v5.0.0a1

MoleditPy 5.0.0a1 is an alpha release from migrate/pyside6-without-openbabel at commit 7f5ba9f8cb9e67ed7f1ac66037a25b222329cfca.

Documentation errata after the alpha release: the README packaged in 5.0.0a1 recommends the older PyPI shortcut helper. That helper's published 3.1.3 release still selects moleditpy-linux on Linux. Install the alpha directly with python -m pip install MoleditPy==5.0.0a1; shortcut setup is optional. The helper update is planned for publication; the installation documentation uses the normal PyPI helper command. Older installer-page claims that Open Babel is bundled are incorrect for this release: the actual wheel dependencies and tested standalone bundles exclude it. Documentation corrections are additive commits after the release; the published tag and artifacts have not been rewritten.

• The GUI now uses PySide6-Essentials. The app selects PySide6 inside its own process so an old QT_API=pyqt6 setting does not cause binding fallback warnings.
• Open Babel is removed from the core and standalone bundles. Core conversion uses RDKit with Direct fallback; additional optimizer engines belong to separate plugins.
• Windows, macOS, and Linux use the single MoleditPy Python package. The separate Linux package and publishing pipeline are retired.
• Python 3.9–3.14 is supported. Python 3.9 uses Qt 6.9; newer supported interpreters use Qt 6.10–6.11. Qt 6.12 is excluded after reproducing a native scene reference-count bug on Linux.
• The core is LGPL-3.0-or-later. Independently developed plugins may choose their own licenses; existing plugin licenses remain unchanged. Source/build and Qt replacement instructions are included.

GUI plugins must migrate to PySide6 for MoleditPy 5. PyQt6, PyQt5, and PySide2 plugins cannot load into the host. Plugin compatibility metadata uses >=5.0.0, <6.0.0; the host's numeric compatibility check also accepts this alpha.

Install the alpha explicitly:

python -m pip install MoleditPy==5.0.0a1

For an old Linux installation, remove the retired packages before installing:

python -m pip uninstall moleditpy-linux openbabel-wheel
python -m pip install MoleditPy==5.0.0a1

Validation: the full local test script passes 2,908 tests. All main-app CI jobs pass, including Linux/macOS/Windows, Python 3.9–3.14 launch probes, native GUI rendering, and the frozen Windows executable. The 37 coordinated migration PRs passed the earlier audit; subsequent CI identified the Linux/Python 3.12 window-lifetime issue described below.

This is a prerelease from the migration branch. The migration PRs have not been merged.

Post-alpha fix on the migration branch: commit bcc81c8 parents UIManager to its native window, so the active style watchdog timer is destroyed with that window. The previous code could leave the manager/timer alive after window destruction and crash in native Qt event processing on Linux/Python 3.12. This fix is not included in the published 5.0.0a1 artifacts; the original tag and files remain unchanged. The regression fails before the fix and passes afterwards; 56 UIManager unit tests and 36 targeted Linux integration tests passed. Fixed-source CI passed, and the fix is included in 5.0.0a2. The published a2 package also passed all 18 OS/Python installation tests.