ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg, Mikhail

September 18, 2023

Agenda

• ViewDockX port to Qt progress
• pip install procedure; use Python or ChimeraX binary; ChimeraX binary goals
• ChimeraX library; feasibility of removing toolshed, user commands
• Wording of LGPL notice / which files to change
• Wisdom of making Qt/chimerax.ui imports fail in nogui mode
• 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

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Discussion

• ViewDockX
  • Mikhail had no progress to report.
  • Has not encountered any difficulties that need our help.

• Toolshed mdtraj install
  • Greg made Toolshed install of PyPi packages use Python executable instead of ChimeraX.
  • This fixed mdtraj compilation error for unknown reasons.
  • Greg also fixed a bug where install was not going into versioned ChimeraX directory.
  • Greg notified developer Barry who encountered this problem installing mdtraj.

• ChimeraX library license
  • Zach proposed text for top of code files that references LGPL license.
  • We discussed some revisions (add copyright UC Regents, add url to ChimeraX further license details).
  • Reviewed that we need toolshed and user command code in library to handle manager/provider and other uses.
  • Ready to propose at group meeting how we can release library for Scooter and Tom Ferrin to comment on.

• Allowing Qt import in nogui
  • Greg added code to disallow importing Qt in nogui mode.
  • Alignment headers test suite produced an error because Qt imported but not used. Code needs some reorganization.
  • Decided we should not disallow Qt imports in nogui. Our code and Toolshed bundles sometimes import Qt at top level to subclass.
  • For ChimeraX library we will be fixing any case where Qt is imported so it is not imported.

• Toolshed issues
  • Hung progress indicator when a Toolshed entry updated, caused by Django update. Greg has not yet investigated.
  • Mike Schmid installing Clipper in daily build, button said not compatible, but pressing it looked like it tried to install. Mike asked me if it failed and if so what went wrong. Toolshed needs be clearer -- no Clipper for 1.7 / python 3.11 available.
  • Toolshed install regularly reports "An error may of occurred" because of a pip upgrade warning to stderr. Should fix this so install works cleanly and user is not confused.
  • Discussed making ChimeraX Toolshed updates available tool give a reason for an update. Eric suggested just a link to release notes would be an improvement.
  • Need to prioritize fixing the many Toolshed rough edges.

• Grafana web service log visualization
  • Greg will install promtail and loki on webservicestest.
  • Zach can prototype some web service dashboards.

• Task Manager
  • Zach has a branch with a Task Manager tool that can save and restore running tasks.
  • Testing it with BLAST Protein tool.
  • Eric is interested in using it.

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Action Items

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