ChimeraX Developer Meeting

Attendance: Greg, Zach, Tom, Eric, Piet

August 12, 2024

Agenda

• Work in progress reports
• Develop ChimeraX 1.9 road map
• Progress updating prereqs
• Make Chimera end-of-life bug report and registration changes.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• ChimeraX Ideas milestone clean-up.

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Discussion

• chimerax-prereqs git repository
  • Zach trying to allow access to our ChimeraX third party packages currently only on plato, when plato is down.
  • Encounters this problem trying to due github builds of the ChimeraX PyPi wheel where plato does not respond.
  • The third party packages are being accessed through a cxtoolshed.rbvi.ucsf.edu. May be more reliable if we use www.rbvi.ucsf.edu/chimerax/www/data.

• Toolshed ScholAR bundle update failing
  • Some toolshed problem is preventing Piet from uploading a new version of the bundle.
  • Greg says franklin was not running mail server so the newly submitted bundle tried to email the submitter that it succeeded and that failed.
  • Greg said subsequent uploads of the same version found the file from the previous upload and tried to make a new name, probably leading to further problems.
  • Greg will get this working.

• Numpy 2
  • Numpy updated from major version 1 to 2 in June, the first major update in over 15 years.
  • We will probably wait until ChimeraX 1.10 to look at updating to numpy 2 since many of the PyPi packages we depend on use numpy and they will have to update to numpy 2.

• Docutils
  • Eric reverted docutils update to get ChimeraX license on download page working.
  • License was missing because docutils command-line program rst2html was missing. It converted the RST markup license file to html.
  • Greg has figured out how the new docutils package provides access to rst2html and may switch to using the new mechanism.

• ChimeraX active user statistics
  • Eric is restoring some web logs from backups so Greg can extract active user info based on ChimeraX toolshed update queries.
  • Greg is using both toolshed update checks and also the ChimeraX web services check for new ChimeraX versions to count unique user ids and platforms.
  • Greg will talk about this at group meeting next week.

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Action Items