Attendees

• Conrad, Elaine, Eric, TomG, Greg, TomF

Agenda

• Review action items from 9/7 meeting
• Chimera 1.12
• Alpha 3
  • Yet another new bundle building change
  • Sessions: msgpack vs pickle
• Alpha 4
  • Undo manager
  • Preferences GUI
• Beta release topics
• Make ChimeraX tickets viewable publicly
• Custom Qt for ChimeraX
• Next meeting
  • ​Glycosylation depiction
  • Who will develop mmCIF writer? ​ticket
  • ChimeraX on Github
  • Rotamer library license

Discussion

• Chimera 1.12 candidate is up for download
  • Wait for a couple weeks for bug reports
  • Eric will poke "turn off indexer" victim
• Alpha 3
  • Sessions: msgpack vs pickle
    • Make v3 (Cython version) the default session format
    • Report error if trying to read v2 file
  • Undo manager
    • infrastructure in place
    • show, hide, style, cartoon, color are implemented except for surfaces
• Alpha 4
  • Preferences GUI
    • Eric
    • Core preferences + 1 example bundle preferences
    • Ensure fetching URL is settable via preferences
  • Zone atomspec
    • Conrad
    • chains still need work, only selects polymer
  • Named targets/selections
    • Eric will create ticket
    • Conrad
    • UI is the focus
  • Rescan tickets, in particular, findclash
• Need to investigate
  • Replace ctypes in atomic with Cython
• Make ChimeraX tickets viewable publicly
  • Private tickets need to start private
  • Alternative, make all tickets public and make UI say "don't send private data"
  • Make tickets public now and add warning later when needed
• Custom Qt for ChimeraX
  1. Ignore the problems
     • tool windows always on top of app (on Mac, ALL apps)
     • tool windows disappear when focus goes to another app (on Mac and Windows)
  2. Fix it for easy platform (Mac)
     • Can recompile Qt and drop in libraries after PyQt installation
  3. Fix it for all platforms
  4. Submit pull request to Qt maintainers
  • b and c requires compiling Qt and rebuilding PyQt
  • d depends on Qt/PyQt maintainers to accept and incorporate pull request
  • Eric will (Mac only) compile Qt, build PyQt wheel, put back on plato
  • Eric will submit pull request to Qt with full changes eventually
• Beta release topics
  • Meeting on Monday
  • Why do we need a beta so soon? Why not leave it as alpha?
  • Is December a realistic target?
  • Will bundles move out from core, e.g., atomic?
  • What are the beta APIs? Toolshed. Atomic. Command...
  • How much "firming up" API is needed?
  • What consists of "the API"? Public methods, even those without Sphinx documentation?
  • Release protocol for "core" bundles?

Action Items

• Greg will make session file format changes
• Elaine will add "no private data" to contacts.html
• Eric will add "no private data" to traceback printout in log
• Conrad will make tickets publicly readable
• Conrad will continue working on ribbon tickets
• Conrad will investigate implementing the "like" operator
  • e.g., to specify polymer in atomspec
• Scooter will investigate making tickets public (possibly marking some tickets private)
• Conrad will send mail to RCSB about bad pdb.org certificate
• Greg will handle Chimera 1.12 branching and release notes migration
• Conrad will go through Chimera 1.12 svn logs for notable bug fixes