Ubuntu 22 ChimeraX installer is replacing symlinks by copies of libraries

[Tristan Croll]

Tristan notes that the ChimeraX Ubuntu 22 installer is copying symlinks for libraries duplicating 180 Mbytes of files during install. He mentioned this in the following ticket.

​https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7857#comment:19

A minor observation I noticed while messing with this: looks like (at least for Ubuntu 22) symlinks are being expanded into real files somewhere in the installation process, leading to spurious extra copies of libpython and libOpenMM amounting to about 180 MB between them:

cd /usr/lib/ucsf-chimerax/lib
ls -l

-rwxr-xr-x  1 root root   362216 Oct 29 00:32 libOpenMMAmoeba.so
-rwxr-xr-x  1 root root    97360 Oct 29 00:32 libOpenMMDrude.so
-rwxr-xr-x  1 root root    80720 Oct 29 00:32 libOpenMMRPMD.so
-rwxr-xr-x  1 root root  3785392 Oct 29 00:32 libOpenMM.so
-rwxr-xr-x  1 root root  3785392 Oct 29 00:32 libOpenMM.so.7.7
-rwxr-xr-x  1 root root 14985688 Nov  7 11:03 libpython3.9.so
-rwxr-xr-x  1 root root 14985688 Nov  7 11:03 libpython3.9.so.1.0
-rwxr-xr-x  1 root root    15112 Nov  7 11:03 libpython3.so
drwxr-xr-x  2 root root     4096 Nov  7 14:13 plugins
drwxr-xr-x 36 root root    20480 Nov  7 14:13 python3.9

Got curious and ran a quick script over the rest of the ChimeraX directory tree, and it looks like these are the only cases of this.

[Greg Couch]

Needed syslinks=True argument to shutil.copytree()