ChimeraX Developer Meeting

Attendance: Piet, Greg, Tom, Eric, Zach

November 18, 2024

Agenda

• Toolshed contact obfuscated email addresses.
• LAMMPS bundle include in distribution?
• Linux candidate builds failing, last night getting ffmpeg from www.rbvi.ucsf.edu failed.
• What to do about Mac external display crashes
• ChimeraX 1.9 release candidates, branch and tickets
• Clean-up ChimeraX 1.9 roadmap wiki page
• 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.
• GitHub Actions builds

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Discussion

• LAMMPS contact email obfuscated
  • The LAMMPS file reader listed email on Toolshed with "at" instead of "@" to avoid spam
  • That makes our nightly email that notifies about Toolshed bundles without Trac accounts constantly notify us developers.
  • Eric will change that notify script to allow exceptions.

• LAMMPS in ChimeraX distribution?
  • LAMMPS developer wants to eliminate need to install from Toolshed by inclusion in ChimeraX distribution.
  • Should we allow that?
  • Bundle has no other dependencies.
  • Bundle is currently licensed GPL -- license would need to be changed.
  • It is about 400 lines of Python code.
  • Developer could submit pull requests to fix bugs.
  • We could remove it if it broke in a new ChimeraX version.
  • Would want some documentation in user guide - Eric will ask Elaine about that.
  • Eric would manage any pull requests.
  • Seems ok if Eric and Elaine are willing.

• Toolshed reload available
  • We tried during meeting to get Toolshed to load LAMMPS metadata to see if it would put the file format in the Open dialog list of formats.
  • Could not get the meta data using "toolshed reload available".
  • Greg said that command is asynchronous so may not have completed.

• Mac display configuration crashes
  • Have 5 crashes reported in 10 days in 1.9 release candidate.
  • We may get crash reports every day if we release this.
  • We don't have any way to reproduce it.
  • Today's report in ChimeraX 1.8 was on an iMac with no external display, probably waking from sleep.
  • Could popup a one time warning on Mac with 2 or more displays about crash when changing displays. But this does not address same crash when computer sleeps -- hard for user to avoid display sleep.
  • We don't have any good ideas for handling this crash.
  • Greg says PyQt 6.8 won't be out until Qt 6.8.1 comes out.
  • Unlikely that Qt 6.8 will fix crash. No Qt bug reports. Probably requires Qt app using OpenGL so is rare among apps.

• ChimeraX 1.9 milestoned tickets
  • Greg and Zach say none of the 15 milestoned 1.9 tickets block release.
  • They will work on remilestoning or closing tickets.

• Nucleotides tethers fixed
  • Greg with Eric's help fixed a tether not going to the ribbon bug with nucleotides.
  • Tether was drawn before nucleotides set the atom hide bit.

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Action Items