Some pictures appear too small in the web reference manual
In the Analysis section e.g. (analysis.rst)
Fig. 50 The window of gmx view showing a box of water
Fig. 55 has the correct rotation but is far too small
Fix reference manual image sizes
Make Imagemagick availability more visible
Changes the message type for the gmxTestImagemagick test to be a warning
when GMX_BUILD_MANUAL is ON, to make sure users see that there may be an
issue with building the full documentation.
Also change the test script to see if the new file actually gets
created, instead of checking the return code.
#1 Updated by Paul Bauer 12 months ago
Checking this out right now when building with I7c9bb695e1dac37b83cdc82a2c0bdb53700a1156
Fig. 50 is the right way round when visualized in Chromium
Fig. 51 the same, right way around for me
Fig. 53 same
Fig. 54 and 55 also look correct for me
Fig. 57 and 58 also look fine for me
Fig. 60 and 61 are too small (62 kind of as well)
#4 Updated by Carsten Kutzner 12 months ago
I found out that the problem I originally reported (wrong rotation of some figures) was not caused by GROMACS but ultimately by the fact that ImageMagick's convert was not able to produce new figures during 'make webpage-sphinx' due to missing permissions. That problem, however, did go unnoticed since there were still old (rotated) versions of these figures in my build tree.
Only after deleting these, I got a proper error message:
[ 93%] Converting Sphinx input graphics file reference-manual/analysis/plots/sgangle.pdf to png
convert: not authorized `/home/ckutzne/eclipse-workspace/git-gromacs-WRITE/docs/reference-manual/analysis/plots/sgangle.pdf'
convert: no images defined `/home/ckutzne/eclipse-workspace/git-gromacs-WRITE/build2/docs/sphinx-input/reference-manual/analysis/plots/sgangle.png'
For security reasons, recent SUSE versions apparently do not allow the use of /usr/bin/convert on PDFs (and other formats) any more unless specified otherwise in the /etc/ImageMagick*/policy.xml file.
Solution for others who run into the same problem:
In the policy.xml file, change
<policy domain="coder" rights="write" pattern="PDF" /> to
<policy domain="coder" rights="read|write" pattern="PDF" />
#6 Updated by Carsten Kutzner 12 months ago
Just tested this again. I am post 2019-beta3, so I1c49d683d971a5bf0b0ce217f7e9ecd60603e6e6 is in.
However, make webpage-sphinx builds quietly (apart from several warnings due to undefined labels etc) and without errors. Only the begin of the reference manual then states "The manual could not be properly build because we could not convert the images for proper display without Imagemagick."
convert is however properly picked up by CMake, just cannot actually convert anything.