Substantial app.py refactor, feature upgrades, hygiene improvements, and more

.gitignore

@@ -60,3 +60,4 @@ planning/
 nul
 /.claude/
 /temp - untracked/
+/logs

.pre-commit-config.yaml

@@ -1,3 +1,5 @@
+fail_fast: true
+
 repos:
   # ── Standard file hygiene ─────────────────────────────────────────────────
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -42,6 +44,7 @@ repos:
     rev: v1.10.0
     hooks:
       - id: mypy
+        stages: [pre-push]
         files: ^quantui/        # type-check the package only, not tests
         args: ["--ignore-missing-imports", "--no-error-summary"]
         additional_dependencies:

launch-native-jupyter.bat

@@ -0,0 +1,72 @@
+@echo off
+echo QuantUI NATIVE JUPYTER MODE -- Local conda env in WSL, no container
+echo Use this when you have edited quantui/*.py and want JupyterLab.
+echo.
+
+REM Convert the Windows repo path to a WSL path for portability
+set "WIN_REPO=%~dp0."
+for /f "delims=" %%i in ('wsl wslpath -a "%WIN_REPO%"') do set WSLPATH=%%i
+if not defined WSLPATH (
+	echo ERROR: Could not resolve a WSL path for %WIN_REPO%
+	echo Try this command manually:
+	echo   wsl wslpath -a "%WIN_REPO%"
+	echo.
+	pause
+	exit /b 1
+)
+set LOGFILE=%~dp0logs\native-jupyter.log
+
+echo Startup log: %LOGFILE%
+echo.
+
+REM Runs JupyterLab directly from the quantui conda env inside WSL.
+REM pip install -e . is skipped when pyproject.toml has not changed since the
+REM last install (.dev_install_stamp). quantui/*.py changes are always live in
+REM editable mode -- reinstall is only needed after pyproject.toml changes or on
+REM first use.
+REM Uses port 8868 to avoid conflict with container-based launchers on 8866 and
+REM native Voila launcher on 8867.
+REM Clears quantui/__pycache__ on every launch to prevent stale .pyc bytecode
+REM (WSL2 DrvFs does not reliably propagate Windows-side mtime changes, so Python
+REM may load pre-edit bytecode even after source changes -- see GOTCHAS.md).
+REM PYTHONDONTWRITEBYTECODE=1 prevents a new stale cache from accumulating.
+start "QuantUI [native-jupyter]" wsl -d Ubuntu --cd "%WSLPATH%" -- bash ./launch-native-jupyter.sh
+
+echo Waiting for JupyterLab to start on localhost:8868...
+set MAX_WAIT=45
+set waited=0
+set OPENED=0
+
+:wait_for_jupyter
+powershell -NoProfile -Command "$client = New-Object Net.Sockets.TcpClient; try { $client.Connect('127.0.0.1', 8868); $client.Close(); exit 0 } catch { exit 1 }" > nul 2>&1
+if %errorlevel%==0 goto open_browser
+if %waited% GEQ %MAX_WAIT% goto startup_timeout
+timeout /t 1 /nobreak > nul
+set /a waited=%waited%+1
+goto wait_for_jupyter
+
+:startup_timeout
+echo.
+echo JupyterLab did not open localhost:8868 within %MAX_WAIT% seconds.
+echo Check the QuantUI [native-jupyter] WSL window for startup errors.
+echo Review startup log: %LOGFILE%
+if exist "%LOGFILE%" start "" "%LOGFILE%"
+echo.
+goto done
+
+:open_browser
+set OPENED=1
+start http://127.0.0.1:8868/lab/tree/notebooks/molecule_computations.ipynb
+
+:done
+
+echo.
+if "%OPENED%"=="1" (
+	echo Native JupyterLab server running at http://127.0.0.1:8868/lab
+	echo All local quantui/*.py changes are live -- no rebuild needed.
+	echo Close the WSL window to stop.
+) else (
+	echo JupyterLab startup not confirmed yet.
+	echo Review the QuantUI [native-jupyter] WSL window for details.
+	echo Startup log: %LOGFILE%
+)

launch-native-jupyter.sh

@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+LOG_FILE="logs/native-jupyter.log"
+mkdir -p "$(dirname "$LOG_FILE")"
+
+{
+    echo
+    echo "=== QuantUI native Jupyter launch: $(date -Iseconds) ==="
+    echo "PWD: $(pwd)"
+} >> "$LOG_FILE"
+
+exec > >(tee -a "$LOG_FILE") 2>&1
+
+source ~/miniconda3/etc/profile.d/conda.sh
+conda activate quantui
+
+echo "Using Python: $(command -v python)"
+echo "Using Jupyter: $(command -v jupyter)"
+
+# Reinstall editable package only when pyproject metadata changed, or on first run.
+if [ ! -f .dev_install_stamp ] || [ pyproject.toml -nt .dev_install_stamp ]; then
+    pip install -e . -q
+    touch .dev_install_stamp
+fi
+
+# Prevent stale bytecode from WSL2 DrvFs mtime quirks.
+rm -rf quantui/__pycache__
+export PYTHONDONTWRITEBYTECODE=1
+
+exec jupyter lab notebooks/molecule_computations.ipynb \
+    --no-browser \
+    --port=8868 \
+    --ServerApp.port_retries=0 \
+    --ServerApp.root_dir="$(pwd)" \
+    --IdentityProvider.token='' \
+    --ServerApp.password=''

notebooks/molecule_computations.ipynb

@@ -78,7 +78,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.15"
+   "version": "3.11.14"
   }
  },
  "nbformat": 4,