Remove venv isolation, use host Python for workers and pin pathsim deps at build time

README.md

@@ -98,6 +98,7 @@ pathview_server/           # Python package (pip install pathview)
 ├── cli.py                 # CLI entry point (pathview serve)
 └── static/                # Bundled frontend (generated at build time)
 
+
 scripts/
 ├── config/                # Configuration files for extraction
 │   ├── schemas/           # JSON schemas for validation
@@ -496,8 +497,9 @@ npm run dev      # Starts Vite dev server (separate terminal)
 
 **Key properties:**
 - **Process isolation** — each session gets its own Python subprocess
+- **Host environment** — workers run with the same Python used to install pathview, so all packages in the user's environment are available in the code editor
 - **Namespace persistence** — variables persist across exec/eval calls within a session
-- **Dynamic packages** — packages from `PYTHON_PACKAGES` (the same config used by Pyodide) are pip-installed on first init
+- **Dynamic packages** — packages from `PYTHON_PACKAGES` (the same config used by Pyodide) are pip-installed on first init if not already present
 - **Session TTL** — stale sessions cleaned up after 1 hour of inactivity
 - **Streaming** — simulations stream via SSE, with the same code injection support as Pyodide
 

pathview_server/app.py

@@ -21,8 +21,6 @@
 from flask import Flask, request, jsonify, send_from_directory
 from flask_cors import CORS
 
-from pathview_server.venv import get_venv_python
-
 # ---------------------------------------------------------------------------
 # Configuration
 # ---------------------------------------------------------------------------
@@ -44,7 +42,7 @@ def __init__(self, session_id: str):
         self.last_active = time.time()
         self.lock = threading.Lock()
         self.process = subprocess.Popen(
-            [get_venv_python(), "-u", WORKER_SCRIPT],
+            [sys.executable, "-u", WORKER_SCRIPT],
             stdin=subprocess.PIPE,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,

pathview_server/cli.py

@@ -7,7 +7,6 @@
 import webbrowser
 
 from pathview_server import __version__
-from pathview_server.venv import VENV_DIR, ensure_venv
 
 
 def main():
@@ -30,8 +29,6 @@ def main():
 
     args = parser.parse_args()
 
-    ensure_venv()
-
     from pathview_server.app import create_app
 
     app = create_app(serve_static=not args.debug)
@@ -52,7 +49,7 @@ def open_browser_when_ready():
         threading.Thread(target=open_browser_when_ready, daemon=True).start()
 
     print(f"PathView v{__version__}")
-    print(f"  Python venv: {VENV_DIR}")
+    print(f"  Python: {sys.executable}")
     print(f"Running at http://{args.host}:{args.port}")
 
     if args.host == "0.0.0.0":

pathview_server/worker.py

@@ -160,7 +160,6 @@ def initialize(packages: list[dict] | None = None) -> None:
                 send({"type": "stderr", "value": f"Optional package {pkg.get('import', '?')} failed: {e}\n"})
 
     # Import numpy AFTER packages are installed (numpy comes with pathsim).
-    # In a fresh venv without simulation packages, numpy won't be available.
     try:
         exec("import numpy as np", _namespace)
     except Exception:

pyproject.toml

@@ -20,6 +20,8 @@ dependencies = [
     "flask-cors>=4.0",
     "numpy",
     "waitress>=3.0",
+    "pathsim",
+    "pathsim-chem==0.2rc3",
 ]
 
 [project.optional-dependencies]

scripts/extract.py

@@ -694,6 +694,10 @@ def extract(self) -> dict:
 class DependencyExtractor:
     """Extract and generate dependency configuration."""
 
+    # Packages managed by the extraction script in pyproject.toml.
+    # These are added/updated automatically; all other dependencies are left untouched.
+    MANAGED_PACKAGE_NAMES = {"pathsim", "pathsim-chem"}
+
     def __init__(self, config_loader: ConfigLoader):
         self.config = config_loader
 
@@ -735,6 +739,59 @@ def extract(self) -> dict:
             "extracted_versions": extracted_versions
         }
 
+    def update_pyproject(self, packages: list[dict], project_root: Path) -> None:
+        """Update pyproject.toml dependencies with pinned package versions.
+
+        Adds/updates entries for packages from requirements-pyodide.txt
+        while leaving all other dependencies (flask, numpy, etc.) untouched.
+        """
+        pyproject_path = project_root / "pyproject.toml"
+        if not pyproject_path.exists():
+            print("  Warning: pyproject.toml not found, skipping")
+            return
+
+        text = pyproject_path.read_text(encoding="utf-8")
+
+        # Build pip specs for managed packages (e.g. "pathsim==0.17.0")
+        new_specs: list[str] = []
+        for pkg in packages:
+            base_name = pkg["pip"].split(">=")[0].split("==")[0].split("<=")[0].split("<")[0].split(">")[0]
+            if base_name in self.MANAGED_PACKAGE_NAMES:
+                new_specs.append(pkg["pip"])
+
+        # Parse the existing dependencies list
+        pattern = re.compile(
+            r'(dependencies\s*=\s*\[)(.*?)(\])',
+            re.DOTALL,
+        )
+        match = pattern.search(text)
+        if not match:
+            print("  Warning: Could not find dependencies in pyproject.toml, skipping")
+            return
+
+        existing_block = match.group(2)
+
+        # Keep non-managed dependencies
+        kept: list[str] = []
+        for line in existing_block.strip().splitlines():
+            dep = line.strip().strip(",").strip('"').strip("'")
+            if not dep:
+                continue
+            dep_name = re.split(r'[><=~!\[]', dep)[0].strip()
+            if dep_name not in self.MANAGED_PACKAGE_NAMES:
+                kept.append(dep)
+
+        # Append managed packages
+        all_deps = kept + new_specs
+
+        # Rebuild the dependencies block
+        dep_lines = ",\n".join(f'    "{d}"' for d in all_deps)
+        new_block = f"dependencies = [\n{dep_lines},\n]"
+        text = text[:match.start()] + new_block + text[match.end():]
+
+        pyproject_path.write_text(text, encoding="utf-8")
+        print(f"  Updated pyproject.toml dependencies: {', '.join(new_specs)}")
+
 
 # =============================================================================
 # TypeScript Generation
@@ -1009,8 +1066,11 @@ def main():
 
     if extract_all or args.deps:
         print("\nExtracting dependencies...")
-        deps = DependencyExtractor(config).extract()
+        dep_extractor = DependencyExtractor(config)
+        deps = dep_extractor.extract()
         generator.write_dependencies(deps)
+        project_root = Path(__file__).parent.parent
+        dep_extractor.update_pyproject(deps["packages"], project_root)
 
     # Track extracted data for registry generation
     blocks = None

src/lib/constants/dependencies.ts

@@ -1,7 +1,7 @@
 // Auto-generated by scripts/extract.py - DO NOT EDIT
 // Source: scripts/config/requirements-pyodide.txt, scripts/config/pyodide.json
 
-export const PATHVIEW_VERSION = '0.6.1';
+export const PATHVIEW_VERSION = '0.7.0';
 
 export const PYODIDE_VERSION = '0.26.2';
 export const PYODIDE_CDN_URL = `https://cdn.jsdelivr.net/pyodide/v${PYODIDE_VERSION}/full/pyodide.mjs`;

tests/conftest.py

@@ -3,13 +3,11 @@
 import pytest
 
 from pathview_server.app import create_app, _sessions, _sessions_lock
-from pathview_server.venv import ensure_venv
 
 
 @pytest.fixture()
 def app():
     """Create a Flask test app (API-only, no static serving)."""
-    ensure_venv()
     application = create_app(serve_static=False)
     application.config["TESTING"] = True
     yield application