Changes between Version 1 and Version 2 of Dev2026-07-13

Timestamp:

Jul 13, 2026, 4:54:09 PM (2 days ago)

Author:

Tom Goddard

Comment:

--

Dev2026-07-13

@@ -7 +7 @@
 = Agenda =
 
-* Use prebuilt Astral Python
-* Update to numpy 2.
 * Update to Python 3.14 (blocked by #20335 and #16848)
 * Inside ribbon color?
@@ -19 +17 @@
 = Discussion =
 
+* Small molecule cif bonds
+ - Tristan says small molecule cif files don't bond atoms by distance for atoms that have bonds to metals.
+ - This is because adding bonds by distance does not operate on atoms that already have 1 or more bonds.
+ - Greg will cache the metal bonds, then add bonds by distance, then add metal bonds back.
+
+* Toolshed Editor vs Contact email addresses
+ - Trac accounts use the Toolshed Contact email.
+ - For the Kurwenal bundle this the contact email was set to the lab PI.  Probably it should instead be set to the bundle developer's email which is currently the Toolshed editor email.
+ - Tom will tell the Kurwenal developer if they want bugs to go to them they need to change the contact email to their email address.
+
+* Qt setCheck() with numpy.bool_
+ - Eric says new bug report in daily build has Qt setCheck() giving an error when passing a numpy.bool_
+ - This may be because of our update from numpy 1 to numpy 2.
+ - Eric will test if ChimeraX 1.12 gives the same error.  1.12 is still using numpy 1.
+
+* Python 3.14 getrefcount()
+ - Python 3.14 returns different values from getrefcount() due to a new optimization.
+ - Tom will check if the getrefcount() calls in the map_data bundle that free data from the volume cache needs updating and inform Zach.
+
+* Avoid making prebuilt prereqs tar file
+ - Zach points out that the ChimeraX build makes a prereqs prebuilt tar file for use in subsequent builds, but on Mac (and possibly Windows) there is nothing used from it since we now use Astral Python builds.
+ - Zach asks if he should remove making the prebuilt tar ball on Mac that contains python.  This saves 1 minute of build time.  Yes.
+
+* SSL_CERT_FILE on Mac ChimeraX builds
+ - ChimeraX builds set SSL_CERT_FILE to a non-existent file in the build site-packages/certifi directory.
+ - This causes the Python 3.14 ChimeraX build to fail building pynmrstar.
+ - Tom worked around this by setting SSL_CERT_FILE to the ChimeraX.app site-packages/certifi which does exist.
+ - Zach will test if setting SSL_CERT_FILE is necessary and will remove it if not needed.
+ - Zach will also test if the curl --insecure option is needed for fetching prereqs from plato.  The code comment says it was needed because of the bad SSL_CERT_FILE path on Mac.
+
+* Segger tar ball in ChimeraX
+ - The ChimeraX Segger tool is installed from a tar ball on plato as a prerequisite.
+ - Zach asks can it be removed from plato?
+ - Tom says the Segger tar ball is made from a github SeggerX repository and we could check that tar ball into our ChimeraX github.
+ - Zach suggests another route would be to make the SeggerX github a subrepository of the ChimeraX repository.  We don't currently use subrepositories.
+ - We discussed whether it is feasible to get rid of all the prereqs downloaded from plato during a ChimeraX build.  Unclear.
+
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 = Action Items =