Updates

README.md

@@ -22,8 +22,9 @@ Built for classroom teaching at the
 - **3D visualization** — interactive py3Dmol or PlotlyMol viewer with a live
   backend toggle when both are installed; post-calculation structure rendered
   automatically in the results panel
-- **In-session calculations** — RHF, UHF, 9 DFT functionals, MP2, and NMR
-  shielding via PySCF, running in your Python kernel (no batch submission)
+- **In-session calculations** — RHF, UHF, 9 DFT functionals, MP2, NMR
+  shielding, TD-DFT UV-Vis, and 1D PES scans via PySCF, running in your
+  Python kernel (no batch submission)
 - **Implicit solvent** — PCM solvation (Water, Ethanol, THF, DMSO,
   Acetonitrile) via a single checkbox
 - **Rich results** — total energy, HOMO-LUMO gap, Mulliken charges, dipole
@@ -148,6 +149,7 @@ Five step-by-step notebooks in [`notebooks/tutorials/`](notebooks/tutorials/):
 | Frequency | Vibrational frequencies, ZPVE, IR intensities, thermochemistry (H/S/G at 298 K), animated normal modes, IR spectrum chart (stick / Lorentzian broadened) |
 | UV-Vis (TD-DFT) | Excitation energies, oscillator strengths, UV-Vis spectrum plot |
 | NMR Shielding | ¹H and ¹³C chemical shifts relative to TMS via GIAO; tabulated by element |
+| PES Scan | 1D potential energy surface along a bond, angle, or dihedral; energy profile chart; geometry animation at each scan point |
 
 ### Basis sets
 
@@ -184,6 +186,7 @@ quantui/                  Main package
   ir_plot.py              IR spectrum chart (stick and Lorentzian broadened)
   tddft_calc.py           TD-DFT UV-Vis excited-state calculations
   nmr_calc.py             NMR shielding + ¹H/¹³C chemical shift prediction
+  pes_scan.py             1D potential energy surface scan
   optimizer.py            QM geometry optimization with trajectory
   visualization_py3dmol.py  3D viewer (py3Dmol + PlotlyMol backends)
   pubchem.py              PubChem molecule search
@@ -197,7 +200,7 @@ quantui/                  Main package
 notebooks/
   molecule_computations.ipynb   Main student-facing interface
   tutorials/                    Step-by-step guided notebooks (01–05)
-tests/                    pytest test suite (575+ tests)
+tests/                    pytest test suite (860+ tests)
 apptainer/                Container definition for reproducible deployment
 local-setup/              Conda environment definition
 pyproject.toml            Package metadata and tool config

launch-native.bat

@@ -12,7 +12,11 @@ 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 8867 to avoid conflict with container-based launchers on 8866.
-start "QuantUI [native]" wsl -d Ubuntu -- bash -c "cd '%WSLPATH%' && source ~/miniconda3/etc/profile.d/conda.sh && conda activate quantui && if [ pyproject.toml -nt .dev_install_stamp ] || ! python -c 'import quantui' 2>/dev/null; then pip install -e . -q && touch .dev_install_stamp; fi && voila notebooks/molecule_computations.ipynb --no-browser --port=8867 --ServerApp.disable_check_xsrf=True"
+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]" wsl -d Ubuntu -- bash -c "cd '%WSLPATH%' && source ~/miniconda3/etc/profile.d/conda.sh && conda activate quantui && if [ pyproject.toml -nt .dev_install_stamp ] || ! python -c 'import quantui' 2>/dev/null; then pip install -e . -q && touch .dev_install_stamp; fi && rm -rf quantui/__pycache__ && PYTHONDONTWRITEBYTECODE=1 voila notebooks/molecule_computations.ipynb --no-browser --port=8867 --ServerApp.disable_check_xsrf=True"
 
 echo Waiting for Voila to start...
 timeout /t 6 /nobreak > nul

local-setup/environment.yml

@@ -46,6 +46,10 @@ dependencies:
       - black>=24.0.0
       - ruff>=0.4.0
       # Install QuantUI in editable mode
-      # On Linux/WSL also run: conda install -c conda-forge pyscf pyscf-properties
-      - pyscf-properties   # NMR and other properties (pyscf.prop); moved out of pyscf core in v2.0
+      # On Linux/WSL also run: conda install -c conda-forge pyscf
+      # (pyscf-properties is pip-only; installed here automatically)
+      # PyPI pyscf-properties 0.1.0 is missing the infrared module and has an NMR
+      # reshape bug fixed in commit 4eee5a4 (2024-11-07, unreleased).  Install
+      # from GitHub source until a new release lands on PyPI.
+      - pyscf-properties @ git+https://github.com/pyscf/properties.git
       - -e ..

pyproject.toml

@@ -40,9 +40,12 @@ packages = ["quantui"]
 [project.optional-dependencies]
 # PySCF requires Linux/macOS/WSL — not available on Windows natively.
 # Use the Apptainer container (apptainer/quantui.def) for Windows.
-# pyscf-properties provides pyscf.prop (NMR, etc.) — moved out of core in PySCF 2.0.
+# pyscf>=2.13.0: pyscf.prop.infrared is in pyscf 2.13.0+ core (creates the
+# pyscf.prop namespace that infrared lives under).
+# pyscf-properties: provides additional pyscf.prop.* modules (EFG, IR, etc.).
+# NMR is accessed via pyscf.nmr (core, not overwritten by pyscf-properties).
 pyscf = [
-    "pyscf>=2.3.0",
+    "pyscf>=2.13.0",
     "pyscf-properties",
 ]