ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

May 15, 2023

Agenda

• Release initial ChimeraX library on PyPi or Conda
• ChimeraX 1.7 roadmap
• Update ChimeraX prereqs
• Python updating plan, binary patch releases only available for 1.5 years after each release.
• Chimera/ChimeraX notarization scripts need updating, Apple deprecated altool command Fall 2023 ​#7234
• ChimeraX Ideas milestone clean-up.
• Install Splunk on plato to monitor web services.
• Back up the Chimera build machine to a solid state drive, Windows 7?
• Toolshed bundle requirement checking
• Discuss possible OpenMM and VR improvements for Tristan and Altos to pursue

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Discussion

• Update ChimeraX to Python 3.11
  • Zach will try compiling ChimeraX for Python 3.11 using a branch he made months ago.
  • Should test building on Mac ARM/Intel, Linux and Windows before making the move to 3.11.
  • Tinyarray, pyopengl-accelerate and tables may need to be compiled by us.

• ChimeraX library
  • User asked on mailing list about using ChimeraX in notebook (possibly Google Colab).
  • Zach has initial version of library with gui code removed.
  • Need examples and documentation to use the library.
  • Might release initially just for linux built for one Python version.
  • CZI grant funding library ends Aug 1, 2023. Probably will ask for extension. But initial library should be released before then.

• Plato update to Rocky 8
  • Power outage Tuesday night 11 pm to Wed 6 am.
  • Plan is to switch to Rocky 8 after outage.

• mmCIF out of memory errors
  • Got another report with user email, but no reply from any user yet.
  • Greg has added a sanity check when allocating size of memory mapped file.
  • Greg changed error message so it is distinct from system out of memory message.

• Memory leak opening and closing atomic models
  • Eric solved biggest memory leak opening and closing atomic models.
  • Looking for source of next biggest leak.
  • Discussed flushing in-memory ligand cache in mmCIF reader so those don't accumulate when loading all PDB models.

• ChimeraX builds with Github actions
  • Might be troublesome accessing licensed PyQt from could machine.

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Action Items

• Present github continuous integration tutorial. Zach
• Beta releases on Toolshed - make ticket for this. Greg