ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom (late), Greg

August 1, 2022

Agenda

• Remilestone or close 1.5 roadmap tickets
• Update PyPi prerequisites
• Make installing on the Mac more obvious
  • More download Notes?
  • README in .dmg?
• 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

I joined the meeting late at 2:30 so missed first half hour discussion. Tom

• Move developer meetings to Monday 3 pm
  • Tom never comes on time at 2 pm (right after lunch)
  • We will try meeting at 3 pm.
  • Tom on vacation next week.

• AmberTools compile on Rocky 8
  • Daily Linux build not working due to AmberTools
  • Renamed centos7 binary prereq on plato to rocky8
  • See if tonight's ChimeraX Linux build works

• Mac universal build
  • Will Toolshed handle ARM vs Intel Mac wheels? Greg says probably yes.
  • Should put Mac universal build as techpreview before replacing daily build.

• Mac universal wheels
  • Zach says bundle builder makes universal wheel but puts arm64 in name instead of "universal2"
  • Greg thinks updating packaging PyPi package may fix it.

• Outdated prereqs email
  • Outdated prereqs email is wrong because it is using old CentOS 7 ChimeraX on plato.
  • Greg is making the outdated notice use Rocky 8 ChimeraX run under singularity.

• New AlphaFold database for BLAST
  • Tom says new alphafold database (214 million sequences) built and tested on plato.
  • ChimeraX 1.4 needs to keep using old database version 2.
  • Zach says BLAST tool client code passes the database version to use with queries.
  • May just need to make put the new v3 database on plato to have it working.

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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