ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg, Mikhail

August 28, 2023

Agenda

• Toolshed website spinning progress never goes away.
• mmCIF out of memory
• Update ChimeraX prereqs
• Release initial ChimeraX library on PyPi or Conda
• ChimeraX Ideas milestone clean-up.
• Install Grafana on plato to monitor web services.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• Toolshed bundle requirement checking
• Discuss possible OpenMM and VR improvements for Tristan and Altos to pursue
• Wording of LGPL notice / which files to change

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Discussion

• ViewDockX
  • Mikhail asked about best way to learn Qt toolkit.
  • Suggested Qt docs, inspecting existing ChimeraX tools.
  • Eric gave tips about basic tool layout.
  • Mikhail is using git clone of chimerax repository, and BlastProtein tool which has a table as an example.

• LGPL ChimeraX library license
  • Not clear who will create new text and modify code files for new license.

• Toolshed problems
  • Search is broken, gives traceback, reported by Tristan. Greg will try to fix today.
  • Tom mentions hard to find tools on web page except by showing them all. Have lots of categories with just a few tools each.
  • Eric suggests the update tool needs to indicate what problems an update fixes. Currently the tool only receives version numbers, name and category for updates.
  • Developer changing toolshed pages appears to hang on submit. Problem caused by Django update. Greg has not looked.
  • Tom asks if we should be considering a toolshed distribution mechanism that does not require so much maintenance and could be taken over by Tristan or others in the future. Greg suggests possibly just use PyPi.

• StrudelScore
  • StrudelScore developer email is dead and core < 1.6 requirement prevents it from running in current ChimeraX even though it works in current ChimeraX.
  • How can we fix this? Could fork the git repository, see if code is the same as current wheel, and create a new wheel that works with ChimeraX 1.x.
  • Then do take over StrudelScore toolshed ownership and update? Or make a new Toolshed submission.
  • No decision yet on how to proceed.
  • Abandoned bundles on toolshed will be common.

• mmCIF out of memory error
  • Eric says we still have no mmCIF out of memory reports in daily build, so possibly it is fixed.

• Grafana web service monitoring
  • Greg installed grafana on plato nodes.
  • Some additional packages needed to make web pages that show web service usage.
  • Zach will provide Greg a list of what packages need to be installed.

• Web services number of workers
  • Agreed at previous meeting to increase number of web service workers from 10 to 20.
  • Greg has updated to 20 workers.

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Action Items

• Present github continuous integration tutorial. Zach
• Beta releases on Toolshed - make ticket for this. Greg