Attendees

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

Agenda

• Review action items from 9/14 meeting
• Vijay's visit
• Beta release discussion
• Next meeting
  • ​Glycosylation depiction
  • Who will develop mmCIF writer? ​ticket
  • ChimeraX on Github
  • Rotamer library license

Discussion

• Beta release discussion (including 9/18 minutes)
  • Why do we need a beta so soon? Why not leave it as alpha?
    • we said we would
    • demonstrates progress, although alphas do that too
    • a beta is a milestone that shows more confidence in the functionality and stability of what we are releasing
    • it looks bad not to have a beta given the time spent in development
    • would send a message to reviewers of our R01 proposal that we have made significant progress on this project
  • What does it mean to release an API?
    • Using mechanism to be established, we label functions/attributes/properties/etc as API if we intend to support semantic versioning for them
    • Developers can use non-API items but have no guarantees that they will continue to work
    • Developers should be able to easily determine whether an item is part of “the API”
  • What consists of "the API"? Public methods, even those without Sphinx documentation?
    • It is easier to mark items as part of the API than to mark items that are NOT part of the API
    • There are methods that should not start with underscore because they are shared among classes internally, but are still not part of “the API”
    • Tentative APIs also should not be labeled as part of the API because we may not support forward compatibility
    • We can use naming conventions (which developers may not know about, might be painful for internal development) [Answer: No, none that could be agreed on]
    • Annotation on non-API items: decorators (does not work with attributes and properties) or doc string markers (e.g., “unsettled”)
      • doc strings will work for attributes, optional arguments
      • we agree that this is a viable solution but not the one we will use
      • will need to go through source code and add everything before beta
    • Annotation on API items: decorators/doc strings
      • Developers will not see non-API items clearly marked
      • Omission of markup less detrimental
      • Less effort
      • Might leave more markup in the long run (if public API outnumbers non-API items)
      • we agree that this is a viable solution and IS THE ONE WE WILL USE
      • we will use doc strings rather than decorators because doc strings work for properties.
      • attributes will be documented in the class doc string
      • Marker string is "Supported API." at the beginning of the doc string
      • will need to go through source code and add everything before beta
    • Have a utility that identifies non-API items in bundles (may not be practical)
  • How much "firming up" API is needed?
    • If it’s ready, it’s ready
    • If it’s iffy, it’s not
  • Will bundles move out from core, e.g., atomic?
    • Do it before beta and there is no API change needed later
    • Most import’s will need to be changed when package is externalized
    • Toolshed images/documentation needs effort
    • Order packages based on dependency
    • Eric will try to bundle-ize core.ui after preferences
  • What are the beta APIs? Toolshed. Atomic. Command…
    • The plan is to write a tutorial for a "simple" bundle supporting commands and HTML widget GUI
    • beta APIs must support everything in the tutorial
  • Release protocol for "core" bundles? (defer for now)
  • Is December a realistic target?
    • it depends whether the milestone is more important or more functionality is more important

• Need to investigate
  • Replace ctypes in atomic with Cython
• Make ChimeraX tickets viewable publicly
  • Private tickets need to start private
  • Alternative, make all tickets public and make UI say "don't send private data"
  • Make tickets public now and add warning later when needed
• Beta release topics
  • Meeting on Monday
  • Why do we need a beta so soon? Why not leave it as alpha?
  • Is December a realistic target?
  • Will bundles move out from core, e.g., atomic?
  • What are the beta APIs? Toolshed. Atomic. Command...
  • How much "firming up" API is needed?
  • What consists of "the API"? Public methods, even those without Sphinx documentation?
  • Release protocol for "core" bundles?

Action Items

• Greg will make session file format changes
• Elaine will add "no private data" to contacts.html
• Eric will add "no private data" to traceback printout in log
• Conrad will make tickets publicly readable
• Conrad will continue working on ribbon tickets
• Conrad will investigate implementing the "like" operator
  • e.g., to specify polymer in atomspec
• Conrad will send mail to RCSB about bad pdb.org certificate