Changes between Version 1 and Version 2 of Dev2026-07-06

Timestamp:

Jul 6, 2026, 4:08:41 PM (9 days ago)

Author:

Tom Goddard

Comment:

--

Dev2026-07-06

@@ -8 +8 @@
 
 
-* Not compiling Python ourselves; use !GitHub
-  - Try as a tech preview
-  - Still do Linux ourselves because of ssh
-* ChimeraX 1.13 updates?
-  - Python 3.14 (blocked by #20335 and #16848)
-  - !PySide 6.11.1
-    - Try it again -- in a week (along with other package updates)
+* Use prebuilt Astral Python
+* Update to numpy 2.
+* Update to Python 3.14 (blocked by #20335 and #16848)
+* Update to PySide 6.11.1
+* Make Chimera 1.20 release with Mac fix.
 * Inside ribbon color?
 * Toolshed reduce query result size.
-* Chimera release?
 * Work in progress reports
 * Make Chimera end-of-life bug report and registration changes.
@@ -25 +22 @@
 = Discussion =
 
+* Use prebuilt Astral Python
+ - Zach will switch to prebuilt Astral Python for ChimeraX daily build on Mac and Windows.
+ - We will still compile Python on Linux to use system OpenSSL.
+
+* Update to numpy 2
+ - Tom will update daily build to use numpy 2 today.
+ - Tom tested all major ChimeraX numpy code with numpy 2.
+ - Fixed 20 file readers, 5 file writers.
+ - Most problems were removed numpy function fromstring, tostring.
+ - Some casting problems (16-bit integer overflows), long long default integer arrays on Windows.
+
+* Update to Python 3.14 (blocked by #20335 and #16848)
+ - Boltz does not work with Python 3.14.
+ - Tom will either make it work with Python 3.14 or make it use its own Python installation.
+ - After Boltz fix we can try updating daily build to Python 3.14.
+
+* Update to PySide 6.11.1
+ - Zach switched daily build from PyQt to PySide last week in daily build to work around main window resize bug with floating tools.
+ - So far no PySide specific bugs reported.
+
+* Make Chimera 1.20 release with Mac fix.
+ - Greg made Chimera 1.20 release with new Tcl/Tk/Tix that fixed Mac graphics window layout bug.
+
+* Nightly build email
+ - Last few days nightly build email says all builds failed, but clicking github links says they worked.
+ - Zach will look at what is going on.
+
+* Mac Chimera nightly build failed
+ - Apple updated terms of service.
+ - Eric notified UCSF Apple signing certificate people who agreed to new terms.
+ - Mac signing should be back to working now.
+
+* Recent toolshed submissions
+ - Tom reviewed Kurwenal toolshed submission, utilities for AI Model Angelo models built in cryoEM maps. Asked that they use normal model specs and keywords in commands.
+ - Tom reviewing toolshed CryoZeta AI model building in cryoEM map, ChimeraX interface to server.
+ - Zach will review carbvis toolshed submission from last week on carbohydrate depictions.
+
+* Dockerhub ChimeraX Linux build image
+ - Greg suggests putting a ChimeraX Linux build environment image on Dockerhub.
+ - Tristan can use this to make a singularity image for his ISOLDE builds.
+
+* Trajectory RMSD maps
+ - Eric working on all-by-all trajectory RMSD plot tool.
+
+* Proofpoint spamming Trac bug reports
+ - Eric filed bug report about ProofPoint sending blocked email digests to Trac.
+ - Frequent digests create spurious bug reports.
+ - Greg notes that email2trac has a blocklist file.  Made file writable by chimdev group so Eric can filter out proofpoint digests.
+
+* Trac migration off CGL email server
+ - Greg has explored how to run Trac bug reporting email2trac using rbvi.org instead of cgl.ucsf.edu.
+
+* Group meeting topic
+ - Greg presenting group meeting on Thursday.
+ - Possible topic is new features in Python 3.14.
 
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