VS Code extension spawns `bionetgen` via PATH (ENOENT / wrong binary) instead of using selected interpreter

[wshlavacek]

Summary

The PyBioNetGen VS Code extension detects/validates bionetgen using the selected workspace interpreter, but when actually running a BNGL file it appears to spawn bionetgen by bare command name (PATH lookup). On macOS this often fails with spawn bionetgen ENOENT or runs the wrong bionetgen (e.g., from conda), because the VS Code extension host PATH can differ from the integrated terminal PATH and may not include the workspace venv.

Observed behavior

Auto-install / checks succeed:

• Found python path: .../.venv/bin/python
• Found bionetgen ... Location: .../.venv/lib/python3.12/site-packages

But execution fails:

bionetgen -req "0.5.0" run -i ".../model.bngl" -o "..." -l "..."
Error: spawn bionetgen ENOENT
process exited with code -2

Earlier, when a different bionetgen existed on PATH (conda), the extension ran that instead of the venv binary (tracebacks showed /Users/.../opt/anaconda3/bin/bionetgen), even though the check phase found bionetgen installed in the workspace venv.

Environment

• macOS
• VS Code + PyBioNetGen extension
• Workspace uses a repo-local venv: ${workspaceFolder}/.venv
• bionetgen installed in .venv

Root cause (likely)

The extension uses the interpreter to verify package presence, but uses something equivalent to Node's child_process.spawn("bionetgen", ...) for execution, relying on PATH. The extension host PATH is not guaranteed to include .venv/bin, and can differ from the integrated terminal.

Workarounds

• Launch VS Code from a terminal where the venv is active / PATH includes .venv/bin (requires the code shell command installed).
• Add a global shim/symlink so bionetgen is discoverable on PATH.
• (If supported) configure the extension to use an explicit executable path or python -m bionetgen (currently no such setting appears exposed).

Proposed fix

Prefer interpreter-based execution rather than PATH-based lookup:

• Use the selected interpreter to run the module:
  • python -m bionetgen ... using the resolved workspace interpreter, or
• Spawn the resolved absolute path to the venv script (the interpreter's scripts dir):
  • <venv>/bin/bionetgen ...

Also consider exposing a setting so users can override the executable/command explicitly.

Expected behavior

If the extension reports it is using a particular interpreter, running a model should use the corresponding bionetgen installation and must not depend on external PATH state.

[wshlavacek]

This is addressed in RuleWorld/BNG_vscode_extension#29 — the extension now uses python -m bionetgen via the resolved workspace interpreter instead of a bare PATH lookup. Once that PR is merged, this issue can be closed.