I found part of my problem with the fonts. Running squarize.py gives me a
bunch of errors. Partial log attached. Fontforge is built with python3
bindings. I don't really know what the error means or how to fix it.

-Br. Elijah Schwab, O.Carm.

On Apr 09, 2015 22:38, Henry So Jr. wrote:
> You might need to clear your luatex font cache
> 
> luaotfload-tool --cache=erase
> 
> since the fonts have changed.  Since the punctum figures are not there,
> it might explain the tightness without actually exhibiting what I'm
> seeing.
> 
> Henry
$ fontforge -script squarize.py gregorio &> errorlog

Copyright (c) 2000-2014 by George Williams. See AUTHORS for Contributors.
 License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
 with many parts BSD <http://fontforge.org/license.html>. Please read LICENSE.
 Based on sources from 18:50 TAHT  2-Apr-2015-ML-D.
 Based on source from git with hash: 
Internal Error (overlap) in uF0442: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0443: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0444: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0445: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0542: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0543: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0544: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF0545: The start of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4C06: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4C0B: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4C10: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4C15: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4C1A: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF5006: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF500B: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF5010: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF5015: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF501A: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4F06: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4F0B: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4F10: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4F15: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4F1A: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4E06: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4E0B: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4E10: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4E15: The end of the monotonic does not match 
that of the containing spline.
Internal Error (overlap) in uF4E1A: The end of the monotonic does not match 
that of the containing spline.
generating horizontal episemus for gregorio
generating pes for gregorio
  * pes
  * pes quilisma
  * pes deminutus
  * pes initio debilis
  * pes initio debilis deminutus
generating pes quadratum for gregorio
  * pes quadratum
  * pes quassus
  * pes quilisma quadratum
  * pes auctus ascendens
  * pes initio debilis auctus ascendens
  * pes quassus auctus ascendens
  * pes quilisma auctus ascendens
  * pes auctus descendens
  * pes initio debilis auctus descendens
  * pes quassus auctus descendens
  * pes quilisma auctus descendens
  * first part of salicus
generating flexus for gregorio
  * flexus
  * flexus deminutus
  * flexus auctus ascendens
  * flexus auctus descendens
generating scandicus for gregorio
generating ancus for gregorio
generating salicus for gregorio
generating torculus for gregorio
  * torculus
  * torculus initio debilis
  * torculus auctus descendens
  * torculus initio debilis auctus descendens
  * torculus auctus ascendens
  * torculus initio debilis auctus ascendens
  * torculus deminutus
  * torculus initio debilis deminutus
Traceback (most recent call last):
  File "squarize.py", line 1283, in <module>
    main()
  File "squarize.py", line 147, in main
    torculus()
  File "squarize.py", line 987, in torculus
    write_torculus(i,j, "idebilis", "deminutus", 'torculus', 
'initiodebilisdeminutus')
  File "squarize.py", line 1009, in write_torculus
    write_deminutus(i,j,glyphnumber, length, firstbar=1)
  File "squarize.py", line 401, in write_deminutus
    paste_and_move("mdeminutus", glyphnumber, length, i*base_height)
  File "squarize.py", line 360, in paste_and_move
    newfont.pasteInto()
KeyboardInterrupt
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