ChimeraX Developer Meeting

Attendance: Piet, Greg, Tom, Eric, Zach

January 6, 2025

Agenda

• Possible updates Python 3.13, numpy 2, PySide6
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes.
• Back up the Chimera build machine to a solid state drive, Windows 7.

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Discussion

• Jinga github security alert
  • Github notice says jinga is used by ChimeraX and needs updating minor version due to security alert.
  • We will update that.

• Python 3.13
  • ChimeraX 1.9 is at Python 3.11.
  • Should we update to Python 3.13 which was released October 2024?
  • Python project is no longer shipping new Python 3.11 binaries with patches.
  • Numpy 1 does not support Python 3.13 so we would have to also update numpy 1 to numpy 2 which may cause other third-party packages we use that want numpy 1 to fail.
  • Eric is seeing if Python 3.13 fixes the crashing kvFinder bundle on Windows.

• Numpy 2
  • Should we update from numpy 1 (the version for the last 20 years) to numpy 2?
  • Probably needed to go to Python 3.13 because numpy 1 does not support Python 3.13. Not sure if that means they just don't make builds, or if in fact it won't build.
  • Numpy 2 made various breaking changes with the Python API (like array casting rules) that will only become apparent at runtime.
  • Numpy 2 also changes the C ABI in small ways (different structures) so all binary PyPi packages that compile against the numpy C API or use ctypes (e.g. openmm, opengl-accelerate, chimerax, ...) will need to be built for numpy 2.

• PySide 6
  • Zach has added a USE_PYSIDE6 environment variable to build ChimeraX using PySide instead of PyQt.
  • This would allow us to not pay commercial license fees for PyQt6 since PySide6 is free and LGPL licensed.
  • It may be that PySide6 is better supported than PyQt6 because it is part of the official Qt project while PyQt is a one developer effort.
  • Alot of testing of the ChimeraX GUI would be needed to catch the API differences between PySide6 and PyQt6.

• Piet progress
  • USC ScholAR developer has made improvements that are ready to be included in the ChimeraX ScholAR bundle.
  • Piet has started winter classes, including C programming, organic chemistry, and bioinformatics.

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Action Items