= 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 =