quantui 0.10.0__tar.gz → 0.11.1__tar.gz

{quantui-0.10.0 → quantui-0.11.1}/CHANGELOG.md

@@ -7,6 +7,303 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 
 ## [Unreleased]
 
+## [0.11.1] - 2026-11-02
+
+### Changed
+
+- Documentation site: an "Open the Viewer" link in the Home sidebar and on
+  the home page, a two-column Features page, and shorter text throughout.
+
+### Fixed
+
+- **IRC no longer ends both directions in the same minimum.** Sella's
+  iterative estimate of the starting Hessian could carry a spurious mode,
+  so from a transition state converged only to the force threshold the
+  first step went sideways and both directions fell into one valley. The
+  IRC now starts from PySCF's analytic Hessian, as the transition-state
+  search already does. If Sella's inner loop fails, the direction is
+  finished by mass-weighted steepest descent before a short-step BFGS;
+  if both ends still match, the verdict says so rather than reporting a
+  connection.
+- Viewer installer builds use the `macos-15` runner (`macos-14` is retired).
+
+## [0.11.0] - 2026-11-01
+
+### Added
+
+- **IRC calc type** (M-TS TS.3, engine Sella): follows the reaction path
+  downhill from a transition state in both directions, in mass-weighted
+  coordinates, to the two minima it connects. Pick the Transition State
+  result under *Start from*. The card gives the barrier from each side and
+  a verdict; the PES Scan panel plots energy against the reaction coordinate
+  (click a point to jump the Trajectory panel there); Trajectory plays
+  reactant → TS → product; History replays both. Steps of 0.2 Å·amu½ with
+  Sella's gamma at 0.4 (measured: 35–71 SCFs per direction where the
+  defaults stalled); if Sella's inner loop gives out near a minimum, that
+  direction is finished by minimizing and the card says so. PCM supported.
+  Also a batch job (`--calc irc`, usually `--from` a Transition State job;
+  no mid-path resume) in `quantui submit`, `quantui-batch` and the app's
+  SLURM path; `results` prints the barriers and verdict.
+- **Full symmetry labels for D4h, D4, C4v and D2d** vibrational modes
+  (square-planar, square-pyramidal and allene-type molecules) instead of
+  their D2h/C2v/D2 subgroup labels. B1 and B2 follow the usual convention
+  (C2′ axes, or σv planes, through the ligands), so a square-planar AB4's
+  B1g is the in-plane stretch. Point-group detection for mode labels no
+  longer drops to a lower group at the loose tolerance (an exact square
+  pyramid was labelled C2v).
+- **The Viewer draws the HOMO and LUMO** (M-VIEWER VW.7): when orbitals are
+  saved (app or batch job), the HOMO and LUMO, each spin for unrestricted
+  results, are also saved as gzipped cubes at the Isosurface panel's
+  default grid (about 0.4 MB each; `frontier_cubes/`). The desktop and
+  browser Viewer, which have no PySCF, draw those; for any other orbital,
+  density or ESP they say to open the result in the full QuantUI. Set
+  `QUANTUI_FRONTIER_CUBES=0` to skip them.
+- **`quantui view` opens the last folder it showed** when started without
+  one (desktop shortcuts), instead of the home directory.
+- **`quantui jobs`** (M-BATCH2 B2.9): your batch jobs, newest first, with
+  where each one is: waiting, running (with the worker's progress),
+  done or failed. With `squeue` on PATH it refreshes the job records from
+  the queue first; without it (an OnDemand session) it reads each job
+  folder. `--running` lists unfinished jobs, `--all` every job.
+- **History lists batch jobs not finished yet** (B2.10): on app start and
+  on Refresh, jobs submitted from a terminal show their state and progress
+  from their job folders, since OnDemand has no `squeue`. A
+  terminal-submitted job's record is marked succeeded when its result is
+  saved to History.
+- **Transition State as a batch job** (M-TS TS.5): `quantui submit`,
+  `quantui-batch submit --calc transition_state` and the app's SLURM path
+  run the same Sella search and frequency check as the window, PCM included.
+  A killed job resumes the search from its last step, never redoes a
+  finished search, and keeps the frequency check's finished displacements.
+  History shows the stationary point found with its search path;
+  `results` prints the verdict; `--from` a TS job starts from its saddle
+  point. A post-HF method is refused before the job queues. Both Apptainer
+  images now install the `[ts]` extra (Sella), which Transition State needs
+  on the cluster in the window as well.
+- **Clarity and layout pass** (M-UIPOLISH, from a rendered-UI walk-through):
+  - Molecules open facing the camera in every viewer (principal axes), so
+    water no longer looks linear and the dipole arrow is visible.
+  - The library finds common names ("water", "ammonia", "benzene"); QM9
+    entries come after the curated ones and duplicates are listed once.
+  - Two-column layouts on wide screens: Calculate (molecule | setup + run),
+    Results (card | structure), and the Analysis viewer, Mulliken,
+    Vibrational and Orbital panels; they stack on narrow windows.
+  - One-line header with the toolbar, a one-line step indicator, the
+    "Calculation complete" links right under Run, and a shorter, resizable
+    log that hides internal bookkeeping lines.
+  - Analysis lists the panels that have data first; plots opened from a
+    collapsed panel fill their width; Raman follows the IR axis direction.
+  - UV-Vis shows vacuum-UV bands (the window started at 100 nm) and lists
+    the excited states; NMR groups equivalent nuclei and uses one
+    Atom | σ | δ table.
+  - Live and History result cards show the same rows; frequencies are
+    listed with their symmetry labels; formulas read NH3, not H3N.
+  - Compare uses checkboxes and renders its chart; History offers recent
+    results as links with the other filters folded away; Help and Report
+    Issue open as side drawers (Esc closes both).
+  - Shorter copy throughout, a 12 px minimum text size, clearer section
+    headings, neutral Report Issue / Exit / idle Cancel buttons.
+  - Fixed: the System Settings GPU row could stay at "checking…" forever.
+- **Vibrational-mode symmetry labels** (M-SPECTRA2 SPC2.4) — after a Frequency
+  calculation each normal mode gets its irreducible representation: a *Sym.*
+  column and a Γvib caption in the Vibrational mode table (NH₃: 2A₁ + 2E), the
+  label in the mode dropdown, and a *Symmetry* line in the IR and Raman stick
+  hovers. Works for live results and History reloads (computed from the saved
+  displacements). Full-group labels for abelian groups, C3v, D3h, D3, D3d, D6h,
+  Td, Oh and linear molecules (σ/π); other groups (e.g. D4h) show labels in
+  PySCF's computational subgroup, said so in the caption.
+  `quantui.symmetry.label_mode_irreps()`.
+- **Diffuse basis sets** — `6-31+G*`, `6-31++G**`, `aug-cc-pVDZ` and
+  `def2-SVPD` join the basis menu (each next to the set it extends), for
+  anions, radical anions and weakly bound species. Available with PySCF in the
+  app, `quantui submit` and `quantui-batch`; PyFock's menu is unchanged.
+  `6-31+G(d)` / `6-31++G(d,p)` are accepted as the same sets. The basis card
+  marks them *Diffuse*, the educational notes explain them and nudge an anion
+  on a non-diffuse basis toward one, and the basis-set help topic has a new
+  *Anions need diffuse functions* paragraph. SLURM memory factors and the time
+  estimator's basis-function table cover the new sets.
+  `config.DIFFUSE_BASIS_SETS` / `config.is_diffuse_basis()` list them.
+- **`quantui results JOB_DIR`** — the `quantui-batch results` summary
+  (convergence, energy, imaginary modes, strongest IR bands, excited states,
+  NMR shifts) from inside the image. Both now also note a saddle-point
+  retry.
+- **Site limits for batch jobs** — `QUANTUI_SLURM_MAX_MEMORY_GB`,
+  `QUANTUI_SLURM_ESTIMATE_MAX_MEMORY_GB` and `QUANTUI_SLURM_MAX_CORES` set the
+  hard limits and the automatic estimate's own memory ceiling (defaults
+  unchanged: 128 GB, 32 cores). Set them in the image environment before
+  `quantui install-launcher` so `quantui-batch` uses the same values.
+- **Viewer mode (`quantui view [FOLDER]`)** — a lightweight QuantUI with only
+  the History and Analysis tabs, pointed at a results folder, needing no quantum
+  engine. `QuantUIApp(viewer=True, results_dir=...)` adds a results-folder bar
+  above the tabs; `quantui view` starts Voilà on a free `127.0.0.1` port and
+  opens the browser. Packaging for two delivery routes lives in
+  `packaging/viewer/` (unsigned conda-constructor desktop installers and a
+  Voici/Pyodide browser build), built by the new `viewer-builds` workflow.
+- **QuantUI Viewer in the docs** — new *QuantUI Viewer* page
+  (`/viewer/`) with a link to the browser Viewer, which the Pages workflow now
+  builds and publishes at `/viewer/app/` on each release and docs change.
+  Publishing a release also attaches the three Viewer installers to it.
+- **SLURM GPU and account settings** — `QUANTUI_SLURM_GRES`,
+  `QUANTUI_SLURM_QOS` and `QUANTUI_SLURM_ACCOUNT` add `#SBATCH --gres`,
+  `--qos` and `--account` lines to generated batch scripts (app, `quantui
+  submit` and `quantui-batch`). A GRES that asks for a GPU also turns on
+  `apptainer exec --nv`; `QUANTUI_SLURM_NV=1`/`0` overrides that.
+- **Batch Geometry Opt results are complete** — a SLURM `geometry_opt`
+  result now records the optimized geometry (`final_molecule`), the final
+  SCF's dipole moment and Mulliken charges, so History and
+  `quantui-batch results` show them without a follow-up single point.
+  `--from` chaining reads the recorded geometry.
+
+### Changed
+
+- **`quantui view` needs a per-run token.** It listened on 127.0.0.1 with
+  no authentication, so any local process or web page could start kernels
+  on its port; it now starts Voila with a random token and opens the URL
+  that carries it. A request without it gets a login page. (Standalone
+  Voila has no XSRF setting, so the `disable_check_xsrf` flag was never in
+  effect for the viewer; DEC-001's container setting is unchanged.)
+- **Frequency results check the geometry** — every Frequency run now
+  computes the forces at the input geometry. When the largest force is above
+  the Geometry Opt threshold (0.05 eV/Å) the result card (live and History)
+  and the Analysis thermochemistry box warn that the geometry is not a
+  stationary point, so its frequencies and thermochemistry are not
+  meaningful, and say how to fix it. `FreqResult.max_force_ev_per_ang`;
+  saved as `spectra.ir.max_force_ev_per_ang`.
+- **IR spectra run 4000 → 400 cm⁻¹ by default** (FTIR convention). An
+  **Axis** dropdown on the IR panel switches back to 400 → 4000; the choice
+  is remembered (`viz.ir_axis` in user settings). `plot_ir_spectrum()` gains
+  `descending=`.
+- **Energy-level diagram hides core orbitals by default** — occupied
+  orbitals more than 50 eV below the HOMO (e.g. water's O 1s) no longer set
+  the Y range and squeeze the valence levels into a sliver; the subtitle says
+  how many are hidden and a **Show core orbitals** checkbox restores them.
+  The HOMO–LUMO gap label no longer overlaps the axis labels.
+- **Dipole arrow convention** — the Mulliken panel says which end the arrow
+  head marks and offers both conventions (− → +, IUPAC/physics, default; or
+  + → −, the chemistry crossed arrow), remembered as `viz.dipole_arrow`.
+- **Frequency card** — title reads "H2O · B3LYP/6-31G* (RKS)"; H and G are
+  shown with their thermal correction vs E in kJ/mol instead of an absolute
+  kJ/mol value.
+- **Less duplication, tidier layout** — viewers no longer repeat the molecule
+  facts in a "Molecule Information" box; the launcher notebook drops its
+  duplicate "QuantUI" heading; result tables are compact and left-aligned;
+  the empty Calculate tab no longer reserves a blank viewer block.
+- **Esc closes the Help panel** (as does its Close button).
+- **Clearer controls** — no more truncated labels or "?.." buttons; PES atom
+  chips read "O1"; XYZ table headers line up; a **Done** button closes the
+  molecule editor; the Help panel has a **Close** button; System Settings
+  groups all settings in one card and says PlotlyMol; the activity indicator
+  is a neutral status chip; History, Compare and the Analysis heading show
+  readable times ("2026-10-25 04:31").
+- **Context-aware extras** — the spin-state helper appears only for molecules
+  with a transition metal; "Use mode → new Frequency calc" only when there
+  are imaginary modes; Analysis panels that don't apply say what they need in
+  their title; dark themes give 3D viewers the panel colour (also in PNG
+  exports) instead of black.
+- `import quantui` no longer loads numpy, RDKit, ASE, Plotly, IPython or
+  requests; every public name is resolved when first used. `quantui`
+  command-line tools and the batch worker start in a fraction of the time,
+  which matters on cluster login nodes (slow shared filesystems, per-user
+  thread limits).
+
+### Fixed
+
+- **"Copy path" in the browser viewer** no longer raises: Pyodide cannot
+  start the thread that resets the label, so the label just stays.
+- **`quantui-batch check` prints a fix hint only under a failed or warning
+  line.** Passing lines showed their hint too (`[ok  ] image …` followed by
+  "ask your instructor: the course image is missing or unreadable"), which
+  read as an error to students.
+- **Generate Isosurface works again for molecular orbitals** — it failed for
+  every MO with `unexpected keyword argument 'esp_range'` since the ESP-map
+  release. The orbital gallery was not affected.
+- **Edit Structure stays available after a molecule loads** — loading or
+  changing a molecule rebuilt the Calculate panel without it.
+- **Mulliken viewer** opens charge-coloured with the dipole arrow when those
+  boxes are ticked, instead of only after a box was toggled.
+- **Sliders are visible on every theme** (ipywidgets 8 sliders were unstyled:
+  no visible track, and a white handle on the Light theme), and the selected
+  option of toggle-button groups and History filter chips is now highlighted.
+- The QM pre-optimization checkbox no longer keeps the PES Scan wording
+  ("…before scan") after switching to another calculation type.
+- The Files tab re-lists its folder when opened, so newly saved results show
+  without clicking Refresh.
+- PES Scan: suggested Start/Stop values are rounded (0.001 Å / 0.1°) and the
+  unit label sits after Stop rather than after Points.
+- **Time-estimate basis-function counts** — the per-element table behind
+  `calc_log.count_basis_functions` had drifted from PySCF for 75 entries
+  (every element in def2-TZVP, e.g. H 14 instead of 6; Li/Be and Na–Ar in
+  the 6-31G*, cc-pV*Z and def2-SVP rows; Al–Ar in 3-21G/6-31G). It is now
+  generated from PySCF's AO counts and a test checks every entry. History
+  records logged before this keep their old `n_basis`, so estimates for
+  def2-TZVP and second-row/heavier molecules settle as new runs are logged.
+- **CPU image no longer overrides a caller's `QUANTUI_RESULTS_DIR` /
+  `QUANTUI_FREQ_PARALLEL`** (M-BATCH2 B2.12). `apptainer/quantui.def`
+  hard-exported both, so a site module or job script setting either was
+  silently clobbered inside the container. Both are now defaults
+  (`${VAR:-default}`), matching `quantui-gpu.def`.
+
+- History's **Refresh** button also saves batch jobs that finished since
+  the app started; before, they appeared only after a restart or a Cluster
+  Jobs refresh.
+- The batch resource estimate knows def2-SVP, def2-TZVP and LANL2DZ (they
+  used a generic factor), treats `6-31G(d)` / `6-31G(d,p)` like `6-31G*` /
+  `6-31G**`, and adds walltime for TD-DFT runs with more than 10 states and
+  PES scans with more than 10 points.
+- Batch `live.log` files no longer contain a copy of QuantUI's worker
+  source. PySCF writes the running script into its output at the log level
+  QuantUI uses; in a batch job that script is the worker (~900 lines per
+  calculation). PySCF's version and input summary are still logged.
+- Batch job and folder names write Pople bases the usual way: `6-31G*` →
+  `6-31Gd`, `6-31G(d,p)` → `6-31Gdp`, `6-31+G*` → `6-31pGd` (was
+  `6-31Gx`, `6-31Gxdxpx`, …).
+- `quantui submit` and `quantui-batch` refuse an XYZ file whose first line
+  gives a different atom count from the atoms listed (a cut-off or padded
+  file). The app still only warns, where you see the structure.
+- `quantui submit` (and Resubmit) syncs job states with the SLURM queue before
+  checking the concurrent-job limit. With no app open, finished jobs stayed
+  "submitted" in the registry and kept counting, so after two submissions
+  every further one was refused.
+- Generated SLURM scripts ask for one task with N CPUs
+  (`--ntasks=1 --cpus-per-task=N`) instead of N tasks, which is what the
+  single multi-threaded worker uses; a `SLURM_CPUS_PER_TASK` inherited from
+  the submitting allocation no longer sets the thread count.
+- `apptainer exec --nv` is no longer used for CPU jobs, and the worker runs
+  the batch image's own `python` instead of the submitting process's
+  interpreter path, which need not exist in that image.
+- SLURM jobs resume again after a resubmission. Since job folders got one
+  attempt folder per run, the checkpoint and the cached pre-opt geometry
+  were kept inside the attempt folder, which the next attempt never sees,
+  so killed geometry optimizations, PES scans and frequency runs restarted
+  from scratch. Both now live in the job folder.
+- The geometry optimization before a Frequency calculation (app and batch)
+  now converges to 0.01 eV/Å instead of 0.05. Residual forces at 0.05 left
+  soft modes such as methyl rotors wrong, or imaginary (CHEM-3200 Lab 4).
+  Plain Geometry Opt and the pre-opt for other calc types are unchanged.
+- When that pre-optimized Frequency run still finds an imaginary mode below
+  20i cm⁻¹ (usually a methyl or other rotor stuck at its eclipsed saddle
+  point), QuantUI displaces along the mode, re-optimizes and repeats the
+  frequencies once (app and batch). The result card and `result.json`
+  (`spectra.ir.imaginary_mode_retry`) say what was done; a mode still
+  imaginary after the retry is reported, not retried again.
+- **Viewer installers: the shortcut opened and closed a console without
+  starting anything.** `quantui view` looked for the `voila` command on
+  `PATH`, which a shortcut launch of an unactivated install does not set; it
+  printed "Voilà is not installed or not on PATH" and exited. It now runs
+  Voilà as `python -m voila` from its own interpreter and puts the install's
+  folders on `PATH` for the server. The Windows shortcut runs through
+  `cmd /c ... || pause`, so any future failure stays on screen. Stopping
+  `quantui view` now stops Voilà too, instead of leaving it serving. The
+  installer CI smoke test starts the viewer the way a shortcut does and
+  fetches a page (it previously only ran `quantui view --help`).
+
+- History → "View Results" / "View Analysis" navigated by fixed tab index, so
+  with the Cluster Jobs tab visible they landed one tab early. They now look
+  the tab up by name.
+- Background renders (vibrational animation, isosurface, export) and the
+  activity-light timer fall back to running inline when threads are
+  unavailable instead of leaving the panel stuck.
+
 ## [0.10.0] - 2026-10-03
 
 ### Added
@@ -1093,7 +1390,9 @@ Initial public scaffolding of the QuantUI package: `quantui` package with
 `calculator.py`, basic notebook launcher, Apptainer container definition,
 MIT license, and project metadata.
 
-[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.10.0...HEAD
+[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.11.1...HEAD
+[0.11.1]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.11.0...v0.11.1
+[0.11.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.10.0...v0.11.0
 [0.10.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.9.0...v0.10.0
 [0.9.0]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.8.2...v0.9.0
 [0.8.2]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.8.1...v0.8.2

{quantui-0.10.0/quantui.egg-info → quantui-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: quantui
-Version: 0.10.0
+Version: 0.11.1
 Summary: An open-source frontend for DFT and post-HF quantum chemistry with PySCF
 Author-email: Jonathan Schultz <nccu-schultz-lab@users.noreply.github.com>
 License: MIT License
@@ -66,7 +66,7 @@ Provides-Extra: pyfock
 Requires-Dist: pyfock<0.3,>=0.1.7; extra == "pyfock"
 Requires-Dist: ase<4,>=3.22.0; extra == "pyfock"
 Requires-Dist: scipy<2,>=1.10; extra == "pyfock"
-Requires-Dist: numba<0.68,>=0.57; extra == "pyfock"
+Requires-Dist: numba<0.69,>=0.57; extra == "pyfock"
 Provides-Extra: ase
 Requires-Dist: ase<4,>=3.22.0; extra == "ase"
 Provides-Extra: xtb
@@ -99,11 +99,11 @@ Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
 Requires-Dist: pytest-mock>=3.10.0; extra == "dev"
 Requires-Dist: pytest-xdist>=3.0.0; extra == "dev"
 Requires-Dist: build>=1.0.0; extra == "dev"
-Requires-Dist: mypy<2.4,>=1.10; extra == "dev"
+Requires-Dist: mypy<2.5,>=1.10; extra == "dev"
 Requires-Dist: types-requests>=2.28.0; extra == "dev"
-Requires-Dist: black~=26.5.1; python_version >= "3.10" and extra == "dev"
+Requires-Dist: black<26.11.0,>=26.5.1; python_version >= "3.10" and extra == "dev"
 Requires-Dist: black~=25.11.0; python_version < "3.10" and extra == "dev"
-Requires-Dist: ruff~=0.16.0; extra == "dev"
+Requires-Dist: ruff<0.18,>=0.16; extra == "dev"
 Requires-Dist: pre-commit>=3.7.0; extra == "dev"
 Dynamic: license-file
 
@@ -404,7 +404,9 @@ pip install "quantui[ts]"
 
 Sella pulls in jax/jaxlib (about 380 MB) and is LGPL-3.0, used as a
 separately installed library. Without it the calc type stays in the menu and
-says how to install it. Local runs only for now (not SLURM batch jobs).
+says how to install it. It also runs as a SLURM batch job
+(`quantui-batch submit FILE --calc transition_state`); both Apptainer images
+include it.
 
 ### Optional: GFN-FF metal pre-optimization (xtb)
 
@@ -625,6 +627,7 @@ Five step-by-step notebooks in [`notebooks/tutorials/`](https://github.com/The-S
 | Single Point | Energy, HOMO-LUMO gap, Mulliken charges, dipole moment |
 | Geometry Opt | Optimised structure, trajectory animation; optional frozen atoms |
 | Transition State | Saddle point near the input geometry (Sella, optional `[ts]` extra), then a frequency check: transition state, minimum, or higher-order saddle point; animated imaginary mode |
+| IRC | Reaction path from a Transition State result, downhill both ways to the minima it connects (Sella); barrier from each side, energy profile and animated path |
 | Frequency | Vibrational frequencies, ZPVE, IR intensities, thermochemistry at any temperature and pressure, 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 |
@@ -636,6 +639,9 @@ Five step-by-step notebooks in [`notebooks/tutorials/`](https://github.com/The-S
 STO-3G (fast, good for learning) → 3-21G → 6-31G / 6-31G\* / 6-31G\*\* →
 cc-pVDZ / cc-pVTZ → def2-SVP / def2-TZVP → LANL2DZ
 
+**Diffuse** sets for anions (including radical anions) and weakly bound species:
+6-31+G\* / 6-31++G\*\* / aug-cc-pVDZ / def2-SVPD.
+
 For **transition metals and heavy elements**, use **def2-SVP** / **def2-TZVP**
 or **LANL2DZ** — these carry the effective core potentials that cover metals,
 whereas the Pople (`6-31G…`) and Dunning (`cc-pV…`) sets do not. QuantUI's
@@ -707,7 +713,7 @@ quantui/                  Main package
 notebooks/
   molecule_computations.ipynb   Main user-facing interface (3-cell launcher)
   tutorials/                    Step-by-step guided notebooks (01–05)
-tests/                    pytest test suite (~3,700 tests; run in parallel via pytest-xdist)
+tests/                    pytest test suite (~4,100 tests; run in parallel via pytest-xdist)
 apptainer/                Container definition for reproducible deployment
 local-setup/              Conda environment definition
 pyproject.toml            Package metadata and tool config

{quantui-0.10.0 → quantui-0.11.1}/README.md

@@ -295,7 +295,9 @@ pip install "quantui[ts]"
 
 Sella pulls in jax/jaxlib (about 380 MB) and is LGPL-3.0, used as a
 separately installed library. Without it the calc type stays in the menu and
-says how to install it. Local runs only for now (not SLURM batch jobs).
+says how to install it. It also runs as a SLURM batch job
+(`quantui-batch submit FILE --calc transition_state`); both Apptainer images
+include it.
 
 ### Optional: GFN-FF metal pre-optimization (xtb)
 
@@ -516,6 +518,7 @@ Five step-by-step notebooks in [`notebooks/tutorials/`](https://github.com/The-S
 | Single Point | Energy, HOMO-LUMO gap, Mulliken charges, dipole moment |
 | Geometry Opt | Optimised structure, trajectory animation; optional frozen atoms |
 | Transition State | Saddle point near the input geometry (Sella, optional `[ts]` extra), then a frequency check: transition state, minimum, or higher-order saddle point; animated imaginary mode |
+| IRC | Reaction path from a Transition State result, downhill both ways to the minima it connects (Sella); barrier from each side, energy profile and animated path |
 | Frequency | Vibrational frequencies, ZPVE, IR intensities, thermochemistry at any temperature and pressure, 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 |
@@ -527,6 +530,9 @@ Five step-by-step notebooks in [`notebooks/tutorials/`](https://github.com/The-S
 STO-3G (fast, good for learning) → 3-21G → 6-31G / 6-31G\* / 6-31G\*\* →
 cc-pVDZ / cc-pVTZ → def2-SVP / def2-TZVP → LANL2DZ
 
+**Diffuse** sets for anions (including radical anions) and weakly bound species:
+6-31+G\* / 6-31++G\*\* / aug-cc-pVDZ / def2-SVPD.
+
 For **transition metals and heavy elements**, use **def2-SVP** / **def2-TZVP**
 or **LANL2DZ** — these carry the effective core potentials that cover metals,
 whereas the Pople (`6-31G…`) and Dunning (`cc-pV…`) sets do not. QuantUI's
@@ -598,7 +604,7 @@ quantui/                  Main package
 notebooks/
   molecule_computations.ipynb   Main user-facing interface (3-cell launcher)
   tutorials/                    Step-by-step guided notebooks (01–05)
-tests/                    pytest test suite (~3,700 tests; run in parallel via pytest-xdist)
+tests/                    pytest test suite (~4,100 tests; run in parallel via pytest-xdist)
 apptainer/                Container definition for reproducible deployment
 local-setup/              Conda environment definition
 pyproject.toml            Package metadata and tool config

{quantui-0.10.0 → quantui-0.11.1}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "quantui"
-version = "0.10.0"
+version = "0.11.1"
 description = "An open-source frontend for DFT and post-HF quantum chemistry with PySCF"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -142,7 +142,7 @@ pyfock = [
     "scipy>=1.10,<2",
     # 0.68.0rc1 can be selected by PyFock's permissive floor and brought a
     # prerelease llvmlite that crashed at import on Linux/Python 3.12.
-    "numba>=0.57,<0.68",
+    "numba>=0.57,<0.69",
 ]
 
 # ASE: structure I/O, extended molecule library, geometry optimisation
@@ -233,7 +233,7 @@ dev = [
     # that let quantui.engines silently vanish from the shipped package
     # while CI, always editable, stayed green).
     "build>=1.0.0",
-    "mypy>=1.10,<2.4",  # pinned, not an open floor — same reasoning as
+    "mypy>=1.10,<2.5",  # pinned, not an open floor — same reasoning as
     # black/ruff below: it must agree with .pre-commit-config.yaml's rev,
     # which is what CI enforces (M-TYPECHECK TYPE.2). A newer mypy silently
     # disagrees: 2.x drops support for python_version = "3.9" (this repo's
@@ -251,9 +251,9 @@ dev = [
     # could differ slightly from CI — CI's authority is the pinned pre-commit rev,
     # whose lint job runs on 3.11, so run `pre-commit run` before pushing if you
     # develop on 3.9. (ruff 0.16 needs only >=3.7, so it needs no split.)
-    "black~=26.5.1; python_version >= '3.10'",
+    "black>=26.5.1,<26.11.0; python_version >= '3.10'",
     "black~=25.11.0; python_version < '3.10'",
-    "ruff~=0.16.0",
+    "ruff>=0.16,<0.18",
     "pre-commit>=3.7.0",
 ]