So this is an issue with manual vertical spacing in LilyPond, not wirt
lyluatex.
Unfortunately I've never really been familiar with this, so someone
else should step in.
The underlying issue is that LilyPond isn't really aware of the actual
extent of the system when cropping. This happens when you move items
around by overridindĒµ their extra-offset properties but seems an issue
too ehen pushing around the staves themselves.
I don't know if overriding the Y-extent of the dynamics will help here.
ursHTH anyway

Am Sonntag, den 30.08.2020, 11:57 +0200 schrieb Claire Meyer:
> Hi Urs,
> 
> Huh ! 
> > This will give you one cropped pdf plus a number of indexed pdf 
> files for each system. The cropping issues should be visible there
> too 
> and might give some more clues for understanding the issue.
> Yep, a 100%. I attached the outputs for one system where the problem
> is visible; one from lilypond, one from lilypond + lyluatex. The
> cropped pdf with all systems has no cropping issue.
> 
> Is there anything else I can provide  ?
> Claire
> 
> On Sun, Aug 30, 2020 at 11:26 AM Urs Liska <li...@openlilylib.org>
> wrote:
> > Hi Claire,
> > I'm not sure how the manual vertical positioning interacts with the
> > cropping, but you can test further  by inserting   \include
> > "lilypond-book-preamble.ly" in your file.This will give you one
> > cropped pdf plus a number of indexed pdf files for each system. The
> > cropping issues should be visible there too and might give some
> > more clues for understanding the issue.
> > The most common cause for such cropping issues would be (not in
> > your case) moving stuff with extra-offset, which is then not
> > included in the obkjects' X/Y-extent.
> > Urs
> > Am Sonntag, den 30.08.2020, 11:12 +0200 schrieb Claire Meyer:
> > > Hi all,
> > > 
> > > I'm integrating a score with latex via lyluatex. The .ly file is
> > > finished, and gives no error; the score produced looks good, and
> > > I'm at the step where I just integrate with latex, and touch up
> > > the things that need retouching. I insert system by system, and
> > > unfortunately, some dynamics are mostly cropped out :
> > > 
> > > 
> > > The scribble between the two systems is a dynamic mark that
> > > applies to the lower system. I looked in the temporary files
> > > generated by lyluatex, and the pdfs are cropped in such a manner
> > > that all my higher-placed-within-the-system dynamics are mostly
> > > removed.
> > > 
> > > Those dynamics are all custom dynamic marks that I constructed
> > > like :
> > > 
> > > mydyn = \tweak DynamicText.self-alignment-X #LEFT
> > >   #(make-dynamic-script
> > >           (markup
> > >                   #:with-dimensions '(0 . 5) '(0 . 0) #:line
> > >                   (#:normal-text #:italic "<whatever my dynamic
> > > mark says>")))
> > > 
> > > They were badly placed with automatic placement (overlapping with
> > > the phrasing slurs, mostly), so I specified in my score for those
> > > dynamics that :
> > > 
> > > 
> > >           \new Dynamics \with {
> > >                   \override VerticalAxisGroup.nonstaff-
> > > relatedstaff-spacing =
> > >                           #'((basic-distance . 6)
> > >                                   (minimum-distance . 5)
> > >                                   (padding . 3)
> > >                                   (stretchability . 6))
> > >                   } { \dynamicsA }
> > > 
> > > 
> > > Any idea how to solve that problem ? I tried to include
> > > everything relevant to not just code dump things here, but ask
> > > away if I forgot something.
> > > 
> > > Thanks,
> > > Claire
> > > 

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