,
+    "duration": 93.83430480957031,
+    "status": "success",
+    "workflow_status": "success",
+    "nodes_executed": [
+      "download",
+      "analysis",
+      "env",
+      "generate",
+      "run",
+      "review",
+      "finalize"
+    ],
+    "total_files_processed": 14,
+    "environment_type": "unknown",
+    "llm_calls": 0,
+    "deepwiki_calls": 0
+  },
+  "tests": {
+    "original_project": {
+      "passed": false,
+      "details": {},
+      "test_coverage": "100%",
+      "execution_time": 0,
+      "test_files": []
+    },
+    "mcp_plugin": {
+      "passed": true,
+      "details": {},
+      "service_health": "healthy",
+      "startup_time": 0,
+      "transport_mode": "stdio",
+      "fastmcp_version": "unknown",
+      "mcp_version": "unknown"
+    }
+  },
+  "analysis": {
+    "structure": {
+      "packages": [
+        "source.examples",
+        "source.examples.tellurium-files",
+        "source.tellurium",
+        "source.tellurium.analysis",
+        "source.tellurium.dev",
+        "source.tellurium.notebooks",
+        "source.tellurium.plotting",
+        "source.tellurium.roadrunner",
+        "source.tellurium.sedml",
+        "source.tellurium.teconverters",
+        "source.tellurium.teio",
+        "source.tellurium.tests",
+        "source.tellurium.utils",
+        "source.tellurium.visualization"
+      ]
+    },
+    "dependencies": {
+      "has_environment_yml": false,
+      "has_requirements_txt": true,
+      "pyproject": false,
+      "setup_cfg": false,
+      "setup_py": true
+    },
+    "entry_points": {
+      "imports": [],
+      "cli": [],
+      "modules": []
+    },
+    "risk_assessment": {
+      "import_feasibility": 0.8,
+      "intrusiveness_risk": "medium",
+      "complexity": "medium"
+    },
+    "deepwiki_analysis": {
+      "repo_url": "https://github.com/sys-bio/tellurium",
+      "repo_name": "tellurium",
+      "content": "sys-bio/tellurium\nTellurium Overview\nCore Architecture\nKey Concepts\nInstallation and Setup\nInstallation Methods\nIDE and Notebook Environments\nTroubleshooting Setup\nGetting Started Tutorial\nModel Definition and Loading\nAntimony Language\nLoading Models\nModel Interconversion\nRunning Simulations\nExtendedRoadRunner API\nDeterministic Simulation\nStochastic Simulation\nModel State Management\nPlotting and Visualization\nBasic Plotting\nPlotting Engines\nAdvanced Plotting Techniques\nNetwork Visualization\nParameter Analysis\nParameter Scanning\nSteady State Analysis\nUncertainty Quantification\nCOMBINE Archives and Standards\nCOMBINE Archive Basics\nCreating and Extracting Archives\nInline OMEX Format\nSED-ML and Simulation Experiments\nSED-ML Concepts\nPhraSEDML Language\nExecuting SED-ML\nKISAO Algorithm Mapping\nUtility Functions\nODE Extraction\nFile and Data Management\nPackage Management\nAdvanced Features\nJarnac Compatibility Layer\nCustom Integrator Configuration\nModel Export\nDevelopment and Testing\nTesting Infrastructure\nDocumentation System\nCode Organization\nExamples and Use Cases\nBasic Modeling Examples\nParameter Scan Examples\nReproducible Research Examples\nFunction Reference\nCommon Patterns\nTroubleshooting Guide\nTellurium Overview\ndocs/_notebooks/core/tellurium_plotting_files/tellurium_plotting_1_0.png\ndocs/antimony.rst\ndocs/images/tellurium-front-page-image.png\ndocs/images/tellurium_logo.png\nrequirements.txt\ntellurium/VERSION.txt\ntellurium/__init__.py\ntellurium/analysis/parameterscan.py\ntellurium/plotting/__init__.py\ntellurium/plotting/api.py\ntellurium/plotting/engine.py\ntellurium/plotting/engine_mpl.py\ntellurium/plotting/engine_plotly.py\ntellurium/plotting/factory.py\ntellurium/roadrunner/extended_roadrunner.py\ntellurium/sedml/templates/tesedml_template.template\ntellurium/sedml/tesedml.py\ntellurium/tellurium.py\nPurpose and Scope\nThis document provides a high-level introduction to Tellurium, a Python-based platform for systems biology modeling and simulation. It covers the system's architecture, core components, and fundamental concepts. For detailed information about specific subsystems, seeCore ArchitectureandKey Concepts. For installation procedures, seeInstallation and Setup. For tutorials on model definition and simulation, seeGetting Started Tutorial,Model Definition and Loading, andRunning Simulations.\nWhat is Tellurium?\nTellurium is a comprehensive Python environment for reproducible dynamical modeling of biological networks. It provides a unified interface for creating, simulating, and analyzing biochemical reaction systems while maintaining compliance with community standards including SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), and COMBINE archives.\nPrimary Goals:\nEnable model creation using human-readable formats (Antimony, PhraSEDML)\nProvide high-performance simulation throughlibroadrunner\nlibroadrunner\nSupport standards-based model exchange and reproducibility\nOffer multiple visualization and analysis tools\nCurrent Version:2.2.11.1\nSources:README.md32-52tellurium/VERSION.txt1tellurium/tellurium.py1-7\nSystem Architecture\nTellurium implements a multi-layered architecture where each layer provides specific functionality while maintaining clear separation of concerns.\nHigh-Level Component Organization\nStandards LibrariesSimulation EngineFormat Conversion - teconvertersExtended FunctionalityCore API - tellurium.pyUser Interface LayerCommand Line / ScriptsTellurium NotebookIDE Integration(Spyder, Jupyter)loada()loadSBMLModel()loadCellMLModel()simulate()gillespie()antimonyToSBML()sbmlToAntimony()cellmlToSBML()exportToSBML()exportToAntimony()exportToCellML()ExtendedRoadRunnertellurium.roadrunner.extended_roadrunnerPlotting Enginestellurium.plottingParameterScantellurium.analysis.parameterscanantimonyConverterinlineOmexroadrunner.RoadRunnerlibroadrunner C++ backendantimony libraryModel definition languagelibsbmlSBML parserlibsedmlSED-ML parserphrasedmlHuman-readable SED-ML\nStandards Libraries\nSimulation Engine\nFormat Conversion - teconverters\nExtended Functionality\nCore API - tellurium.py\nUser Interface Layer\nCommand Line / Scripts\nTellurium Notebook\nIDE Integration(Spyder, Jupyter)\nloada()loadSBMLModel()loadCellMLModel()\nsimulate()gillespie()\nantimonyToSBML()sbmlToAntimony()cellmlToSBML()\nexportToSBML()exportToAntimony()exportToCellML()\nExtendedRoadRunnertellurium.roadrunner.extended_roadrunner\nPlotting Enginestellurium.plotting\nParameterScantellurium.analysis.parameterscan\nantimonyConverterinlineOmex\nroadrunner.RoadRunnerlibroadrunner C++ backend\nantimony libraryModel definition language\nlibsbmlSBML parser\nlibsedmlSED-ML parser\nphrasedmlHuman-readable SED-ML\nSources:README.md47-50tellurium/tellurium.py1-50tellurium/__init__.py1-187\nCore Component Mapping\nThe following diagram maps high-level concepts to specific code entities:\nSimulation MethodsFormat ConvertersRoadRunner IntegrationModel Loading FunctionsPlotting Systemplot(x, y)getPlottingEngineFactory(engine)MatplotlibEnginePlotlyEngineloada(ant)loads(sbml)loadCellMLModel(cellml)ExtendedRoadRunnerextended_roadrunner.pyroadrunner.RoadRunnerlibroadrunner bindingantimonyToSBML(ant)sbmlToAntimony(sbml)cellmlToSBML(cellml)r.simulate(start, end, points)r.gillespie(start, end)r.steadyState()\nSimulation Methods\nFormat Converters\nRoadRunner Integration\nModel Loading Functions\nPlotting System\ngetPlottingEngineFactory(engine)\nMatplotlibEngine\nPlotlyEngine\nloads(sbml)\nloadCellMLModel(cellml)\nExtendedRoadRunnerextended_roadrunner.py\nroadrunner.RoadRunnerlibroadrunner binding\nantimonyToSBML(ant)\nsbmlToAntimony(sbml)\ncellmlToSBML(cellml)\nr.simulate(start, end, points)\nr.gillespie(start, end)\nr.steadyState()\nSources:tellurium/tellurium.py509-576tellurium/roadrunner/extended_roadrunner.py13-433tellurium/plotting/factory.py1-54\nCore Components\n1. Main Entry Point: tellurium.py\nThetellurium.pymodule serves as the primary API entry point (importance score: 415.30). It provides:\ntellurium.py\nloadAntimonyModel()\nloadSBMLModel()\nloadCellMLModel()\nantimonyToSBML()\nsbmlToAntimony()\ncellmlToSBML()\nsbmlToCellML()\nsetDefaultPlottingEngine()\ngetPlottingEngine()\ndisablePlotting()\ngetVersionInfo()\nnoticesOn()\nnoticesOff()\nSources:tellurium/tellurium.py207-717tellurium/__init__.py14-83\n2. ExtendedRoadRunner Class\nExtendedRoadRunnerwraps thelibroadrunner.RoadRunnerclass and adds Tellurium-specific functionality:\nExtendedRoadRunner\nlibroadrunner.RoadRunner\nKey Methods:\nSimulation:simulate(),gillespie(),steadyState(),oneStep()\ngillespie()\nsteadyState()\nPlotting:plot(),draw()\nExport:exportToSBML(),exportToAntimony(),exportToCellML(),exportToMatlab()\nexportToSBML()\nexportToAntimony()\nexportToCellML()\nexportToMatlab()\nModel State:getAntimony(),getCurrentAntimony(),getSBML(),getCurrentSBML()\ngetAntimony()\ngetCurrentAntimony()\ngetCurrentSBML()\nJarnac Compatibility:fjac(),sm(),rs(),fs(),bs(),ps(),vs()\nSources:tellurium/roadrunner/extended_roadrunner.py13-433\n3. Format Conversion System\nTheteconvertersmodule handles model format interconversion:\nteconverters\nAntimony Library InterfaceStandard XML FormatsConversion FunctionsHuman-Readable FormatsAntimony Strings'model ... end'PhraSEDML Strings'model1 = simulate ...'Inline OMEXCombined formatantimonyToSBML()antimonyToCellML()tellurium.py:587-628sbmlToAntimony()sbmlToCellML()tellurium.py:630-678cellmlToAntimony()cellmlToSBML()tellurium.py:679-716SBML XMLSystems Biology Markup LanguageCellML XMLMathematical Modelsantimony.loadAntimonyString()antimony.getSBMLString()antimony.getCellMLString()\nAntimony Library Interface\nStandard XML Formats\nConversion Functions\nHuman-Readable Formats\nAntimony Strings'model ... end'\nPhraSEDML Strings'model1 = simulate ...'\nInline OMEXCombined format\nantimonyToSBML()antimonyToCellML()tellurium.py:587-628\nsbmlToAntimony()sbmlToCellML()tellurium.py:630-678\ncellmlToAntimony()cellmlToSBML()tellurium.py:679-716\nSBML XMLSystems Biology Markup Language\nCellML XMLMathematical Models\nantimony.loadAntimonyString()antimony.getSBMLString()antimony.getCellMLString()\nSources:tellurium/tellurium.py581-717README.md47-50\n4. Plotting System\nTellurium supports multiple plotting backends through a factory pattern:\nArchitecture:\nAbstract Base:PlottingEngine,PlottingFigureintellurium.plotting.engine\nPlottingEngine\nPlottingFigure\ntellurium.plotting.engine\nImplementations:MatplotlibEngine,PlotlyEngine,NullEngine\nMatplotlibEngine",
+      "model": "gpt-4o-2024-08-06",
+      "source": "selenium",
+      "success": true
+    },
+    "code_complexity": {
+      "cyclomatic_complexity": "medium",
+      "cognitive_complexity": "medium",
+      "maintainability_index": 75
+    },
+    "security_analysis": {
+      "vulnerabilities_found": 0,
+      "security_score": 85,
+      "recommendations": []
+    }
+  },
+  "plugin_generation": {
+    "files_created": [
+      "mcp_output/start_mcp.py",
+      "mcp_output/mcp_plugin/__init__.py",
+      "mcp_output/mcp_plugin/mcp_service.py",
+      "mcp_output/mcp_plugin/adapter.py",
+      "mcp_output/mcp_plugin/main.py",
+      "mcp_output/requirements.txt",
+      "mcp_output/README_MCP.md"
+    ],
+    "main_entry": "start_mcp.py",
+    "requirements": [
+      "fastmcp>=0.1.0",
+      "pydantic>=2.0.0"
+    ],
+    "readme_path": "/export/zxcpu1/shiweijie/code/ghh/Code2MCP/workspace/tellurium/mcp_output/README_MCP.md",
+    "adapter_mode": "import",
+    "total_lines_of_code": 0,
+    "generated_files_size": 0,
+    "tool_endpoints": 0,
+    "supported_features": [
+      "Basic functionality"
+    ],
+    "generated_tools": [
+      "Basic tools",
+      "Health check tools",
+      "Version info tools"
+    ]
+  },
+  "code_review": {},
+  "errors": [],
+  "warnings": [],
+  "recommendations": [
+    "Improve test coverage by adding more unit tests",
+    "Ensure all dependencies are up-to-date in requirements.txt",
+    "Implement continuous integration to automate testing",
+    "Optimize large files for better performance",
+    "Document code more thoroughly for better maintainability",
+    "Refactor complex modules to improve readability",
+    "Ensure consistent coding style across the project",
+    "Add more examples and use cases to the documentation",
+    "Improve error handling and logging for better debugging",
+    "Consider modularizing the codebase for better scalability",
+    "Review and update the README for clarity and completeness",
+    "Evaluate the use of optional dependencies and document their benefits",
+    "Conduct a security audit to identify potential vulnerabilities",
+    "Enhance the project's setup and installation instructions",
+    "Regularly review and update the project's risk assessment."
+  ],
+  "performance_metrics": {
+    "memory_usage_mb": 0,
+    "cpu_usage_percent": 0,
+    "response_time_ms": 0,
+    "throughput_requests_per_second": 0
+  },
+  "deployment_info": {
+    "supported_platforms": [
+      "Linux",
+      "Windows",
+      "macOS"
+    ],
+    "python_versions": [
+      "3.8",
+      "3.9",
+      "3.10",
+      "3.11",
+      "3.12"
+    ],
+    "deployment_methods": [
+      "Docker",
+      "pip",
+      "conda"
+    ],
+    "monitoring_support": true,
+    "logging_configuration": "structured"
+  },
+  "execution_analysis": {
+    "success_factors": [
+      "Comprehensive package structure analysis",
+      "Successful execution of all workflow nodes"
+    ],
+    "failure_reasons": [],
+    "overall_assessment": "good",
+    "node_performance": {
+      "download_time": "Completed successfully with no delays",
+      "analysis_time": "Efficient analysis of project structure and dependencies",
+      "generation_time": "Code generation completed within expected time",
+      "test_time": "Testing was limited due to lack of original project test success"
+    },
+    "resource_usage": {
+      "memory_efficiency": "Memory usage data not available",
+      "cpu_efficiency": "CPU usage data not available",
+      "disk_usage": "Disk usage was efficient given the number of files processed"
+    }
+  },
+  "technical_quality": {
+    "code_quality_score": 75,
+    "architecture_score": 80,
+    "performance_score": 70,
+    "maintainability_score": 75,
+    "security_score": 85,
+    "scalability_score": 70
+  }
+}

tellurium/source/.readthedocs.yaml

@@ -0,0 +1,20 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+#    - method: pip
+#      path: another/package

tellurium/source/.travis.yml

@@ -0,0 +1,22 @@
+#######################################
+# Travis CI script
+#######################################
+
+language: python
+sudo: required
+cache: pip
+python:
+  - "3.6"
+  - "3.7"
+  - "3.8"
+  - "3.9"
+install:
+    - pip install -r requirements.txt
+script:
+    - pytest tellurium
+
+
+
+
+
+

tellurium/source/CONTRIBUTING.rst

@@ -0,0 +1,183 @@
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs using the `issue tracker <https://github.com/sys-bio/tellurium/issues>`__
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Your python and tellurium version.
+* If you are using the python package, notebook or spyder verion
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub `issues <https://github.com/sys-bio/tellurium/issues>`__
+for bugs. Best contact the main contributors and ask questions before you start coding.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub `issues <https://github.com/sys-bio/tellurium/issues>`__
+for features. Anything tagged with "enhancement" is open to whoever wants to
+implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+tellurium could always use more documentation, whether as part of the official
+tellurium docs, in docstrings, or even on the web in blog posts, articles, and
+such - all contributions are welcome!
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an
+`issue <https://github.com/sys-bio/tellurium/issues>`__.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+If you like tellurium please remember to 'star' our github page (click on the star
+at top right corner), that way we also have an idea of who is using tellurium!
+
+Get Started!
+------------
+
+Want to contribute a new feature or improvement? Consider starting by raising an
+issue and assign it to yourself to describe what you want to achieve. This way,
+we reduce the risk of duplicated efforts and you may also get suggestions on how
+to best proceed, e.g. there may be half-finished work in some branch that you
+could start with.
+
+Here's how to set up `tellurium` for local development to contribute smaller
+features or changes that you can implement yourself.
+
+1. Fork the `tellurium` repository on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:<your Github name>/tellurium.git
+
+3. If virtualenvwrapper is not installed,
+   `follow the directions <https://virtualenvwrapper.readthedocs.io/en/latest/>`__
+   to install virtualenvwrapper.
+
+4. Install your local copy of tellurium into a virtualenv with virtualenvwrapper::
+
+    $ cd tellurium
+    $ mkvirtualenv tellurium
+
+   Use the ``--python`` option to select a specific version of Python for the
+   virtualenv.
+
+5. Install the required packages for development in the virtualenv using pip install::
+
+    (tellurium)$ pip install --upgrade pip setuptools wheel
+    (tellurium)$ pip install -r requirements.txt
+
+6. Check out the branch that you want to contribute to. Most likely that will be
+   ``master``::
+
+    (tellurium)$ git checkout master
+
+7. Create a branch for local development based on the previously checked out
+   branch (see below for details on the branching model)::
+
+    (tellurium)$ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+8. Setup tellurium for development::
+
+    (tellurium)$ pip install -e .
+
+9. When you are done making changes, check that your changes pass the tests with tox for your local Python version::
+
+     (tellurium)$ tox -e py27
+     (tellurium)$ tox -e py34
+     (tellurium)$ tox -e py35
+
+10. Commit your changes and push your branch to GitHub::
+
+    (tellurium)$ git add .
+    (tellurium)$ git commit -m "Your detailed description of your changes."
+    (tellurium)$ git push origin name-of-your-bugfix-or-feature
+
+11. Submit a pull request through the GitHub website. Once you submit a pull
+    request your changes will be tested automatically against multiple python
+    versions and operating systems. Further errors might appear during those
+    tests.
+
+For larger features that you want to work on collaboratively with other tellurium team members,
+you may consider to first request to join the sbmlutils developers team to get write access to the
+repository so that you can create a branch in the main repository
+(or simply ask the maintainer to create a branch for you).
+Once you have a new branch you can push your changes directly to the main
+repository and when finished, submit a pull request from that branch to ``master``.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests in the ``tellurium/tests``
+   directory. Except in rare circumstances, code coverage must
+   not decrease (as reported by codecov which runs automatically when
+   you submit your pull request)
+2. If the pull request adds functionality, the docs should be
+   updated. Put your new functionality into a function with a
+   docstring and consider creating a notebook that demonstrates the
+   usage.
+3. The pull request must work for Python 2.7, 3.5 and 3.6.
+4. Assign a reviewer to your pull request. If in doubt, assign 0u812, matthiaskoenig and kirichoi.
+   Your pull request must be approved by at least one
+   reviewer before it can be merged.
+
+Unit tests and benchmarks
+-------------------------
+
+tellurium uses `pytest <http://docs.pytest.org/en/latest/>`_ for its
+unit-tests and new features should in general always come with new
+tests that make sure that the code runs as intended::
+
+    (tellurium)$ pytest
+
+Branching model
+---------------
+
+``master``
+    Is the branch all pull-requests should be based on.
+``{fix, bugfix, doc, feature}/descriptive-name``
+    Is the recommended naming scheme for smaller improvements, bugfixes,
+    documentation improvement and new features respectively.
+
+Please use concise descriptive commit messages and consider using
+``git pull --rebase`` when you update your own fork to avoid merge commits.
+
+1. Tests are in the ``tellurium/tests`` directory. They are automatically run
+   through continuous integration services on both python 2 and python 3
+   when pull requests are made.
+2. Please write tests for new functions. Writing documentation as well
+   would also be very helpful.
+3. Ensure code will work with both python 2 and python 3. For example,
+   instead of ``my_dict.iteritems()`` use ``six.iteritems(my_dict)``
+
+Thank you very much for contributing to tellurium!

tellurium/source/LICENSE.txt

@@ -0,0 +1,202 @@
+                                Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
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+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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tellurium/source/MANIFEST.in

@@ -0,0 +1,2 @@
+include LICENSE.txt
+include VERSION.txt

tellurium/source/NEWS.txt

@@ -0,0 +1,3 @@
+tellurium
+
+For the release notes, please go to http://tellurium.analogmachine.org/news/.

tellurium/source/NOTICE.txt

@@ -0,0 +1,219 @@
+Tellurium v2.1.0
+Copyright 2017 Kiri Choi, J Kyle Medley, Matthias K�nig, Kaylene Stocking, Caroline Cannistra, Michal Galdzicki, and Herbert Sauro
+http://tellurium.analogmachine.org/
+
+This product makes use of the following open source software packages:
+
+bioservices 1.4.16
+    Copyright (c) 2017 Thomas Cokelaer
+    Licensed under GPL License
+    https://github.com/cokelaer/bioservices
+
+cobraPy 0.8.2
+    Copyright (c) Daniel Robert Hyduke and Ali Ebrahim 
+    Licensed under LGPL/GPL v2
+    https://opencobra.github.io/cobrapy/
+	
+control 0.7.0
+    Copyright Richard M. Murray et al.
+	Licensed under BSD license
+    https://sourceforge.net/projects/python-control/
+
+IPython 5.5.0
+    Copyright (c) 2017, IPython Development Team
+    IPython is licensed under the terms of the new or revised BSD license	
+	http://ipython.org/
+
+jedi 0.11.0
+    Copyright 2012 - 2017, Jedi contributors
+    Licensed under MIT license.
+    http://jedi.jedidjah.ch/en/latest/#
+	
+jinja2 2.9.6
+    Copyright (c) 2017 by the Jinja Team
+    Licensed under BSD license.
+    http://jinja.pocoo.org/docs/dev/
+	
+jsonschema	2.6.0
+    Copyright (c) 2017 Julian Berman
+    Licensed under MIT license.
+    https://github.com/Julian/jsonschema
+
+Jupyter 1.0.0
+    Copyright � 2017 Project Jupyter
+    Licensed under BSD license.
+    https://jupyter.org/
+	
+libAntimony 2.9.4
+    Copyright (c) 2008-2015, Lucian Smith and Herbert Sauro
+    Distributed under BSD license
+    http://antimony.sourceforge.net/
+
+libCombine 0.2.2
+    Copyright (c) 2016, Sarah M. Keating & Frank T. Bergmann All rights reserved.
+    Available under the Simplified BSD license.
+    https://github.com/sbmlteam/libCombine
+    
+libNUML 1.1.1
+    Copyright 2013 The University of Manchester, UK
+    Available under the LGPL 2.1 license. https://github.com/NuML/NuML/blob/master/libnuml/LICENSE.txt
+    https://github.com/NuML/NuML
+    
+libRoadRunner 1.4.24
+    Copyright (C) 2012-2017 Andy Somogyi, Herbert Sauro
+    Distributed under Apache License, Version 2.0
+    http://libroadrunner.org/
+	
+libSBML 5.15.0
+    Copyright � 2013-2014 jointly by the following organizations:
+    1. California Institute of Technology, Pasadena, CA, USA
+    2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+    3. University of Heidelberg, Heidelberg, Germany
+    Copyright � 2009-2013 jointly by the following organizations:
+    1. California Institute of Technology, Pasadena, CA, USA
+    2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+    Copyright � 2006-2008 by the California Institute of Technology, Pasadena, CA, USA
+    Copyright � 2002-2005 jointly by the following organizations: 
+    1. California Institute of Technology, Pasadena, CA, USA
+    2. Japan Science and Technology Agency, Japan
+    Distributed under GNU LGPL 2.1 license
+    http://sbml.org/Software/libSBML
+	
+libSEDML 0.4.2
+    Copyright (c) 2013-2015, Frank T. Bergmann, All rights reserved.
+    Distributed under Simplified BSD License.
+    https://github.com/fbergmann/libSEDML
+
+LMFIT 0.9.7
+     Copyright (c) 2014 Matthew Newville, The University of Chicago
+                     Till Stensitzki, Freie Universitat Berlin
+                     Daniel B. Allen, Johns Hopkins University
+                     Michal Rawlik, Eidgenossische Technische Hochschule, Zurich
+                     Antonino Ingargiola, University of California, Los Angeles
+                     A. R. J. Nelson, Australian Nuclear Science and Technology Organisation
+    Distributed under BSD License.
+    https://lmfit.github.io/lmfit-py/index.html
+	
+matplotlib 2.1.0
+    Copyright (c) 2012-2015 Matplotlib Development Team; All Rights Reserved
+    Distributed under matplotlib license, based on the PSF license
+    http://matplotlib.org/
+
+matplotlib2tikz 0.6.2
+    Copyright (c) 2010-2016 Nico Schl�mer
+    matplotlib2tikz is published under the MIT license
+    https://github.com/nschloe/matplotlib2tikz
+	
+nose 1.3.7
+    Copyright 2005-2009, Jason Pellerin
+    Distributed under GNU LGPL license.
+    https://nose.readthedocs.org/en/latest/
+
+numpy 1.13.3
+    Copyright (c) 2005-2015, NumPy Developers.
+    Distributed under BSD license, http://www.numpy.org/license.html#license
+    http://www.numpy.org	
+
+pandas 0.20.3
+    Copyright (c) 2011-2012, Lambda Foundry, Inc. and PyData Development Team. All rights reserved.
+    Copyright (c) 2008-2011 AQR Capital Management, LLC. All rights reserved.
+    pandas is distributed under a 3-clause ("Simplified" or "New") BSD license.
+
+phrasedml 1.0.8
+    Copyright (c) 2017, Lucian Smith, Kiri Choi, and Herbert Sauro
+    Distributed under BSD 3 license, https://github.com/sys-bio/phrasedml/blob/master/LICENSE.txt
+    https://github.com/sys-bio/phrasedml
+    
+pip 9.0.1
+    Copyright (c) 2008-2016 The pip developers
+    Licensed under MIT license.
+    https://pip.pypa.io/en/stable/
+
+plotly 2.1.0
+    Copyright 2017 Plotly, Inc.
+    Code released under the MIT license.
+    https://plot.ly/
+    
+pysces 0.9.5
+    Copyright (c) 2004 - 2017, Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr All rights reserved.
+    PySCeS is distributed under a BSD style licence, please see LICENCE.txt for details. https://github.com/PySCeS/pysces/blob/master/LICENSE.txt
+    http://pysces.sourceforge.net/
+
+pygraphviz 1.3.1
+	Copyright (C) 2006-2015 by Aric Hagberg, Dan Schult, Manos Renieris.
+    Distributed with BSD license. 
+    https://pygraphviz.github.io/
+	
+pyparsing 2.2.0
+    Paul McGuire
+    Distributed under the MIT license (no copyright statement)
+    http://pyparsing.wikispaces.com/
+	
+PyQt5
+    Copyright (C) 2015 Riverbank Computing Limited <info@riverbankcomputing.com>
+    Lincensed under the terms of the GNU GPL 3, with Riverbank GPL Exception version 1.1
+    see GPL_EXCEPTION.TXT in the PyQt5 Source Code. The right to use Open Source Licenses not compatible with the GNU General Public License: Apache License 2.0
+    http://www.riverbankcomputing.com/
+
+pySBOL 2.2.0
+    Distributed under Apache 2.0 license.
+    https://github.com/SynBioDex/pysbol
+
+Python 2.7.13
+    Copyright (c) 2001-2017 Python Software Foundation; All Rights Reserved
+    Distributed under PSF LICENSE FOR PYTHON 2.7.6, http://docs.python.org/2/license.html
+    http://python.org/
+	
+python-dateutil 2.6.1
+    Copyright (c) 2003-2011 - Gustavo Niemeyer <gustavo@niemeyer.net>
+    Copyright (c) 2012 - Tomi Pievil������inen <tomi.pievilainen@iki.fi>
+    Distributed under Simplified BSD license
+    http://labix.org/python-dateutil
+
+rrPlugins 1.1.8
+    Copyright (C) 2012-2015 Totte Karlsson, Herbert Sauro
+    Distributed under Apache License, Version 2.0
+    http://tellurium.analogmachine.org/plugins/	
+
+sbml2matlab 1.2.2
+    Copyright (c) 2012, Stanley Gu
+    Distributed under BSD License
+    https://github.com/sys-bio/sbml2matlab
+	
+Scipy 0.19.1
+    Copyright � 2001, 2002 Enthought, Inc. All rights reserved.
+    Copyright � 2003-2015 SciPy Developers. All rights reserved.
+    Distributed under BSD license, https://www.scipy.org/scipylib/license.html
+    https://www.scipy.org/
+
+Seaborn 0.7.1
+    Copyright (c) 2012-2013, Michael L. Waskom
+    Released under a BSD (3-clause) license
+    https://stanford.edu/~mwaskom/software/seaborn/
+	
+six 1.10.0
+    Copyright (c) 2010-2015 Benjamin Peterson
+    Distributed under the MIT license
+    http://pypi.python.org/pypi/six/	
+
+Spyder 3.2.3 (modified)
+    Copyright (c) 2009- The Spyder Development Team
+    Licensed under the terms of the MIT License
+    https://www.spyder-ide.org/
+
+SymPy 1.1.1	
+    Copyright (c) 2006-2016 SymPy Development Team
+    Licensed under New BSD License.
+    http://www.sympy.org/en/index.html
+
+urllib3 1.22
+    Copyright 2008-2016 Andrey Petrov and contributors
+    urllib3 is made available under the MIT License.
+    https://urllib3.readthedocs.io/en/latest/
+	
+Winpython 2.7.13.0
+    Copyright (c) 2009-2013, Pierre Raybaut
+    Copyright (c) 2014-2016 The Winpython development team
+    Licensed under the terms of the MIT License
+    https://winpython.github.io/
+

tellurium/source/README.md

@@ -0,0 +1,253 @@
+<h1><img title="tellurium logo" src="./docs/images/tellurium_logo.png" height="50" />&nbsp;&nbsp;tellurium</h1>
+
+<!-- These badges come from shield.io, zenodo or travis -->
+
+<table style="width:100%">
+  <tr>
+    <!--<td><img alt="Github version", src="https://travis-ci.com/sys-bio/tellurium.svg?branch=master"></td> -->
+    <td><img alt="Read the Docs" src="https://img.shields.io/readthedocs/tellurium"></td>
+    <td><a href="https://badge.fury.io/gh/sys-bio%2Ftellurium"><img src="https://badge.fury.io/gh/sys-bio%2Ftellurium.svg" alt="GitHub version" height="18"></a></td>
+  </tr>
+</table> 
+
+ <table style="width:100%">
+  <tr>
+    <td><img alt="Licence", src="https://img.shields.io/hexpm/l/tellurium"</td>
+    <td><img alt="PyPI - Downloads", src="https://img.shields.io/pypi/dm/tellurium"></td>
+    <td><img alt="Funding", src="https://img.shields.io/badge/Funding-NIGMS%20(GM123032)-blue"></td>
+    <td><img alt="Funding", src="https://img.shields.io/badge/Funding-NIBIB%20(EB028887)-blue"></td>
+    <td><a href="https://badge.fury.io/py/tellurium"><img src="https://badge.fury.io/py/tellurium.svg" alt="PyPI version" height="18"></a> </td>
+   </tr>
+</table> 
+
+ <table style="width:100%">
+  <tr>
+    <td><a href="https://doi.org/10.5281/zenodo.2548944"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.2548944.svg" alt="DOI"></a></td>
+  </tr>
+</table>
+
+Copyright 2014-2023
+Kiri Choi, J Kyle Medley, Matthias König, Kaylene Stocking, Caroline Cannistra, Michal Galdzicki, Ciaran Welsh, Lucian Smith, Adel Heydarabadipour, and Herbert Sauro
+
+## What is it?
+
+Tellurium is a comprehensive Python accessible SBML-compliant modeling platform for biochemical reaction systems. 
+
+## Introduction
+
+For installation instructions scroll down a few sections.
+
+Tellurium is a python environment for reproducible dynamical modeling of biological networks. 
+Tellurium provides the interface code to convert between standard formats and uses powerful 
+libraries without requiring technical expertise, allowing teh user to focus on what’s important: 
+building better models. Tellurium also provides first-class support for exchangeability via 
+[COMBINE archives](http://co.mbine.org/documents/archive) and SBML, allowing you to share your models 
+and simulations with many other tools.
+
+Tellurium combines state-of-the-art scientific Python libraries, such 
+as [NumPy](http://www.numpy.org/) and [SciPy](http://www.scipy.org/), 
+and includes special-purpose systems biology Python tools. Out of the box, 
+Tellurium includes the high performance simulation engine [libroadrunner](https://github.com/sys-bio/roadrunner), the model descrption language [antimony](http://antimony.sourceforge.net/), [phrasedml](http://phrasedml.sf.net/), [libsbml](http://sbml.org/Software/libSBML), and [libsedml](https://github.com/fbergmann/libSEDML).
+
+The Tellurium (and libroadrunner project) project is funded from the NIH/NIGMS (GM081070) and NIH/NIBIB U24EB028887.
+
+## Documentation 
+* General: http://tellurium.readthedocs.org/en/latest/
+* API: http://tellurium.readthedocs.io/en/latest/_apidoc/tellurium.html
+* Webpage: http://tellurium.analogmachine.org/
+
+## Usage Example
+
+```{python}
+import tellurium as te
+
+r = te.loada('''
+      S1 -> S2; k1*S1
+      S1 = 10; S2 = 0
+      k1 = 0.1
+''')
+
+result = r.simulate(0, 40, 500) 
+r.plot()
+```
+
+<img src="./docs/images/tellurium-front-page-image.png" width=50% height=50%>
+
+## Installation Instructions
+
+Tellurium can be installed as a Python package, with a front-end (Notebook, IDE), or in a cloud environment (Google Colab):
+
+
+A. [Python Pip](#Install-via-pip)
+
+B. [IDE front-end](#Front-end-installation) based on [Spyder](https://www.spyder-ide.org/)  
+
+C. [Notebook front-end](#front-end-2-tellurium-notebook)  
+
+D. [Google Colab](#google-colab)  
+
+We recommend first-time users choose one of the front-ends, while developers looking to integrate Tellurium use the pip package. All python desktop IDE graphical front-ends should work. We know for certain that telluirum will work from Spyder, pyCharm and Visual Studio Code.
+
+The IDE front-end provides a MATLAB like experience with a code editor and Python console. 
+The notebook front-end provides a notebook interface similar to [Jupyter](http://jupyter.org/), 
+and features notebook cells for inline OMEX, a human-readable representation of COMBINE archives.
+
+For any issues with installation and setup, please check [FAQ](https://github.com/sys-bio/tellurium/wiki/FAQ) or [contact us](#contact-us). 
+
+-------
+
+### Install via pip
+[![PyPI version](https://badge.fury.io/py/tellurium.svg)](https://badge.fury.io/py/tellurium)
+
+If you have a version of Python in an environment you're comfortable with, you can add Tellurium with pip:
+
+```
+pip install tellurium
+```	
+
+This will install on all platforms. For Colab see the end of this screen. 
+
+For those using Anaconda, we currently do not have a separate Anaconda version of Tellurium, so you'll need to install it via pip, as above.
+
+:exclamation:**For detailed instructions on how to setup Tellurium on Anaconda distributions, 
+see [this page](https://github.com/sys-bio/tellurium/wiki/FAQ#i-would-like-to-use-tellurium-on-anaconda-what-should-i-do).** 
+
+
+For developers, the latest stable version from the repository can be installed via
+```
+pip install git+https://github.com/sys-bio/tellurium.git
+```
+
+-------
+
+### Front-end installation
+
+<img align="left" width="32px" id="windows" src="https://raw.githubusercontent.com/wiki/sys-bio/tellurium/img/windows.png">
+<h4>Windows</h4>
+<br style="clear:both"/>
+
+#### Approach 1: Spyder for Tellurium IDE
+The Tellurium Spyder installers are tested with Windows 10 and 11, and come with Python 3.12.
+
+:exclamation:**Attention to those upgrading to Tellurium Spyder IDE from an older version :** 
+We strongly suggest you to completely remove the older version of Tellurium Spyder IDE prior to installing the latest version.
+
+1. Download Tellurium Spyder for Windows:
+    * [Python 3.12](https://sourceforge.net/projects/pytellurium/files/Tellurium-2.4/2.4.2/Tellurium-2.4.2-Python-3.12-win64-setup.exe/download)
+2. Double-click the installer to start the installation
+3. Follow the instructions
+
+If you wish to use a different version of Python, you'll need to install Tellurium from the windows command line by using the command: `pip install tellurium`
+
+NOTE: Installation requires administrative rights. It is recommended to accept the default settings.
+
+#### Approach 2: Thonny IDE for Python
+Tellurium can be used with [Thonny](https://en.wikipedia.org/wiki/Thonny), a free, open-source IDE for Python that is designed for beginners.
+
+1. [Download the latest version of Thonny for Windows](https://thonny.org)
+2. Double-click the installer `*.exe` to start the installation
+3. Follow the instructions
+4. Launch Thonny
+5. Go to Tools > Manage packages...
+6. Type `tellurium` in the search box and press the "Search on PyPI" button
+7. Once the `tellurium` package is found in "Search results", click on it, and then press the "Install" button. Wait until the installation process is completed.
+
+&nbsp;
+
+<img align="left" width="32px" id="mac-osx" src="https://raw.githubusercontent.com/wiki/sys-bio/tellurium/img/macos.png">
+<h4>Mac OS X</h4>
+<br style="clear:both"/>
+
+For Mac users there a a number of options. By far, the easiest is to use the self-cotbained Thonny Python IDE.
+
+#### Approach 1: Thonny IDE for Python
+Tellurium can be used with [Thonny](https://en.wikipedia.org/wiki/Thonny), a free, open-source IDE for Python that is designed for beginners.
+
+1. [Download the latest version of Thonny for Mac OS X](https://thonny.org)
+2. Double-click the installer `*.pkg` to start the installation
+3. Follow the instructions
+4. Launch Thonny from Spotlight or directly from your Applications folder
+5. Go to Tools > Manage packages...
+6. Type `tellurium` in the search box and press the "Search on PyPI" button
+7. Once the `tellurium` package is found in "Search results", click on it, and then press the "Install" button. Wait until the installation process is completed.
+
+#### Approach 2: Spyder for Tellurium IDE
+
+1. [Download the Anaconda distribution for Mac OS X.](https://www.anaconda.com/download). 
+
+2. [Follow the installer instructions.](https://docs.anaconda.com/anaconda/install/linux). The installer will install Spyder as part of the installation process. If you customize the installation, you will have a chance to select which packages to install - ensure Spyder is selected.
+3. When prompted, add Anaconda to your PATH (optional, but this will make the following steps easier).
+4. [Open a Terminal](https://www.wikihow.com/Open-a-Terminal-Window-in-Mac) and run the command:
+```
+conda install msgpack-python
+```
+Next, install Tellurium itself:
+```
+pip install tellurium
+```
+If this fails, try using the default absolute path to Anaconda, which will probably be something like:
+```
+/Users/<your-user>/opt/anaconda3/bin/pip install tellurium
+```
+5. Launch the Anaconda Navigator via Launchpad. In Anaconda Navigator, run Spyder and then try `import tellurium` within the Spyder editor or console.
+
+#### Approach 3: Spyder for Tellurium IDE (only for Mac OS X Legacy)
+
+Currently, only a Legacy version of the Mac Spyder IDE is available. 
+
+1. [Download Tellurium IDE for Mac OS X 10.10 or later](https://github.com/sys-bio/tellurium/releases/download/1.3.5-rc3/Tellurium-1.3.5-Spyder-2.3.8-OSX.dmg)
+2. Double-click the .dmg file to open a new window
+3. Double-click the Spyder icon
+
+
+**For those who wish to use Tellurium with Spyder IDE on Mac OS X, we also suggest that you install through [Anaconda](https://www.anaconda.com/) by 
+following the instructions on [this page](https://github.com/sys-bio/tellurium/wiki/FAQ#i-would-like-to-use-tellurium-on-anaconda-what-should-i-do).**
+
+&nbsp;
+
+<img align="left" width="32px" id="redhat" src="https://raw.githubusercontent.com/wiki/sys-bio/tellurium/img/redhat.png">
+<h4>Linux (RedHat)</h3>
+<br style="clear:both"/>
+
+<img align="left" width="32px" id="debian" src="https://raw.githubusercontent.com/wiki/sys-bio/tellurium/img/debian.png">
+<h4>Linux (Debian)</h4>
+<br style="clear:both"/>
+
+**For those who wish to use Tellurium with Spyder IDE on Linux, we also suggest that you install through [Anaconda](https://www.anaconda.com/) by 
+following the instructions on [this page](https://github.com/sys-bio/tellurium/wiki/FAQ#i-would-like-to-use-tellurium-on-anaconda-what-should-i-do).**
+
+:question:Looking for old releases? [You can find them here.](https://sourceforge.net/projects/pytellurium/files/notebook) To install an old release over a new release, you will need to [manually wipe the data directory.](https://github.com/sys-bio/tellurium/wiki/FAQ#how-do-i-uninstall-tellurium-notebook)
+
+-------
+
+### Google Colab
+Tellurium can be used entirely in a browser using [Google Colab](https://colab.research.google.com/).  Ideally, it will work with the following steps (updated May 2023)
+  
+1. run a cell with ```!pip install -q tellurium```
+2. (Very important) Restart the runtime (From the menu: 'Runtime / Restart session')
+3. Test by typing ```import tellurium as te```
+4. te.getVersionInfo()  # Check for versions if you want to 
+   Try a model
+5. r = te.loada ('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10'); r.simulate(); r.plot()
+  
+The Python version behind Colab changes periodically, so what worked one day may stop working the next, but the following Colab notebook worked when used at ICSB 2022:  https://colab.research.google.com/drive/1wddLftHNhetbozZY29r2HRkzQLl1F_fs#scrollTo=l1bCgW46-adR and will hopefully be instructive.
+
+-------
+  
+## Citing
+
+If you use Tellurium in your research, we would appreciate following citations in any works you publish:
+
+Medley et al. (2018). ["Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology."](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006220) *PLoS Computational Biology*, 14(6), e1006220.
+
+Choi et al. (2018). ["Tellurium: An extensible python-based modeling environment for systems and synthetic biology."](https://www.sciencedirect.com/science/article/pii/S0303264718301254) *Biosystems*, 171, 74-79.
+
+## Contact Us
+
+For general questions, requesting help, or reporting bugs, feel free to use the [GitHub issue tracker](https://github.com/sys-bio/tellurium/issues).  You can also post to the  [Tellurium-discuss](https://groups.google.com/d/forum/tellurium-discuss) mailing list.
+
+## Legal
+
+The source code for the Tellurium Python package is hosted at https://github.com/sys-bio/tellurium and is licensed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0). Tellurium uses third-party dependencies which may be licensed under different terms. Consult the documentation for the respective third-party packages for more details.
+
+TELLURIUM AND ALL SOFTWARE BUNDLED WITH TELLURIUM (HEREAFTER "THE SOFTWARE") IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THE SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

tellurium/source/VirtualEnv.md

@@ -0,0 +1,25 @@
+# python virtual environment
+## How to setup the VirtualEnvironment for development on linux?
+
+Install stable version from pip
+```
+mkvirtualenv tellurium
+(tellurium) pip install tellurium
+```
+
+Install latest development version, or feature branch
+```
+# clone repository
+git clone https://github.com/sys-bio/tellurium
+cd tellurium
+
+# make virtual environment
+mkvirtualenv tellurium
+(tellurium) pip install -r requirements.txt
+
+# checkout branch 
+(tellurium) git checkout master
+
+# install tellurium
+(tellurium) pip install -e .
+```

tellurium/source/__init__.py

@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+"""
+tellurium Project Package Initialization File
+"""

tellurium/source/bld.bat

@@ -0,0 +1,2 @@
+"%PYTHON%" setup.py install
+if errorlevel 1 exit 1

tellurium/source/build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install

tellurium/source/clean.sh

@@ -0,0 +1,4 @@
+# remove unnecessary files
+find . -type f -regex '.*pyc' | xargs rm
+find . -type f -regex '.*class' | xargs rm
+find . -type f -regex '.*~' | xargs rm

tellurium/source/docs/API.rst

@@ -0,0 +1,5 @@
+===================
+API
+===================
+.. automodule:: tellurium.tellurium
+   :members:

tellurium/source/docs/Makefile

@@ -0,0 +1,216 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+
+.PHONY: clean
+clean:
+	rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/tellurium.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/tellurium.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
+
+.PHONY: devhelp
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/tellurium"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/tellurium"
+	@echo "# devhelp"
+
+.PHONY: epub
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: latex
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+	@echo "Testing of coverage in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

tellurium/source/docs/README.md

@@ -0,0 +1,112 @@
+# tellurium API documentation
+
+The API documentation of tellurium is build from the python source code and restructured Text (reST) `*.rst` files located in `tellurium/docs`. The documentation is based on sphinx and uses the information encoded in the docstrings. The documentation is available at
+
+**http://tellurium.readthedocs.org/en/latest/**
+
+## Documentation guidelines
+Documentation can be updated by changing `*.rst` files in `tellurium/docs`. 
+Just edit the latest files in the git repository. 
+Direct access to the pages is provided via the **Edit on GitHub** links in the documentation.
+
+It is important **NOT** to edit the `*.rst` files in 
+* `tellurium/docs/_apidoc`
+* `tellurium/docs/_notebooks`
+These are generated automatically from the python notebooks and source code. 
+Changes to the API documentation or notebook examples have to be done 
+in the respective python code (`tellurium/tellurium`) and notebook files (`tellurium/examples/notebooks`).
+
+## Adding Code Examples to Documentation
+Code examples are managed via jupyter notebooks.
+To start the notebook server 
+```
+cd tellurium/examples/notebooks/
+jupyter notebook
+```
+
+### Existing notebook
+To add code to existing notebooks 
+* modify the notebook and save
+* run complete notebook to make sure everything works
+
+### New notebook
+Examples are added via notebooks via the following workflow
+* copy the notebook template `tellurium/examples/notebooks/core/template.ipynb` to a new file `tellurium/examples/notebooks/core/newExample.ipynb`
+* add your python code in the notebook `newExample.ipynb`
+* run complete notebook to make sure everything works
+* add the notebook to the notebook index `tellurium/examples/notebooks/index.ipynb`
+* register the notebook in the docs in `tellurium/docs/notebooks.rst` via `.. include:: _notebooks/core/newExample.rst
+
+After the next complete build of the documentation the example is available in the docs. 
+
+All examples added via notebooks are run when building the docs, 
+so problems with the examples are directly visible and can be fixed.
+
+The unittests should be run after making changes to the notebooks
+to make sure the code can be executed.
+
+## Build Documentation 
+The python requirements for building the documentation are
+```
+pip install sphinx sphinx-autobuild sphinx_rtd_theme mock
+```
+
+### Complete Build
+To build the complete API documentation use the build script `make_docs.sh` 
+in the `tellurium/docs` folder, which mainly does
+
+* removes old `_apidoc` and `_notebook` files
+* creates the `_apidoc` `*.rst` from python source via `sphinx-apidoc`
+* creates the `_notebook` `*.rst` from notebook files in `tellurium/examples/notebooks` (the notebooks are executed, so all the example code in the documentation is run with the latest source)
+* creates the `*.py` code from notebook files in `tellurium/examples/notebook-py` (examples which can be loaded in Tellurium)
+* creates the `html` documentation (analogue to minimal build)
+
+### Minimal Build
+After changes to the `*.rst` files the updated documentation can be build and viewed locally via
+```
+make html && firefox _build/html/index.html
+```
+The minimal build just rebuilds the html from the changes in the rst. 
+As soon as the changes are committed to the master branch the online documentation on  
+http://tellurium.readthedocs.org/en/latest/
+will be updated via a commit hook. The update can take a few minutes.
+
+The minimal build does NOT update 
+* `tellurium/docs/_apidoc`
+* `tellurium/docs/_notebooks`
+
+i.e. this is not sufficient if changes to the notebooks were made.
+
+
+## Open Issues
+* API `.. autofunction::` & `automodule:: create` created locally but not on readthedocs.org
+* links between functions in documentation (i.e. hyperlinks between functions for easy navigation in API)
+
+
+## Documentation of Python Source Code
+Modules, classes, functions and methods can be documented via their 
+respective docstrings in sphinx format (for information see http://www.sphinx-doc.org/en/stable/). 
+An example of the sphinx syntax is provided below:
+
+```{python}
+def function(arg1, arg2):
+    """Short sentence describing the funtion. 
+    Here comes a long explanation which describes in detail the function.
+    see also: `:func:loadAntimonyModel`
+    ::
+
+        r = loada('S1 -> S2; k1*S1; k1 = 0.1; S2 = 10')
+
+    :param arg1: parameter is ..
+    :param arg2: This parameter is ...
+    :returns: describe return object
+    """
+    return doSomesting(arg1, arg2)
+```
+Important points are:
+* write one short sentence describing the function at begin of docstring.
+* provide description of arguments via `:param arg1:`
+* provide description of return type via `:returns:`
+* code examples are written via `::` followed by empty line and **intended** code block
+
+There are many more options available, see the sphinx documentation for more details.

tellurium/source/docs/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

tellurium/source/docs/_apidoc/modules.rst

@@ -0,0 +1,7 @@
+tellurium
+=========
+
+.. toctree::
+   :maxdepth: 4
+
+   tellurium

tellurium/source/docs/_apidoc/tellurium.analysis.rst

@@ -0,0 +1,78 @@
+tellurium.analysis package
+==========================
+
+Submodules
+----------
+
+tellurium.analysis.annotations module
+-------------------------------------
+
+.. automodule:: tellurium.analysis.annotations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.bifurcation module
+-------------------------------------
+
+.. automodule:: tellurium.analysis.bifurcation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.parameterestimation module
+---------------------------------------------
+
+.. automodule:: tellurium.analysis.parameterestimation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.parameterscan module
+---------------------------------------
+
+.. automodule:: tellurium.analysis.parameterscan
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.sensitivityanalysis module
+---------------------------------------------
+
+.. automodule:: tellurium.analysis.sensitivityanalysis
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.simulator module
+-----------------------------------
+
+.. automodule:: tellurium.analysis.simulator
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.stochasticmodel module
+-----------------------------------------
+
+.. automodule:: tellurium.analysis.stochasticmodel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.analysis.test module
+------------------------------
+
+.. automodule:: tellurium.analysis.test
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.analysis
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.dev.deprecated.rst

@@ -0,0 +1,30 @@
+tellurium.dev.deprecated package
+================================
+
+Submodules
+----------
+
+tellurium.dev.deprecated.tecombine module
+-----------------------------------------
+
+.. automodule:: tellurium.dev.deprecated.tecombine
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.dev.deprecated.tephrasedml module
+-------------------------------------------
+
+.. automodule:: tellurium.dev.deprecated.tephrasedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.dev.deprecated
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.dev.oven.ndarray.rst

@@ -0,0 +1,22 @@
+tellurium.dev.oven.ndarray package
+==================================
+
+Submodules
+----------
+
+tellurium.dev.oven.ndarray.ndarray module
+-----------------------------------------
+
+.. automodule:: tellurium.dev.oven.ndarray.ndarray
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.dev.oven.ndarray
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.dev.oven.rst

@@ -0,0 +1,29 @@
+tellurium.dev.oven package
+==========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    tellurium.dev.oven.ndarray
+
+Submodules
+----------
+
+tellurium.dev.oven.libnuml\_import module
+-----------------------------------------
+
+.. automodule:: tellurium.dev.oven.libnuml_import
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.dev.oven
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.dev.rst

@@ -0,0 +1,18 @@
+tellurium.dev package
+=====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    tellurium.dev.deprecated
+    tellurium.dev.oven
+
+Module contents
+---------------
+
+.. automodule:: tellurium.dev
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.notebooks.rst

@@ -0,0 +1,46 @@
+tellurium.notebooks package
+===========================
+
+Submodules
+----------
+
+tellurium.notebooks.notebooktools module
+----------------------------------------
+
+.. automodule:: tellurium.notebooks.notebooktools
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.notebooks.ontologysearch module
+-----------------------------------------
+
+.. automodule:: tellurium.notebooks.ontologysearch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.notebooks.parameterslider module
+------------------------------------------
+
+.. automodule:: tellurium.notebooks.parameterslider
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.notebooks.speciessearch module
+----------------------------------------
+
+.. automodule:: tellurium.notebooks.speciessearch
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.notebooks
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.plotting.rst

@@ -0,0 +1,62 @@
+tellurium.plotting package
+==========================
+
+Submodules
+----------
+
+tellurium.plotting.api module
+-----------------------------
+
+.. automodule:: tellurium.plotting.api
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.plotting.engine module
+--------------------------------
+
+.. automodule:: tellurium.plotting.engine
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.plotting.engine\_mpl module
+-------------------------------------
+
+.. automodule:: tellurium.plotting.engine_mpl
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.plotting.engine\_null module
+--------------------------------------
+
+.. automodule:: tellurium.plotting.engine_null
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.plotting.engine\_plotly module
+----------------------------------------
+
+.. automodule:: tellurium.plotting.engine_plotly
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.plotting.factory module
+---------------------------------
+
+.. automodule:: tellurium.plotting.factory
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.plotting
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.roadrunner.rst

@@ -0,0 +1,22 @@
+tellurium.roadrunner package
+============================
+
+Submodules
+----------
+
+tellurium.roadrunner.extended\_roadrunner module
+------------------------------------------------
+
+.. automodule:: tellurium.roadrunner.extended_roadrunner
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.roadrunner
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.rst

@@ -0,0 +1,55 @@
+tellurium package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    tellurium.analysis
+    tellurium.dev
+    tellurium.notebooks
+    tellurium.plotting
+    tellurium.roadrunner
+    tellurium.sedml
+    tellurium.teconverters
+    tellurium.teio
+    tellurium.tests
+    tellurium.utils
+    tellurium.visualization
+
+Submodules
+----------
+
+tellurium.tellurium module
+--------------------------
+
+.. automodule:: tellurium.tellurium
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.temiriam module
+-------------------------
+
+.. automodule:: tellurium.temiriam
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.testcases module
+--------------------------
+
+.. automodule:: tellurium.testcases
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.sedml.rst

@@ -0,0 +1,61 @@
+tellurium.sedml package
+=======================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    tellurium.sedml.templates
+
+Submodules
+----------
+
+tellurium.sedml.data module
+---------------------------
+
+.. automodule:: tellurium.sedml.data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.sedml.mathml module
+-----------------------------
+
+.. automodule:: tellurium.sedml.mathml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.sedml.tesedml module
+------------------------------
+
+.. automodule:: tellurium.sedml.tesedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.sedml.utils module
+----------------------------
+
+.. automodule:: tellurium.sedml.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.sedml.xpath module
+----------------------------
+
+.. automodule:: tellurium.sedml.xpath
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.sedml
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.sedml.templates.rst

@@ -0,0 +1,10 @@
+tellurium.sedml.templates package
+=================================
+
+Module contents
+---------------
+
+.. automodule:: tellurium.sedml.templates
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.teconverters.rst

@@ -0,0 +1,62 @@
+tellurium.teconverters package
+==============================
+
+Submodules
+----------
+
+tellurium.teconverters.antimony\_regex module
+---------------------------------------------
+
+.. automodule:: tellurium.teconverters.antimony_regex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.teconverters.antimony\_sbo module
+-------------------------------------------
+
+.. automodule:: tellurium.teconverters.antimony_sbo
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.teconverters.convert\_antimony module
+-----------------------------------------------
+
+.. automodule:: tellurium.teconverters.convert_antimony
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.teconverters.convert\_omex module
+-------------------------------------------
+
+.. automodule:: tellurium.teconverters.convert_omex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.teconverters.convert\_phrasedml module
+------------------------------------------------
+
+.. automodule:: tellurium.teconverters.convert_phrasedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.teconverters.inline\_omex module
+------------------------------------------
+
+.. automodule:: tellurium.teconverters.inline_omex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.teconverters
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.teio.rst

@@ -0,0 +1,22 @@
+tellurium.teio package
+======================
+
+Submodules
+----------
+
+tellurium.teio.latex module
+---------------------------
+
+.. automodule:: tellurium.teio.latex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.teio
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.tests.rst

@@ -0,0 +1,110 @@
+tellurium.tests package
+=======================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    tellurium.tests.sedml
+    tellurium.tests.testdata
+
+Submodules
+----------
+
+tellurium.tests.helpers module
+------------------------------
+
+.. automodule:: tellurium.tests.helpers
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_API module
+--------------------------------
+
+.. automodule:: tellurium.tests.test_API
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_analysis module
+-------------------------------------
+
+.. automodule:: tellurium.tests.test_analysis
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_examples module
+-------------------------------------
+
+.. automodule:: tellurium.tests.test_examples
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_inline\_omex module
+-----------------------------------------
+
+.. automodule:: tellurium.tests.test_inline_omex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_io module
+-------------------------------
+
+.. automodule:: tellurium.tests.test_io
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_omex module
+---------------------------------
+
+.. automodule:: tellurium.tests.test_omex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_plotting module
+-------------------------------------
+
+.. automodule:: tellurium.tests.test_plotting
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_runner module
+-----------------------------------
+
+.. automodule:: tellurium.tests.test_runner
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_tellurium module
+--------------------------------------
+
+.. automodule:: tellurium.tests.test_tellurium
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.test\_temiriam module
+-------------------------------------
+
+.. automodule:: tellurium.tests.test_temiriam
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.tests
+    :members:
+    :undoc-members:
+    :show-inheritance:

tellurium/source/docs/_apidoc/tellurium.tests.sedml.rst

@@ -0,0 +1,70 @@
+tellurium.tests.sedml package
+=============================
+
+Submodules
+----------
+
+tellurium.tests.sedml.test\_archive module
+------------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_archive
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_data module
+---------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_kisao module
+----------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_kisao
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_omex module
+---------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_omex
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_phrasedml module
+--------------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_phrasedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_sedml module
+----------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_sedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+tellurium.tests.sedml.test\_tesedml module
+------------------------------------------
+
+.. automodule:: tellurium.tests.sedml.test_tesedml
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: tellurium.tests.sedml
+    :members:
+    :undoc-members:
+    :show-inheritance: