= 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  - Greg says weekly outdated package notification and benchmark failed because ChimeraX does not run on CentOS 7.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