quantui 0.5.1__tar.gz

quantui-0.5.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to QuantUI are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.5.1] - 2026-07-31
+
+### Fixed
+
+- **The "Geometry optimization before calculation" checkbox no longer gets
+  stuck disabled.** Selecting a seed geometry on Frequency or UV-Vis disables
+  that checkbox (a seed is already an optimised geometry, so re-optimising
+  first would be redundant) — but switching to a different calculation type
+  afterwards used to leave it disabled with no way to re-enable it short of
+  going back and clearing the seed selection.
+- **The Geometry Opt seed dropdown now updates when you change molecules
+  while already on that panel.** It previously only refreshed when you
+  switched *into* the Geometry Opt calculation type, so loading a new
+  molecule without leaving the panel could leave it listing matches for the
+  wrong molecule.
+
+### Changed
+
+- **Internal cleanup:** the Geometry Opt / Frequency / UV-Vis seed-geometry
+  dropdowns, refresh buttons, and status notes are now one shared widget group
+  instead of three near-identical copies. No user-visible change — the same
+  dropdown, filtering, and messages appear on each calculation type as before.
+
+## [0.5.0] - 2026-07-31
+
+First release published to **PyPI** — `pip install quantui`.
+
+### Added
+
+- **Seed geometry for Geometry Optimization runs** — a run can now start from
+  the final geometry of a previous optimization instead of the current molecule,
+  which makes the standard "optimize at a cheap level of theory, then refine at
+  a higher one" workflow a single dropdown choice. Frequency and UV-Vis already
+  supported this; Geometry Opt now matches them.
+- **A "still working" heartbeat in the live log.** Long silent phases — the
+  TD-DFT excited-state solve most of all — could leave the output log unchanged
+  for minutes while the calculation was running normally, which reads as a hang.
+  The log now reports `… still working — <stage> · <elapsed>` whenever it has
+  been quiet for 25 seconds. The saved `pyscf.log` is unaffected; it stays a
+  faithful record of the calculation's own output.
+- **Basis-set names now show their alternate notation.** `6-31G*` and `6-31G(d)`
+  are the same basis set written two ways, and nothing in the UI said so. The
+  basis card now notes the equivalent spelling, and the basis-set help topic
+  explains the star/parenthesis convention, the `+`/`++` diffuse markers and
+  when anions need them, and why Dunning sets (`cc-pVDZ`) have no star at all.
+- **The launcher terminal now prints the QuantUI wordmark** instead of two bare
+  lines of text.
+- **Reorganization energy (Marcus 4-point)** — a new "Reorganization Energy"
+  calculation type that computes the internal reorganization energy λ for hole
+  (cation) and/or electron (anion) charge transfer. It optimizes the neutral and
+  ion geometries and evaluates the four single-point energies of the 4-point
+  scheme (λ = [E_ion(R_neutral) − E_ion(R_ion)] + [E_neutral(R_ion) −
+  E_neutral(R_neutral)]), reporting λ, its λ₁ (ion) and λ₂ (neutral) relaxation
+  components, in eV and kcal/mol. `mode="both"` shares the neutral optimization
+  across both channels. Open-shell HF ions are automatically promoted to UHF.
+- **One-click "Calc. Reorganization Energy" button** — sets the calculation type
+  to Reorganization Energy, defaults the channel to both hole + electron, and
+  launches the run in a single click.
+- **GPU offload can now be switched off from the UI** — Status tab → Settings →
+  "Use GPU when available". The preference persists across launches. This exists
+  because GPU offload is not always faster: quantum-chemistry SCF is
+  double-precision throughout, and consumer/workstation GPUs gate FP64 to roughly
+  1/32–1/64 of their FP32 rate, so offload on such a card can be *slower* than a
+  many-core CPU. `QUANTUI_DISABLE_GPU=1` still overrides the setting for scripted
+  runs.
+- **A warning when a detected GPU is unlikely to help.** `quantui gpu check` and
+  the Status tab now flag consumer-class devices with a note that double
+  precision is weak on them and offload may be slower than CPU, instead of
+  presenting any detected CUDA device as free speed.
+
+### Changed
+
+- **The live calculation log no longer snaps back to the bottom while a run is
+  in progress**, so you can scroll up and read earlier output mid-calculation.
+  It still follows new output automatically when you are at the bottom. The log
+  is now a container QuantUI owns and appends to, rather than a widget that
+  rebuilt itself on every line.
+- **No pre-optimization preview when the geometry barely moves.** Previously a
+  relaxation that changed essentially nothing still opened an animation pane and
+  a Keep/Revert choice between two effectively identical structures. Below
+  0.05 Å RMS displacement QuantUI now just reports the number and proceeds with
+  your geometry.
+- **All launcher scripts moved into a `launchers/` folder** to declutter the repo
+  root. Behaviour is unchanged — each launcher now resolves the repo root as its
+  parent directory. `launchers/launch-app.bat` still finds `quantui.sif` next to
+  itself (student download) or in the repo root (dev build). Docs and shortcuts
+  that referenced the old top-level paths were updated.
+- **Apptainer container now builds on `condaforge/miniforge3` with the `mamba`
+  (libmamba) solver.** The previous `continuumio/miniconda3` base used conda's
+  classic solver, which could hang for hours resolving the PySCF + RDKit +
+  JupyterLab dependency set. The build now installs from conda-forge only
+  (`--override-channels`, strict channel priority), which resolves in minutes and
+  avoids the base image's implicit `defaults` channel. No change to the shipped
+  package set or runtime behavior.
+
+### Fixed
+
+- **The live log and run header render in a fixed-width font again.** A
+  system-font rule was applying to the log, which garbled the ASCII wordmark and
+  pushed the run header's `Label : value` columns out of alignment.
+- **`quantui gpu check` no longer reports a broken CUDA install as "gpu4pyscf not
+  installed".** `ModuleNotFoundError` is a subclass of `ImportError`, so catching
+  the latter conflated "the package is absent" with "the package is present but
+  its CUDA libraries are missing" — the second case was reported as the first,
+  sending users back to an install step they had already completed. The two are
+  now distinguished, the underlying exception is included in the message (e.g.
+  the missing `libnvJitLink.so`), and both cases are logged. The reason string
+  now comes from the detection probe itself rather than being re-derived by the
+  CLI, so the message can no longer contradict what the run dispatcher decided.
+- **Exit is now a two-stage confirmation, so one click can no longer tear down an
+  HPC allocation.** Exit shuts the server down by sending `SIGTERM` to the parent
+  process. On a laptop that parent is just Voilà, but on a cluster interactive
+  session (e.g. NCShare) that parent process *is* the job — so a single stray
+  click destroyed the entire allocation. The first click now only arms the
+  shutdown: Exit re-labels to "Confirm shutdown" and an inline warning plus a
+  Cancel button appear. Only a second click runs the shutdown, which is otherwise
+  unchanged. An armed Exit auto-reverts after 15 seconds so a stray click doesn't
+  leave the button primed.
+
+## [0.4.1] - 2026-07-16
+
+Bug-fix and hardening release from a full repository audit. No new features and
+no breaking changes — it fixes correctness bugs across orbital isosurfaces,
+Molden export, the XYZ parser, NMR references, PES scans, and IR intensities,
+plus a range of edge-case, packaging, and hygiene issues found by reading the
+codebase end to end.
+
+### Added
+
+- Single-atom molecules (e.g. a lone He or Ne atom) are now accepted as XYZ input
+  and run end to end — atomic calculations are legitimate targets.
+
+### Changed
+
+- **Python 3.9 is now covered by CI.** The minimum supported version was
+  previously claimed but untested; adding it surfaced and fixed real
+  geometry-optimization and frequency failures on the older ASE that resolves for
+  Python 3.9.
+- **Faster `quantui` CLI startup** — the command-line tool no longer imports the
+  full notebook/GUI stack (ipywidgets, IPython, the app module) just to tail a
+  log.
+- **No more logging hijack** — importing `quantui` no longer reconfigures the
+  root logger, so it won't override or duplicate logging in a host application or
+  notebook.
+- **Faster time estimates over long sessions** — the performance log is cached and
+  re-read only when it changes, instead of being fully parsed on every UI update.
+
+### Fixed
+
+- **Orbital isosurfaces for charged and open-shell molecules** — the isosurface
+  viewer previously errored for every odd-electron system (radicals, and ions
+  such as H₃O⁺, NH₄⁺, OH⁻); charge and spin are now carried through to the cube
+  generator.
+- **Molden export from frequency calculations** — the exported geometry was
+  inflated (Bohr coordinates read as Ångström) and internally inconsistent, so it
+  rendered wrong in Avogadro/IQmol; frequency geometries are now stored and
+  written in the correct units. This also fixes history replay of frequency
+  orbital isosurfaces.
+- **Export Script and method notes for `wB97X-D`** — "Export Script" failed with
+  a "method not supported" error and the educational notes silently disappeared
+  for `wB97X-D`; mixed-case method names are now matched correctly.
+- **2D structure images from XYZ input** — this path never worked (it always
+  returned nothing) and now renders.
+- **XYZ files with a blank or comment (`#`) title line** no longer silently drop
+  the first atom — a very common file layout was losing an atom with only a
+  warning.
+- **NMR reference provenance** — chemical shifts no longer silently fall back to
+  the B3LYP/6-31G\* TMS constants for other method/basis combinations; the
+  reference that was actually applied is now recorded, and the lookup is
+  case-insensitive.
+- **IR intensities for open-shell / UHF-singlet frequency runs** no longer abort
+  the whole IR-intensity step.
+- **PES scans** — a failed scan point no longer records a bogus geometry frame or
+  poisons the energy/barrier statistics with NaN, and angle/dihedral scans work
+  with current ASE releases.
+- **UHF calculations** now report a dipole moment and Mulliken charges (these were
+  silently skipped).
+- **Clearer errors for unsupported input** — elements outside the supported H–Kr
+  range, and post-Hartree–Fock methods (MP2 / CCSD / CCSD(T)) requested for
+  calculation types that don't support them, now fail with an explicit message
+  instead of a misleading one or an uninformative crash.
+- **Windows exports** no longer fail when the basis-set name contains `*` (e.g.
+  `6-31G*`) — export filenames are sanitized.
+- **Method-notes panel** renders bold text correctly instead of leaking literal
+  `**` markers.
+- **Robustness** — the event log is no longer subject to lost entries under
+  concurrent writes; a thumbnail-save failure no longer aborts saving a result;
+  PubChem availability checks respect the configured throttle and timeout; and
+  results carrying NumPy scalar values now save correctly.
+
+## [0.4.0] - 2026-06-18
+
+Interactive-visualization and offline-readiness release. Adds molecular-orbital
+isosurfaces and an interactive pre-optimization preview, reworks the 3D viewers
+to preserve camera orientation across frames, makes all 3D rendering work
+offline, and substantially speeds up startup.
+
+### Added
+
+- **Molecular-orbital isosurfaces (py3Dmol)** — interactive HOMO / LUMO / MO
+  isosurface viewer rendered with py3Dmol; the downsampled Plotly path remains a
+  fallback.
+- **Interactive classical pre-optimization** — a **Preview** button relaxes the
+  geometry with a fast bonded force field (RDKit MMFF94 → UFF) and animates the
+  relaxation in place; **Keep this geometry** adopts it as the active structure
+  or **Revert** discards it. Stepper controls (play/pause, prev/next, scrub
+  slider, and an input ⇄ relaxed flip) let you compare geometries, and the
+  captured trajectory is sampled at even RMSD spacing for smooth playback.
+- **Cancel button** — stop a running calculation cooperatively at the next SCF
+  cycle / optimization step.
+- **Live vibrational-animation framerate** — the Vib fps setting updates the
+  running animation immediately.
+
+### Changed
+
+- **Single persistent 3D viewers** — the trajectory and vibrational-mode viewers
+  now load all frames into one py3Dmol viewer and switch frames/modes
+  client-side, so the camera (rotation/zoom) is preserved across steps and modes
+  and there is no per-frame rebuild or flicker.
+- **Pre-optimization is Preview-only** — the silent "classical pre-optimize"
+  checkbox is gone; pre-optimization happens only through the transparent
+  Preview → Keep/Revert flow, so nothing relaxes the geometry invisibly. (The
+  separate QM "geometry optimization before calculation" option is unchanged.)
+- **Offline-first 3D rendering** — 3Dmol.js is vendored and loaded per-view from
+  a local `data:` URI instead of a CDN, so every 3D view works with no network
+  (the build fails if the vendored asset is missing). Native launchers tolerate
+  offline `pip install`.
+- **Faster startup** — GPU detection and History/Compare population are deferred
+  off the synchronous construction path, so the UI paints in ~1 s instead of
+  ~15 s; the GPU status badge and dropdowns fill in shortly after.
+- **Clear** of the live calculation log is disabled while a calculation runs.
+
+### Fixed
+
+- **GPU-offloaded result extraction** — HOMO–LUMO gap, dipole moment, and
+  Mulliken charges are now reported for GPU runs. CuPy arrays are copied to host
+  before extraction, and Mulliken falls back to the CPU object (gpu4pyscf does
+  not implement population analysis on the GPU).
+- **Vibrational animation glitchiness** — stacked animation loops (a new loop
+  started on every mode switch) made playback jittery and too fast and ignored
+  the framerate setting; exactly one loop now runs.
+- **Cancel status** no longer sticks on "Cancelling…" after a calculation is
+  cancelled.
+- **Stale run status** — "Pre-optimized geometry accepted." is cleared when a new
+  molecule is loaded or a preview is reverted.
+- Structure provenance is reported and the input viewer is persisted across
+  reloads.
+
+## [0.3.0] - 2026-06-11
+
+Structure-sourcing release. Repairs the external-database structure search and
+replaces the 20-entry inline molecule list with an indexed, three-tier bundled
+library, alongside visualization and result-card fixes.
+
+### Added
+
+- **External structure search** — resolve molecules by name, PubChem CID, InChI,
+  InChIKey, SMILES, or CAS number. Input is routed by type: SMILES/InChI resolve
+  locally via RDKit with no network, while names and identifiers query PubChem
+  through a hardened client (URL-encoding, request throttling, bounded retry on
+  server throttling). NCI CACTUS acts as a fallback resolver, and an offline
+  bundled-library fallback keeps the search usable without a network connection.
+- **Disambiguation pick-list** — an ambiguous query (e.g. a name with several
+  PubChem matches) presents a selectable list instead of silently choosing the
+  first hit.
+- **Three-tier bundled molecule library** — 20 presets, 156 curated named
+  molecules, and ~1,900 bulk QM9 structures (CC0), held in an indexed,
+  lazily-loaded package-data store. Bulk entries are reachable via search.
+- **Library browse/search tab** — category filter plus name/formula search,
+  replacing the flat preset dropdown.
+
+### Changed
+
+- The molecule preset list moved from an inline `config.py` dictionary into the
+  indexed library store; `config.MOLECULE_LIBRARY` is preserved as a
+  backward-compatible accessor.
+- Frequency / UV-Vis seed-geometry dropdown entries are now labeled as optimized
+  geometries so their source is explicit.
+
+### Fixed
+
+- **Orbital isosurface could exhaust browser memory** — the full volumetric grid
+  was serialized into the Plotly figure. The rendered surface is now downsampled
+  to a bounded point count (the saved cube file remains full-resolution).
+- **CCSD / MP2 result cards** now show the HF reference and correlation-energy
+  breakdown (plus the (T) triples correction for CCSD(T)); these fields are also
+  persisted with saved results.
+- The live calculation log no longer jumps to the top while streaming output.
+- Structures fetched as 2D records are re-embedded in 3D, and salt/counterion
+  fragments are separated so bond perception does not misread them.
+
+## [0.2.0] - 2026-05-22
+
+First substantial release after `v0.1.0`. The codebase moved from a single
+monolithic `app.py` to a modular package, added six PySCF-backed calculation
+types end-to-end, introduced a results-persistence layer with history replay,
+and shipped a complete visualization stack (3D viewer with selectable backend,
+trajectory animation, IR/UV-Vis/PES plots, orbital isosurfaces, vibrational
+mode animation with caching). UI runs as a Voilà app suitable for classroom
+deployment.
+
+### Added
+
+#### Calculations
+
+- **Geometry optimization** (`optimizer.py`) — ASE-BFGS driver around a custom
+  PySCF calculator; per-step trajectory persisted.
+- **Vibrational frequency analysis** (`freq_calc.py`) — Hessian via
+  `pyscf.hessian`, ZPVE, thermochemistry (H/S/G at 298 K), IR intensities via
+  `pyscf.prop.infrared` or a numerical-derivative fallback for compatibility
+  across PySCF versions.
+- **TD-DFT UV-Vis** (`tddft_calc.py`) — excitation energies, oscillator
+  strengths, wavelengths; full spectrum plot in the Analysis tab.
+- **NMR shielding** (`nmr_calc.py`) — GIAO shielding via `pyscf.nmr` (core
+  preferred over `pyscf-properties` to dodge a known upstream bug); ¹H/¹³C
+  chemical shifts relative to TMS.
+- **1D PES scan** (`pes_scan.py`) — bond / angle / dihedral; energy profile +
+  per-step geometry animation.
+- **PCM implicit solvent** — Water, Ethanol, THF, DMSO, Acetonitrile via a
+  single checkbox in the Calculate tab.
+- **MP2** post-HF method support.
+
+#### Analysis & visualization
+
+- **Analysis tab with 8 always-in-DOM panels** (Energies, Trajectory,
+  Vibrational, IR Spectrum, PES Scan, Isosurface, UV-Vis, NMR) wired through
+  a `_PANEL_REGISTRY` so live runs and history replay share one code path.
+- **IR spectrum chart** (`ir_plot.py`) — stick plot + Lorentzian-broadened
+  curve; broadening toggle and FWHM slider.
+- **UV-Vis spectrum plot** — Plotly chart with wavelength/energy axes.
+- **Orbital visualization** (`orbital_visualization.py`) — energy-level
+  diagram (matplotlib → Plotly HTML) and cube-file isosurface viewer with
+  HOMO-1/HOMO/LUMO/LUMO+1 toggle.
+- **Trajectory animation** — atomic Output-children swap to avoid
+  Voilà-deferred-display blank frames; py3Dmol-only render path with
+  prev/next arrow navigation.
+- **Vibrational mode animation** — py3Dmol multi-frame XYZ renderer with
+  amplitude scaling, prev/next mode nav, and dropdown skipping near-zero
+  modes.
+- **3D visualization backend router** (`viz_backend_router.py`) — pure
+  function that picks py3Dmol or plotlymol3d per `VizTask` based on user
+  preference and runtime availability; immutable `Decision` carries chosen
+  backend, fallback, and reason.
+- **Lifecycle telemetry** — `_viz_render_event` context manager emits
+  `viz_render_start` / `viz_render_done` / `viz_render_error` JSONL events
+  with backend, task, `elapsed_ms`, and extras at every render dispatch.
+- **Side-by-side Compare tab** — pick any two saved calculations and view a
+  diff table.
+
+#### Persistence & logging
+
+- **Results storage** (`results_storage.py`) — every run is saved to a
+  timestamped directory containing `result.json` (schema v2, additive-only),
+  `pyscf.log`, optional `trajectory.json` / `orbitals.npz` / `thumbnail.png`.
+- **History tab** — browse and replay saved calculations after a kernel
+  restart; replay path is identical to live-run analysis activation.
+- **Performance log** (`calc_log.py`) — `perf_log.jsonl` per converged run +
+  `event_log.jsonl` for startup/calc/error events; 7-day auto-prune.
+- **Time estimator** — 4-strategy priority chain (N_basis-normalised → cross-method
+  electron-count) populates "Estimated time" before each run.
+- **Benchmark suite** (`benchmarks.py`) — one-click calibration suite to
+  populate the time-estimator history with real machine data.
+- **Issue tracker** (`issue_tracker.py`) — in-app bug-report UI writing to a
+  local `issues.db`.
+- **Persistent user settings** (`user_settings.py`) — stored at
+  `~/.quantui/settings.json` (override via `QUANTUI_SETTINGS_PATH`). Schema
+  is section-based for additive growth, with atomic writes and graceful
+  fallback to defaults on corruption.
+- **Vibrational-animation disk cache** (`vib_cache.py`) — per-result-dir
+  `vib_frames/` of pre-rendered py3Dmol HTML keyed by
+  `(mode, n_frames, amplitude, renderer, fps)`. Mode switches on repeat
+  visits and history replay are instant.
+- **Vib FPS user preference** — `viz.vib_framerate_fps` exposed as an
+  IntSlider in the Status tab (clamped 1–120, default 10); included in the
+  vib cache key so changing FPS invalidates cleanly.
+
+#### UI
+
+- **Modular UI package** — `app.py` (orchestration) plus `app_analysis.py`,
+  `app_builders.py`, `app_exports.py`, `app_formatters.py`, `app_history.py`,
+  `app_runflow.py`, `app_visualization.py`.
+- **Seven-tab layout** — Calculate, Results, Analysis, History, Compare, Log,
+  Status — with a floating Help overlay (not a tab).
+- **Light / Dark theme selector** — dark by default on startup.
+- **Status tab** — environment info, performance-history accordion (two-step
+  reset), default-3D-backend toggle, vib-FPS slider.
+- **Files tab + activity indicator** for browsing saved results.
+- **Plot export UI** — save IR, UV-Vis, PES, orbital diagram plots as HTML.
+- **Scroll guard** for the run output area to keep long PySCF logs from
+  jumping the page.
+- **Welcome header**, completion banner, structured log header/footer.
+- **Compare-tab Copy-path button** (replaced a broken Open-folder action).
+- **Result directory label + log accordion** showing inline `pyscf.log`.
+- **Structure exports** — XYZ, MOL/SDF, PDB, plus a standalone runnable `.py`
+  script export.
+
+#### Tooling & dev
+
+- **Test suite grew from a handful to 1004 passed / 97 skipped** (Windows
+  `quantui-win` env baseline; the 97 skips are PySCF-gated Linux-only tests).
+- New analysis-history end-to-end tests for every calc type
+  (`test_sp_analysis_history.py`, `test_geo_opt_analysis_history.py`,
+  `test_freq_analysis_history.py`, `test_tddft_analysis_history.py`,
+  `test_nmr_analysis_history.py`, `test_pes_scan_analysis_history.py`).
+- `test_code_quality.py` enforces:
+  - No `include_plotlyjs="cdn"` anywhere (fails silently in offline Voilà).
+  - No bare `except: pass` blocks.
+- `test_viz_backend_router.py` + `test_viz_backend_sync.py` — full
+  task × preference × availability matrix and Calculate/Analysis toggle sync.
+- `test_vib_cache.py`, `test_vib_py3dmol_render.py`,
+  `test_viz_render_telemetry.py` — vib animation + telemetry coverage.
+- `_layout(...)` helper sanitises `widgets.Layout` kwargs to eliminate a
+  4808 → 13 traitlets warning regression.
+- `_safe_cb` wrapper around every `.observe()` callback so exceptions surface
+  in the Log tab instead of disappearing into the Voilà kernel console.
+- Kernel `io_loop` is cached at startup; thread-spawned callbacks are queued
+  onto the main thread to avoid `RuntimeError: no current event loop`.
+- Native launchers: `launch-native.bat` (Windows / WSL) and
+  `launch-native.command` (macOS / Linux) — double-clickable, port `8867`,
+  stamp-based editable-install skip, browser auto-open. README documents
+  pinning each to the Start menu / Dock as a real app.
+- Native JupyterLab launcher (`launch-native-jupyter.bat`) and Apptainer
+  launcher improvements.
+
+#### Docs
+
+- `.github/copilot-instructions.md` — canonical AI-assistant context (now
+  the single source of truth for any AI assistant working on this repo).
+- `CLAUDE.md` — Claude-specific session/workflow context (git-ignored).
+- Site favicons (ICO + SVG) for the GitHub Pages docs site.
+
+### Changed
+
+- **Visualization is py3Dmol-first.** `plotlymol3d` remains an optional
+  fallback for non-trajectory tasks; trajectory rendering is hard-wired to
+  py3Dmol to avoid Plotly/RequireJS flicker.
+- **Plotly figures are rendered via `plotly.io.to_html(..., include_plotlyjs="require")`**
+  inside `widgets.HTML`, not `display(fig)`, so threaded renders work and
+  offline Voilà loads correctly.
+- **`pyscf` is now an optional extra** (`pip install quantui[pyscf]`); the
+  package imports cleanly on Windows with PySCF unavailable.
+- Repo renamed from `QuantUI-local` to `QuantUI`.
+
+### Fixed
+
+- **Trajectory accordion blank on first expand** — switched `traj_output`
+  from `Output` to `VBox` and use atomic children-swap so deferred
+  widget-display is no longer a blank-frame risk.
+- **Vib mode races on rapid switching** — render-token guard (`_vib_render_token`)
+  causes stale background renders to bail rather than overwriting newer
+  output.
+- **Camera state lost on mode switch** — JS hook caches the active
+  `$3Dmol.GLViewer` state across atomic HTML swaps; reset only on a
+  genuinely new frequency result.
+- **PySCF API drift** — robust handling for v2 NMR / thermo API and the
+  `pyscf.prop.infrared` rename; both `Infrared.kernel()` and the older
+  IR API are supported.
+- **Result-dir name collisions** — timestamps now include microseconds; same
+  formula + method + basis no longer overwrite each other.
+- **IR x-axis** — corrected wavenumber axis on the IR Plotly figure.
+- **Plotly figures invisible after accordion show** — figures are re-rendered
+  on accordion expand to handle RequireJS / display-deferral edge cases.
+
+### Removed
+
+- `visualization.py` (PlotlyMol fallback) — replaced by the router-backed
+  `visualization_py3dmol.py` path.
+- All SLURM-era infrastructure already removed during the downstream port:
+  `job_manager.py`, `storage.py`, `slurm_errors.py`, SLURM config templates.
+
+## [0.1.0] - 2026
+
+Initial public scaffolding of the QuantUI package: `quantui` package with
+`molecule.py`, `pubchem.py`, `config.py`, `visualization_py3dmol.py`,
+`calculator.py`, basic notebook launcher, Apptainer container definition,
+MIT license, and project metadata.
+
+[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.5.1...HEAD
+[0.5.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.5.0...v0.5.1
+[0.5.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.4.1...v0.5.0
+[0.4.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.4.0...v0.4.1
+[0.4.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.3.0...v0.4.0
+[0.3.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.2.0...v0.3.0
+[0.2.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.1.0...v0.2.0
+[0.1.0]: https://github.com/The-Schultz-Lab/QuantUI/releases/tag/v0.1.0

quantui-0.5.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 The Schultz Lab, North Carolina Central University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

quantui-0.5.1/MANIFEST.in

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+# Source-distribution contents (M-PYPI PYPI.3).
+#
+# setuptools already picks up the package itself, README, LICENSE and
+# pyproject.toml. This file fixes the two things it gets wrong for us:
+# CHANGELOG.md was missing, and tests/ was being shipped.
+#
+# Policy — what belongs in the sdist:
+#   INCLUDE  the package, its bundled data, and the documents a user or a
+#            downstream packager needs to understand what they installed.
+#   EXCLUDE  anything only useful from a git clone. A pip user cannot run the
+#            test suite meaningfully (it needs dev extras and PySCF), cannot
+#            build the container, and does not get the notebooks in a usable
+#            location — those all stay in the repo.
+
+include CHANGELOG.md
+include SECURITY.md
+
+# Tests need the dev extras + PySCF to run and are not importable from an
+# installed copy; shipping them roughly doubles the sdist for no benefit.
+prune tests
+
+# Repo-only material: container recipes, launcher scripts, tutorial notebooks,
+# the docs site, and the environment file are all clone-time artifacts.
+prune apptainer
+prune docs
+prune launchers
+prune notebooks
+prune local-setup
+prune scripts
+
+# Build/dev droppings that must never reach an artifact.
+prune .github
+global-exclude *.py[cod]
+global-exclude __pycache__
+global-exclude .DS_Store
+exclude .dev_install_stamp
+exclude .pre-commit-config.yaml
+exclude AUDIT_FINDINGS.md
+exclude quantui.sif