ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

September 14, 2022 (Wednesday)

Agenda

• pyproject.toml can replace bundle_info.xml now
• Discuss possible OpenMM and VR improvements for Tristan and Altos to pursue
• 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

• pyproject.toml
  • Zach has made pyproject.toml able to replace bundle_info.xml
  • DICOM, blastprotein, cxwebservices are using pyproject.toml
  • Documentation for ChimeraX pyproject.toml
  • Bundle writing tutorial could use pyproject.toml section

• Tristan Altos visit
  • Tom had lunch with Tristan, Adam and Hana on Monday.
  • Altos talked with OpenMM team (Peter Eastman, John Chodera, 3 others).
  • Tristan had meetings with Altos people every hour.
  • Adam asks what the ChimeraX 5-year plan at UCSF is.

• Chimera builds
  • Windows failing. Host james not turned on after power outage. Tom will turn it on.
  • Mac, essex2 having compile problems with ambertools, Eric working on it.

• MODRES records in mmCIF files
  • Greg discussed difficulties if CCD templates not available

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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