Attendees

Eric, TomG, Greg, Zach

Agenda

• Action items
• ChimeraX
  • Programmer doc string formats and sphinx extensions #5120, Zach
  • Update 1.3 release roadmap, adding completed stuff, moving other stuff to 1.4.
  • Web service discontinued status checking for AlphaFold predict.
  • Task termination at app quit
  • VirtualGL documentation #4783
  • Rename ChimeraX.exe on Windows?
  • Should we remove the HTML tool tutorial and promote only Qt GUIs?
• Chimera

Discussion

• Versioning web services
  • ChimeraX and Chimera blast and modeler services may need to diverge when backend update is not compatible with old Chimera.
  • Modeller service has modelerV9 in name.
  • Eric will think more about how to handle web service backend versions.

• REST services and http vs https
  • REST web services currently all using http.
  • Eric suggests getting https working and keep http working as long as possible.
  • Our current web servers is apache
  • Discussed switching to nginx
  • Apache hard to configure https for multiple sites.

• Sphinx and doc strings
  • Zach suggests we use the Sphinx napolean extension included with Sphinx instead of numpydoc.
  • Napolean handles numpy and google doc string formats.
  • Zach will test it and show us good examples of how to format our doc strings.

• Python type hints
  • Discussed the advantages and disadvantages of Python type hints in function arguments and class attributes.
  • Eric points out ChimeraX plugin developers may find these hints confusing.
  • Greg points out speed optimizers for Python are trying to use type hints. Guido has come out of retirement trying to increase CPython speed 2 fold.
  • Zach says type hints produce runtime error when wrong argument type passed that helps him debug code faster.
  • Zach suggests using a Sphinx extension so the type hints do not appear in function signatures in the documentation.
  • Decided that each developer can choose whether to use type hints.
  • Greg thinks might be possible that ChimeraX command registration could introspect function argument type hints instead of declaring the argument types in the registration call.

• Blast threading
  • Zach asks how to avoid blocking after BLAST rest returns results while code is fetching files containing results. Can QThread be used?
  • Could use a Task.
  • Current blast gui in ChimeraX 1.2.5 blocks for 40 seconds on 4v6x chain A (900 hits) while loading results.
  • Suggest Zach complete new Qt blast gui before worrying about optimization.

• mmCIF saving error
  • Greg says user tried to save NMR ensemble where chain names were changed, gave traceback.
  • Will put in error checking.
  • mmCIF save tries to extract info from chimerax data structures that can be inconsistent and needs checking for compatibility with mmcif requirements.

• Roadmap for 1.3 release
  • Everyone update the 1.3 roadmap moving stuff that won't make it into 1.3 to the 1.4 milestone.

Action Items

• Put download web page checksums on separate page. Zach
• Propose registering only once at group meeting, see if TomF agrees - Everyone.
• Add 1.3 goals to roadmap for next group meeting - Everyone.
• Get cron jobs to build mailing list site map for google indexing working - Greg.
• Make Windows build redirect installer build to separate log so password not shown - Greg.
• Make Updates tool started from menu Tools / Utilities / Updates show only updates, not all available bundles - Greg
• Change milestone on all 1.2 enhancement tickets that won't be in 1.2 to milestone 1.3 - Greg
• Check that all Toolshed bundles that install in 1.2 actually start -- add core<1.2 dependency to those that fail - Greg