ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

August 22, 2022

Agenda

• Discuss possible OpenMM improvements
• Remilestone or close 1.5 roadmap tickets
• Weekly build scripts using singularity
• Plan to fix command-line parser
• Arrow graphic for Mac dmg file
• Mac universals builds
• Mac app notarization
• SSD drives for plato
• DICOM improvements
• Updating Linux compilers from CentOS7 for ISOLDE
• Github Actions continuous integration
• Mac M1 port
• Put parser fix (#4842) on roadmap?
• ISOLDE is installing into 1.5 (#7381)

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Discussion

• Weekly ChimeraX scripts on CentOS 7
  • Greg says weekly outdated package notification and benchmark failed because ChimeraX does not run on CentOS 7.
  • Will fix by running under singularity

• Command-line parser fix plan
  • Command-line parser crashes on long atom specs and slow
  • Uses obsolote parser package grako
  • Eric proposes someone research how to fix it for ChimeraX 1.5 and actually fix it for 1.6
  • Greg mentions Python 3.10 and 3.11 use new PEG parser that might be usable.
  • Greg mentions that successor to grako should be reevaluated.
  • Greg or Eric are most likely candidates for doing this. Did not decide who.

• Mac dmg installation arrow graphic
  • Eric asks if the Mac distribution DMG now shows an arrow suggesting dragging to the Applications folder.
  • Zach says he tried it but has not committed anything yet.

• Universal Mac builds
  • Next step on Mac M1 native build is to make a universal build nightly. Tom will probably do it, or Zach.

• Mac app notarization
  • Tom increased notarization retries from 2 to 5 ten days ago and so far no notarization failures.
  • Notarization failures reported online to be caused by firewalls blocking Apple's signed timestamp server.

• SSD drive for plato
  • Tom says SSD drive makes AlphaFold database 100 times faster than beegfs on plato.
  • May want to get SSD local drives for plato nodes. Still evaluating if it is worth the trouble.

• DICOM
  • Zach refactored DICOM code to create model hierarchy in clearer way.

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Action Items

• Update Linux base system from CentOS 7 to Debian 10 or equivalent. Greg
• Provide Singularity image of compiler environment. Greg
• Present github continuous integration tutorial. Zach

General

ChimeraX

General

Build System

1) Supporting IDEs

• may only need editable installs (will require workaround as namespace packages cannot be installed in this mode automatically)
• editable installs should also let us call ChimeraX with Python for rapid iteration and the C launcher for detailed crash info
• Zach mentioned PyCharm, LSP (Language Server Protocol), XCode
• Greg mentioned Visual Studio

2) API for getting C headers: get_include (see: numpy.get_include)

• native-packaging moves bundle header and source files to bundle/src/include/module \
• maybe just use header files?

3) API for getting library directories: get_libdir

4) macOS compiler call in Makefiles

Infrastructure

1) Beta releases on Toolshed

2) Decoupling core bundle version number from the ChimeraX release number

3) Prereq audit after 27 June

4) arm64 port

Chimera

1) Back up the build machine to a solid state drive