ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric

June 24, 2024

Agenda

• Should we update to Python 3.12 for ChimeraX 1.9?
• Work in progress reports
• Make Chimera end-of-life bug report and registration changes for 1.18 release in Spring 2024.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• ChimeraX Ideas milestone clean-up.
• Regular Chimera release.

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Discussion

• ChimeraX 1.8
  • Have seen a few Mac bug reports with no C stack provided by Mac crash reporter.
  • Can tweet 1.8 release as it seems it is working fine.

• Make distclean
  • Greg made "make clean" not remove downloaded third-party packages (from plato archive) so if plato is down we can still build using already downloaded packages.
  • Use "make distclean" to remove downloaded packages.

• ChimeraX dark mode
  • Greg has ChimeraX behaving better in operating system Dark Mode.
  • Uses Qt 6.7 for html panels, Log, file history.
  • Some icons are hard to see (black on transparent background), and new ones could be made. Greg will add mechanism to use a dark mode icon if one is available.

• Python 3.12 for ChimeraX 1.9?
  • Discussed whether to update ChimeraX to Python 3.12.
  • Python 3.12 released October 2023 and is now at 3.12.4.
  • Greg says Python has 3 years of support where they distribute builds with security fixes. So 3.11 from October 2022 is supported until October 2025 (3 ChimeraX releases from now).
  • After 3 year support Python still includes security fixes for another 3 years but does not provide builds, so you have to build yourself to get those.
  • Zach will try a Python 3.12 ChimeraX build to see how many third-party packages cause problems (not yet available for 3.12).

• Chimera 1.18 release
  • Chimera fails reading AlphaFold 3 mmCIF files because of a "." in some mandatory field (chain id?).
  • Greg will make 1.18 release, no candidates, just build and release.

• ChimeraX 1.9 roadmap
  • Eric suggests we finally fix long atom spec parsing crashes.
  • Greg interested in making linux flatpack use system python.

• Linux package manager ChimeraX versions
  • Greg would like to have ChimeraX distributed through standard Ubuntu package repository.
  • Would require agreeing to license in a different way, e.g. on ChimeraX startup.
  • Flatpaks also have repository want to update automatically which presents licensing issues.

• Scan web logs for ChimeraX use statistics
  • Greg suggests we try scanning web logs for statistics on active number of ChimeraX users for future grant applications.

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Action Items

• Zach remove direct use of pip in Makefile.bundle. Use something like $(PYTHON) -m pip so the correct Python is used.