The-Schultz-Lab · NCCU-Schultz-Lab · Jul 31, 2026 · Jul 31, 2026 · Jul 31, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,8 +7,30 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 
 ## [Unreleased]
 
+## [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
@@ -20,9 +42,30 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
 - **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
@@ -36,22 +79,11 @@ and this project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.ht
   avoids the base image's implicit `defaults` channel. No change to the shipped
   package set or runtime behavior.
 
-### Added
-
-- **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.
-
 ### 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
@@ -429,7 +461,8 @@ 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/v0.4.1...HEAD
+[Unreleased]: https://github.com/The-Schultz-Lab/QuantUI/compare/v0.5.0...HEAD
+[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

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,39 @@
+# 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
diff --git a/README.md b/README.md
@@ -1,8 +1,9 @@
 # QuantUI
 
+[![PyPI](https://img.shields.io/pypi/v/quantui)](https://pypi.org/project/quantui/)
 [![CI](https://github.com/The-Schultz-Lab/QuantUI/actions/workflows/ci.yml/badge.svg)](https://github.com/The-Schultz-Lab/QuantUI/actions/workflows/ci.yml)
 [![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://the-schultz-lab.github.io/QuantUI/)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/The-Schultz-Lab/QuantUI/blob/main/LICENSE)
 [![Python](https://img.shields.io/badge/python-3.9%20|%203.10%20|%203.11-blue)](https://www.python.org)
 
 A powerful open-source frontend for DFT and post-HF quantum chemistry.
@@ -78,9 +79,9 @@ research and classroom use.
 ### Windows users: Apptainer container
 
 PySCF does not install on Windows natively. The
-[`apptainer/quantui.def`](apptainer/quantui.def) container bundles
+[`apptainer/quantui.def`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/quantui.def) container bundles
 the complete environment and runs anywhere Apptainer/Singularity is available.
-See [`apptainer/README.md`](apptainer/README.md) for build and run instructions.
+See [`apptainer/README.md`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md) for build and run instructions.
 
 ---
 
@@ -105,7 +106,7 @@ python -m pip install quantui[pyscf,ase,app]
 
 ### Option C — Apptainer container (Windows / reproducible deployment)
 
-See [apptainer/README.md](apptainer/README.md).
+See [apptainer/README.md](https://github.com/The-Schultz-Lab/QuantUI/blob/main/apptainer/README.md).
 
 ### Optional: GPU acceleration (NVIDIA + Linux / WSL)
 
@@ -194,9 +195,9 @@ no rebuild.
 
 | Platform | File | Action |
 | --- | --- | --- |
-| Windows | [`launchers/launch-native.bat`](launchers/launch-native.bat) | Activates the `quantui` conda env inside WSL Ubuntu, runs Voilà, and opens `http://localhost:8867` |
-| macOS | [`launchers/launch-native.command`](launchers/launch-native.command) | Activates the local `quantui` conda env directly (no WSL needed) and does the same |
-| Linux / WSL | [`launchers/launch-native.sh`](launchers/launch-native.sh) | Run `./launchers/launch-native.sh` from a Linux or WSL terminal; activates `quantui` and does the same |
+| Windows | [`launchers/launch-native.bat`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/launchers/launch-native.bat) | Activates the `quantui` conda env inside WSL Ubuntu, runs Voilà, and opens `http://localhost:8867` |
+| macOS | [`launchers/launch-native.command`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/launchers/launch-native.command) | Activates the local `quantui` conda env directly (no WSL needed) and does the same |
+| Linux / WSL | [`launchers/launch-native.sh`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/launchers/launch-native.sh) | Run `./launchers/launch-native.sh` from a Linux or WSL terminal; activates `quantui` and does the same |
 
 All launchers reuse port `8867`, so you can keep the same browser tab pinned
 across platforms. They **auto-detect your conda installation** — miniforge
@@ -221,7 +222,7 @@ prefix — so no path editing is needed regardless of which you installed.
 
 ### Windows — pin to the Start menu
 
-1. Right-click [`launchers/launch-native.bat`](launchers/launch-native.bat) in
+1. Right-click [`launchers/launch-native.bat`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/launchers/launch-native.bat) in
    File Explorer → **Send to** → **Desktop (create shortcut)**.
 2. Rename the shortcut to something friendly like `QuantUI`.
 3. *(Optional)* Right-click the shortcut → **Properties** → **Change Icon...**
@@ -242,7 +243,7 @@ in your browser.
 ### macOS — pin to the Dock / Launchpad
 
 **Quickest:** double-click
-[`launchers/launch-native.command`](launchers/launch-native.command)
+[`launchers/launch-native.command`](https://github.com/The-Schultz-Lab/QuantUI/blob/main/launchers/launch-native.command)
 from Finder. macOS will open Terminal, run the script, and pop the app open
 in your browser. The first launch is gated by Gatekeeper: right-click the
 file → **Open** → **Open** to clear it (one time only).
@@ -293,7 +294,7 @@ quantui gpu check             # is GPU offload available right now?
 quantui analytics build --open  # build dashboard.html + open in browser
 ```
 
-Full reference with all flags and examples: [docs/CLI.md](docs/CLI.md).
+Full reference with all flags and examples: [docs/CLI.md](https://github.com/The-Schultz-Lab/QuantUI/blob/main/docs/CLI.md).
 
 ---
 
@@ -311,21 +312,21 @@ or any spreadsheet without screen-scraping. The quick reference:
 | Spectrum data in Excel | `*_data_*.csv` | Excel, LibreOffice, pandas |
 | Share whole result | `<result>.zip` (Export bundle) | Any unzip tool |
 
-Full per-tool walkthrough with troubleshooting: [docs/IMPORTING-INTO-AVOGADRO.md](docs/IMPORTING-INTO-AVOGADRO.md).
+Full per-tool walkthrough with troubleshooting: [docs/IMPORTING-INTO-AVOGADRO.md](https://github.com/The-Schultz-Lab/QuantUI/blob/main/docs/IMPORTING-INTO-AVOGADRO.md).
 
 ---
 
 ## Tutorials
 
-Five step-by-step notebooks in [`notebooks/tutorials/`](notebooks/tutorials/):
+Five step-by-step notebooks in [`notebooks/tutorials/`](https://github.com/The-Schultz-Lab/QuantUI/tree/main/notebooks/tutorials/):
 
 | Notebook | Topic |
 | --- | --- |
-| [01_first_calculation.ipynb](notebooks/tutorials/01_first_calculation.ipynb) | Your first RHF calculation |
-| [02_basis_set_study.ipynb](notebooks/tutorials/02_basis_set_study.ipynb) | Comparing STO-3G, 6-31G, cc-pVDZ |
-| [03_multiplicity_radicals.ipynb](notebooks/tutorials/03_multiplicity_radicals.ipynb) | Open-shell molecules and UHF |
-| [04_charged_species.ipynb](notebooks/tutorials/04_charged_species.ipynb) | Ions and charged systems |
-| [05_comparing_results.ipynb](notebooks/tutorials/05_comparing_results.ipynb) | Side-by-side result analysis |
+| [01_first_calculation.ipynb](https://github.com/The-Schultz-Lab/QuantUI/blob/main/notebooks/tutorials/01_first_calculation.ipynb) | Your first RHF calculation |
+| [02_basis_set_study.ipynb](https://github.com/The-Schultz-Lab/QuantUI/blob/main/notebooks/tutorials/02_basis_set_study.ipynb) | Comparing STO-3G, 6-31G, cc-pVDZ |
+| [03_multiplicity_radicals.ipynb](https://github.com/The-Schultz-Lab/QuantUI/blob/main/notebooks/tutorials/03_multiplicity_radicals.ipynb) | Open-shell molecules and UHF |
+| [04_charged_species.ipynb](https://github.com/The-Schultz-Lab/QuantUI/blob/main/notebooks/tutorials/04_charged_species.ipynb) | Ions and charged systems |
+| [05_comparing_results.ipynb](https://github.com/The-Schultz-Lab/QuantUI/blob/main/notebooks/tutorials/05_comparing_results.ipynb) | Side-by-side result analysis |
 
 ---
 
@@ -438,4 +439,4 @@ CHANGELOG.md              Release history (Keep a Changelog format)
 
 ## License
 
-[MIT](LICENSE) — Copyright 2026 The Schultz Lab, North Carolina Central University
+[MIT](https://github.com/The-Schultz-Lab/QuantUI/blob/main/LICENSE) — Copyright 2026 The Schultz Lab, North Carolina Central University
diff --git a/apptainer/quantui.def b/apptainer/quantui.def
@@ -21,7 +21,7 @@ FROM: condaforge/miniforge3:latest
 %labels
   Maintainer "Jonathan Schultz"
   Purpose "Local teaching interface for quantum chemistry calculations"
-  Version "0.4.1"
+  Version "0.5.0"
 
 %environment
   export PATH="/opt/conda/bin:${PATH}"

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,10 +1,14 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=9.2.2"]
+# setuptools_scm was listed here historically but never configured — there is
+# no [tool.setuptools_scm] table and `version` below is static, so nothing
+# consumed it. Dropped for the first PyPI release rather than shipping a
+# build dependency that does nothing.
+requires = ["setuptools>=64", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "quantui"
-version = "0.4.1"
+version = "0.5.0"
 description = "An open-source frontend for DFT and post-HF quantum chemistry with PySCF"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -23,20 +27,55 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    # PyPI shows the licence from this classifier in the sidebar; the
+    # [project] license table alone is not enough for the old-style display.
+    "License :: OSI Approved :: MIT License",
+    # PySCF is Linux/macOS only, so Windows users need the container. Saying so
+    # in metadata means `pip` users see it before they hit an install failure.
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Environment :: Web Environment",
+    "Framework :: Jupyter",
 ]
 
+# Runtime dependencies carry MAJOR-version caps, not open floors (M-PYPI
+# PYPI.2). QuantUI is installed by students as an application, not consumed as
+# a library, so the usual "don't cap in a library" advice does not apply — a
+# resolution conflict is a worse outcome for them than a slightly stale pin,
+# but a silent break from a new major is worse still.
+#
+# The concrete motivation: Voila 0.5.x declares no upper bound on jupyterlab,
+# so a fresh install already resolves a Lab newer than Voila was built against
+# and logs federated-extension errors in the browser console (see GOTCHAS,
+# "Voila 0.5.x does not bound JupyterLab"). Harmless today because the failing
+# extension is Notebook's, which Voila does not use — but shipping an unbounded
+# stack means the next major can break a student with no error we control.
+#
+# Caps are at the MAJOR boundary only: minor/patch updates still flow, and the
+# bounds reflect what has actually been tested rather than pretending to more.
+# Revisit when a new major of any of these is validated.
 dependencies = [
-    "jupyter>=1.0.0",
-    "ipywidgets>=8.0.0",
-    "notebook>=7.0.0",
-    "numpy>=1.24.0",
-    "requests>=2.28.0",
-    "py3Dmol>=2.0.0",
-    "matplotlib>=3.7.0",
-    "plotly>=5.0.0",
-    "plotlymol>=0.2.1",
+    "jupyter>=1.0.0,<2",
+    "ipywidgets>=8.0.0,<9",
+    "notebook>=7.0.0,<8",
+    "numpy>=1.24.0,<3",
+    "requests>=2.28.0,<3",
+    "py3Dmol>=2.0.0,<3",
+    "matplotlib>=3.7.0,<4",
+    "plotly>=5.0.0,<7",
+    "plotlymol>=0.2.1,<1",
 ]
 
+[project.urls]
+# Rendered as the sidebar links on the PyPI project page. "Homepage" and
+# "Source" are the two PyPI actually highlights; the rest appear under
+# "Project links".
+Homepage = "https://github.com/The-Schultz-Lab/QuantUI"
+Source = "https://github.com/The-Schultz-Lab/QuantUI"
+Documentation = "https://the-schultz-lab.github.io/QuantUI/"
+Changelog = "https://github.com/The-Schultz-Lab/QuantUI/blob/main/CHANGELOG.md"
+Issues = "https://github.com/The-Schultz-Lab/QuantUI/issues"
+
 [project.scripts]
 # ``quantui`` CLI — small toolkit for inspecting QuantUI state from
 # the terminal (``quantui log tail -n 50``, etc.). See ``quantui/cli.py``.
@@ -67,20 +106,25 @@ quantui = [
 # pyscf.nmr (that module doesn't exist in released pyscf); it's
 # pyscf.prop.nmr, provided by pyscf-properties below.
 pyscf = [
-    "pyscf>=2.13.0",
+    # .github/dependabot.yml already ignores pyscf MAJOR bumps ("may break
+    # API — review manually"); this cap makes that policy binding for
+    # installers too, not just for our dependency bot.
+    "pyscf>=2.13.0,<3",
     "pyscf-properties",
 ]
 
 # ASE: structure I/O, extended molecule library, geometry optimisation
 ase = [
-    "ase>=3.22.0",
+    "ase>=3.22.0,<4",
 ]
 
 # Voilà app server — hides notebook code; students see only the widget UI.
 # Run with: voila notebooks/molecule_computations.ipynb
 app = [
-    "voila>=0.5.0",
-    "ipykernel>=6.0.0",
+    # Capped for the same reason as the runtime stack above: Voila is the
+    # component whose own bounds are too loose, so ours have to hold the line.
+    "voila>=0.5.0,<0.6",
+    "ipykernel>=6.0.0,<8",
 ]
 
 # GPU acceleration via gpu4pyscf + cupy (M-GPU). Linux + NVIDIA CUDA only.
@@ -111,7 +155,7 @@ gpu-cuda13x = [
 # Notebook smoke-test dependencies
 notebook = [
     "nbmake>=1.4.0",
-    "ipykernel>=6.0.0",
+    "ipykernel>=6.0.0,<8",
 ]
 
 # Development dependencies

diff --git a/quantui/__init__.py b/quantui/__init__.py
@@ -7,7 +7,7 @@
 PySCF requires Linux/macOS/WSL. Windows users should use the Apptainer container.
 """
 
-__version__ = "0.4.1"
+__version__ = "0.5.0"
 
 import logging
 from typing import Any