Windows build fails due to symbolic link docs/devel/apps

[Tom Goddard]

Building ChimeraX on Windows 11 (vizvault.cgl.ucsf.edu) fails apparently because it cannot access

docs/devel/apps/ChimeraX/ChimeraX-icon.svg

because docs/devel/apps is a symbolic link. The link is correct but I am guessing that the symbolic link handling on Windows is flakey so the sphinx code fails to follow it.

make -C devel install
make[3]: Entering directory '/home/goddard/ucsf/chimerax/docs/devel'
rm -rf _build/* conf.py index.rst _static/cxlinks.js pycache _static/devdocs.css \

apps chimerax modules

sed -e 's/PYTHON_VERSION/3.11/' \

-e 's/CHIMERAX_VERSION/1.10/' \
-e 's/CHX_FULL_VERSION/1.10/' \
< conf.py.in > conf.py

sed '/===/d' /home/goddard/ucsf/chimerax/copyright.txt | \

sed $'/COPYRIGHT_NOTICE/{r /dev/stdin\nd\n}' \
index.rst.in > index.rst

mkdir -p _static
cp ../js/cxlinks.js _static/cxlinks.js
cp ../css/devdocs.css _static/devdocs.css
# This code path handles a built ChimeraX, for the Plato build
# system or on a user's local machine. On readthedocs, the
# symlinks are made in Makefile.readthedocs
if [ -d /home/goddard/ucsf/chimerax/ChimeraX.app/bin/Lib/site-packages ]; then \

ln -s /home/goddard/ucsf/chimerax/ChimeraX.app/bin/Lib/site-packages/chimerax chimerax ; \
INTERNAL_CHIMERAX=1 /home/goddard/ucsf/chimerax/utils/build/doc_symlinks.sh ; \

fi
/home/goddard/ucsf/chimerax/ChimeraX.app/bin/python.exe -I 'C:/cygwin64/home/goddard/ucsf/chimerax/ChimeraX.app/bin/Scripts/sphinx-build.exe' -b html -d _build/doctrees . _build/html
[01mRunning Sphinx v8.2.3[39;49;00m

[01mloading translations [en]... [39;49;00mdone

[01mmaking output directory... [39;49;00mdone

[91mExtension error (sphinx.builders.html)![39;49;00m

Versions

========

• Platform: win32; (Windows-10-10.0.26100-SP0)

• Python version: 3.11.4 (CPython)

• Sphinx version: 8.2.3

• Docutils version: 0.21.2

• Jinja2 version: 3.1.6

• Pygments version: 2.18.0

Last Messages

=============

None.

Loaded Extensions

=================

None.

Traceback

=========

File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\Lib\site-packages\sphinx\events.py", line 415, in emit

raise ExtensionError(

sphinx.errors.ExtensionError: Handler <function validate_html_logo at 0x0000023AB7B84900> for event 'config-inited' threw an exception (exception: 1920 The file cannot be accessed by the system: 'C:
cygwin64
home
goddard
ucsf
chimerax
docs
devel
apps
ChimeraX
ChimeraX-icon.svg')

The full traceback has been saved in:

C:\Users\goddard\AppData\Local\Temp\sphinx-err-1wur_5r5.log

To report this error to the developers, please open an issue at <​https://github.com/sphinx-doc/sphinx/issues/>. Thanks!

Please also report this if it was a user error, so that a better error message can be provided next time.

make[3]: * [Makefile:90: html] Error 2
make[3]: Leaving directory '/home/goddard/ucsf/chimerax/docs/devel'
make[2]: * devel.install Error 2
make[2]: Leaving directory '/home/goddard/ucsf/chimerax/docs'
make[1]: * [Makefile:36: install] Error 2
make[1]: Leaving directory '/home/goddard/ucsf/chimerax'
make: * [Makefile:217: build-from-scratch] Error 2