ChimeraX Developer Meeting

Attendance: Eric, Zach, Tom, Greg

September 11, 2023

Agenda

• pip install procedure; use Python or ChimeraX binary; ChimeraX binary goals
• ChimeraX library; feasibility of removing NoGUI mode, 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

---

Discussion

• mdtraj pip install error
  • Bundle developer Barry has had problems getting C source code mdtraj PyPi package to install.
  • Eric will advise Barry how to include the compiled mdtraj in his bundle for Linux, and possibly for Windows and Mac.
  • Greg and Zach discussed pip install technical issues about getting the bundles into the ChimeraX user location.
  • Greg will try to figure out the mdtraj pip install error when installing Barry's bundle and report this Thursday.

• ChimeraX library, user commands and Toolshed
  • Need to include toolshed in library since every bundle init.py imports it.
  • Won't have toolshed module contact web server when using library.
  • Would like user commands to be runnable with the Python run() function as this is used in many Python scripts.
  • Commands are registered by Toolshed using distinfo files in site-packages that include command declarations that came from bundle_info.xml or pyproject.toml.
  • In a future library release we can try to make run() work to execute user commands.

• LGPL license text for ChimeraX library
  • Looked at examples of LGPL license text to put at the top of source code files.
  • Zach will propose what text to use.

• Qt imports for ChimeraX library
  • Qt won't be part of ChimeraX library so code we provide should not import Qt even if it is not used.
  • Greg made the ChimeraX app in nogui mode give an error if Qt imported, and this broke the sequence alignment header nogui test suite code.
  • Decided we should not generate an error when Qt imported in ChimeraX app in nogui since this will break user scripts. We need to do adequate testing before making such a change. Also Toolshed bundles are likely to have top level Qt imports in custom init code.

---

Action Items

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