= ChimeraX Developer Meeting =

Attendance: Eric, Zach, Tom, Greg

August 29, 2022

= Agenda =

* 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)

--------------------------
= Discussion =

* OpenMM needs for Tristan
  - Tristan is now at Altos Labs and has resources to work on ChimeraX.
  - Do we have suggestions for what ChimeraX developments to pursue?
  - Eric is a few months away from getting Dock Prep done.  Then he will look at minimization with OpenMM and there may be some needs.
  - ISOLDE has many enhancements to OpenMM that could be modularized for use outside ISOLDE like handling glycans that we could use for minimization or simulations that resolve clashes.
 - Greg about working on OpenMM user install to get matching CUDA distribution.  Or to setup for a new AMD GPU.
  - Maybe work to simplify binary builds for third-party developers.

* VR needs for Tristan
  - Tristan says head of Altos software development is excited about VR use with ISOLDE.
  - VR user interface and performance issues are likely.
  - Mostly needs someone to spend months trying to use ISOLDE in VR to identify biggest obstacles.

* Meet with Tristan
  - We should meet with Tristan to discuss how Altos can help ChimeraX.
  - UCSF team all ok with 9 AM meeting, not Thursday.
  - Tom will arrange a meeting.

* Linux compilers
  - Greg updated linux compilers uses for ChimeraX.
  - Not sure if Tristan is using these compilers yet.  Need to ask.

* Mac universal builds
  - Greg says to make it another platform in build system.
  - Tom suggests offering universal, arm and intel separate downloads.
  - Eric asks if javascript can distinguish arm vs intel.  Apparently not.
  - Might drop 10.14 for ChimeraX 1.5 release -- it does not support LZMA compression.  If we keep it we need to use old compression, maybe just for the intel distribution.

* Singularity build scripts
  - Greg and Zach propose moving singularity build scripts from the private build_tools repository to the chimerax repository.
  - Could put in a new directory named CI or build_tools, or build_env.
  - Zach has continuous integration scripts currently in a util directory that could also go in this new build tools directory.

* Atom spec parsing crashes.
  - Eric or Greg might look at this.  Zach says he could possibly.  Eric says it is on his TODO list.
  - Plan is to fix it for ChimeraX 1.6, research solutions now.
  - Needs PEG parser.
  - Python 3.10 or 3.11 uses a new PEG parser which may be suitable.

--------------------------
= 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