This is a summary of discussions relevant to ChimeraX that took place at some group meetings.

Attendees

• Eric, Conrad, TomG, Elaine, Greg, TomF, Scooter

Agenda

• Action items
• ChimeraX
  • Should 2D models be selectable as shown w/ green outline for later actions?
  • More general REST interface
  • Permissions on ChimeraX wiki
  • Mechanism for updating from 1.0 to 1.1
  • RBVI bundles on toolshed
    • Change build process to trim down list of bundles in standard release while still testing toolshed-only bundles
  • Stable APIs, #922
  • Documentation strategy
  • 1.0 features (roadmap)

Discussion

• ChimeraX
  • Should 2D models be selectable as shown w/ green outline for later actions?
    • Summary from group meeting.
    • See #2365 for more details.
    • 2D models should be selectable and shown with green outlines.
    • Commands that do not depend on coordinate systems, e.g., "color" and "display", should apply to 2D models when they are included in the atomspec
    • Commands that do depend on coordinate systems, e.g., "move" and "turn", should not apply to 2D models even when they are included in the atomspec
  • More general REST interface
    • Summary from earlier group meeting.
    • Tristan's implementation is "over the top", including:
      • registration that automatically pulls argument types from function
      • GET queries return the list of registered functions
      • Python client that will mimic the registered functions so client-side code looks very similar to server-side code
    • Scooter suggested insisted that the implementation must support Swagger (now known as ​OpenAPI). Python's ​FastAPI may be the perfect fit, but it is very heavyweight in terms of dependent packages.
    • Need to investigate whether FastAPI is compatible with Tristan's approach (a real-life client).
  • Permissions on ChimeraX wiki
    • Should move ancient crud to archeological part of site
    • Option 1:
      • Adopt Chimera wiki permission plugin
      • Move selected private links to protected area (are there any?)
      • Open most of site
    • Option 2:
      • Move private stuff to another site (wiki, GoogleDocs)
      • Open all of site
    • Option 3:
      • Move to github?
  • Mechanism for updating from 1.0 to 1.1
    • Option 1: 1 site-packages for all versions, need to delete/update old bundles
    • Option 2: 1 site-packages per version, need to install/copy old bundles
    • Option 3: 1 site-packages per version, sys.path = new_personal:installed:old_personal:...
    • Option 4: do not use Python import statement; use toolshed.load_module (or something) to get modules
    • Need decision before 1.0 release
  • Putting RBVI bundles on toolshed
    • Want separate run-time vs build-time dependencies in bundle_info.xml
    • Visit the bundle-release page (from intranet) and release your bundles
    • Need to segregate "standard" bundles from "extra" bundles
  • Stable APIs
    • See action items
  • Move to github
    • Move to private RBVI github project
      • Easier to share with collaborators with github admin tools
      • "pull requests" should simplify enhancement/fix submission
      • will not happen that soon

Action Items

• Scooter and Conrad will investigate moving wiki pages to private subtree
• Greg will update rotamer library license in ChimeraX embedded license page
• Scooter will look into private wiki pages in Trac
• Greg will update Linux notes on download page
• Greg will add "VR Notes" link below "Platform Notes" link (https://www.rbvi.ucsf.edu/chimerax/docs/user/vr.html)
• Conrad will investigate how Tristan's mechanism works and start discussion on what style of REST is best (how to specify arguments, etc.)