ChimeraX Developer Meeting

Attendance: Greg, Tom, Eric

March 4, 2024

Agenda

• Should we make a 1.7.3 release with garbage collection fix?
• Work in progress reports
• Update prereqs - most done.
• What ChimeraX 1.8 work/tickets should we prioritize for January?
• Worm ribbon implementation, ticket #9942
• Log slow to update when it gets long, Tristan ticket #9909
• Create Grafana dashboards to monitor web services.
• 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.

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Discussion

• ChimeraX mailing list problems
  • Elaine's email to mailing list bounced with "reason: 500 Line too long (see RFC5321 4.5.3.1.6)". Greg thinks this is a bug in the python smtp module breaking and reassembling message lines.
  • Moderated chimerax-users email message that Eric approved appeared in archive but was not set to mailing list members. Apparently these message when to mailman/var/queue/shunted due to errors. Greg unshunted them and they were delivered.
  • A possible 3rd problem is that mailman "queue runners" die and are not restarted, a bug fixed in the next mailman. But that newer mailman requires Python 3.9 while plato has Python 3.8.

• ChimeraX bundle builder atomic_lib problems
  • ChimeraX cannot build atomic_lib a second time on Mac without an explicit "make clean" apparently because libtmpl.a is not "fat".
  • Eric will make a ticket.

• ChimeraX atomic_lib dependency problem
  • After updating the atomic_lib version number trying to rebuild the 7 dependent bundles (atomic, mmcif, pdb, ...) fails with various dependency errors.
  • It seems the only fix is to rebuild all of ChimeraX.
  • Eric will make a ticket.

• Cython deprecates "IF" macro
  • ChimeraX atomic cymol.pyx cython code uses the "IF" macro to handle Windows pointers needing long long integer while unix needing long.
  • Cython has deprecated "IF" with no equivalent replacement.
  • Eric may try "sed" to patch the cymol.pyx code at build time.

• ChimeraX 1.7.3 release?
  • Eric has fixed the garbage collection crash.
  • We have 40 reports so far since December with this crash.
  • Eric suggests we not do a 1.7.3 release and just tell reporters to use the daily build.

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Action Items