Changes between Version 1 and Version 2 of Dev2025-1-6


Ignore:
Timestamp:
Jan 6, 2025, 3:48:12 PM (10 months ago)
Author:
Tom Goddard
Comment:

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  • Dev2025-1-6

    v1 v2  
    77= Agenda =
    88
    9 * !GitHub Actions builds
    10 * Clean-up ChimeraX 1.9 roadmap wiki page
     9* Possible updates Python 3.13, numpy 2, PySide6
    1110* Work in progress reports
    1211* Make Chimera end-of-life bug report and registration changes.
    … …  
    1615= Discussion =
    1716
     17* Jinga github security alert
     18  - Github notice says jinga is used by ChimeraX and needs updating minor version due to security alert.
     19  - We will update that.
     20
     21* Python 3.13
     22  - ChimeraX 1.9 is at Python 3.11.
     23  - Should we update to Python 3.13 which was released October 2024?
     24  - Python project is no longer shipping new Python 3.11 binaries with patches.
     25  - 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.
     26  - Eric is seeing if Python 3.13 fixes the crashing kvFinder bundle on Windows.
     27
     28* Numpy 2
     29  - Should we update from numpy 1 (the version for the last 20 years) to numpy 2?
     30  - 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.
     31  - Numpy 2 made various breaking changes with the Python API (like array casting rules) that will only become apparent at runtime.
     32  - 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.
     33
     34* PySide 6
     35  - Zach has added a USE_PYSIDE6 environment variable to build ChimeraX using PySide instead of PyQt.
     36  - This would allow us to not pay commercial license fees for PyQt6 since PySide6 is free and LGPL licensed.
     37  - 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.
     38  - Alot of testing of the ChimeraX GUI would be needed to catch the API differences between PySide6 and PyQt6.
     39
     40* Piet progress
     41  - USC ScholAR developer has made improvements that are ready to be included in the ChimeraX ScholAR bundle.
     42  - Piet has started winter classes, including C programming, organic chemistry, and bioinformatics. 
    1843
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