From b949f34f31a045eb0fb242b81a223178fb6994d3 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Mon, 6 Sep 2021 21:53:32 +0200
Subject: gnu: Use the non-deprecated TeX packages.

This commit leaves 'dblatex' and 'texlive-hyperref' as users of
deprecated packages, but these have many dependents.

* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use
non-deprecated TeX Live packages.
(velvet)[native-inputs]: Likewise.
* gnu/packages/chez.scm (chez-scheme)[native-inputs]: Likewise.
(chez-web)[native-inputs]: Likewise.
* gnu/packages/engineering.scm (fastcap)[native-inputs]: Likewise.
* gnu/packages/guile-xyz.scm (emacsy)[native-inputs]: Likewise.
* gnu/packages/maths.scm (hypre)[native-inputs]: Likewise.
* gnu/packages/music.scm (lilypond)[native-inputs]: Likewise.
* gnu/packages/ocaml.scm (ocaml-bibtex2html)[native-inputs]: Likewise.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-numpy-documentation)[native-inputs]:
Likewise.
(python-matplotlib-documentation)[native-inputs]: Likewise.
(python-ipython-documentation)[native-inputs]: Likewise.
(python-nbconvert)[native-inputs]: Likewise.
(python-pypandoc)[native-inputs]: Likewise.
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Likewise.
* gnu/packages/tex.scm (texlive-pstool)[propagated-inputs]: Likewise.
(teximpatient)[native-inputs]: Likewise.
(texlive-latex-pgf)[propagated-inputs]: Likewise.
(texlive-beamer)[propagated-inputs]: Likewise.
---
 gnu/packages/bioinformatics.scm |  6 +++---
 gnu/packages/chez.scm           | 10 +++++-----
 gnu/packages/engineering.scm    |  2 +-
 gnu/packages/guile-xyz.scm      |  2 +-
 gnu/packages/maths.scm          |  4 ++--
 gnu/packages/music.scm          |  2 +-
 gnu/packages/ocaml.scm          |  2 +-
 gnu/packages/plotutils.scm      |  2 +-
 gnu/packages/python-xyz.scm     | 42 ++++++++++++++++++++---------------------
 gnu/packages/statistics.scm     |  6 +++---
 gnu/packages/tex.scm            | 14 +++++++-------
 11 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0718b5e31c..430551887d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3110,9 +3110,9 @@ data and settings.")
      `(("texlive" ,(texlive-updmap.cfg (list texlive-cm
                                         texlive-amsfonts
 
-                                        texlive-latex-doi
+                                        texlive-doi
                                         texlive-latex-examplep
-                                        texlive-latex-hyperref
+                                        texlive-hyperref
                                         texlive-latex-ms
                                         texlive-latex-natbib
                                         texlive-bibtex         ; style files used by natbib
@@ -12776,7 +12776,7 @@ to an artifact/contaminant file.")
        ("zlib" ,zlib)))
     (native-inputs
      `(("texlive" ,(texlive-updmap.cfg (list texlive-latex-graphics
-                                        texlive-latex-hyperref)))))
+                                        texlive-hyperref)))))
     (home-page "https://www.ebi.ac.uk/~zerbino/velvet/")
     (synopsis "Nucleic acid sequence assembler for very short reads")
     (description
diff --git a/gnu/packages/chez.scm b/gnu/packages/chez.scm
index a886e59130..ccb4800d1c 100644
--- a/gnu/packages/chez.scm
+++ b/gnu/packages/chez.scm
@@ -114,8 +114,8 @@
        ;; for docs
        ("stex" ,stex)
        ("xorg-rgb" ,xorg-rgb)
-       ("texlive" ,(texlive-updmap.cfg (list texlive-latex-oberdiek
-                                             texlive-generic-epsf)))
+       ("texlive" ,(texlive-updmap.cfg (list texlive-oberdiek
+                                             texlive-epsf)))
        ("ghostscript" ,ghostscript)
        ("netpbm" ,netpbm)))
     (native-search-paths
@@ -316,10 +316,10 @@ and 32-bit PowerPC architectures.")
       (native-inputs
        `(("chez-scheme" ,chez-scheme)
          ("ghostscript" ,ghostscript)
-         ("texlive" ,(texlive-updmap.cfg (list texlive-latex-oberdiek
-                                          texlive-generic-epsf
+         ("texlive" ,(texlive-updmap.cfg (list texlive-oberdiek
+                                          texlive-epsf
                                           texlive-metapost
-                                          texlive-fonts-charter
+                                          texlive-charter
                                           texlive-pdftex
                                           texlive-context
                                           texlive-cm
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index 57f4687005..8a1ee88f81 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -524,7 +524,7 @@ featuring various improvements and bug fixes.")))
      ;; FIXME: with texlive-tiny citation references are rendered as question
      ;; marks.  During the build warnings like these are printed:
      ;; LaTeX Warning: Citation `nabors91' on page 2 undefined on input line 3.
-     `(("texlive" ,(texlive-updmap.cfg (list texlive-fonts-amsfonts)))
+     `(("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts)))
        ("ghostscript" ,ghostscript)))
     (arguments
      `(#:make-flags '("CC=gcc" "RM=rm" "SHELL=sh" "all")
diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm
index feefa3a5f6..28964fbce2 100644
--- a/gnu/packages/guile-xyz.scm
+++ b/gnu/packages/guile-xyz.scm
@@ -3313,7 +3313,7 @@ API.")
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("texinfo" ,texinfo)
-       ("texlive" ,(texlive-updmap.cfg (list texlive-generic-epsf)))))
+       ("texlive" ,(texlive-updmap.cfg (list texlive-epsf)))))
     (inputs
      `(("dbus-glib" ,dbus-glib)
        ("guile" ,guile-3.0)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 1f8b592ff7..9ce31ba633 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5100,7 +5100,7 @@ set.")
                                              texlive-latex-framed
                                              texlive-latex-geometry
                                              texlive-latex-hanging
-                                             texlive-latex-hyperref
+                                             texlive-hyperref
                                              texlive-latex-multirow
                                              texlive-latex-natbib
                                              texlive-latex-needspace
@@ -5112,7 +5112,7 @@ set.")
                                              texlive-latex-tocloft
                                              texlive-latex-upquote
                                              texlive-latex-varwidth
-                                             texlive-latex-wasysym
+                                             texlive-wasysym
                                              texlive-latex-wrapfig)))))
     (inputs
      `(("blas" ,openblas)
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 178f23c821..de49e1541a 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1535,7 +1535,7 @@ and auto-mapping slices to MIDI note numbers.")
        ("imagemagick" ,imagemagick)
        ("netpbm" ,netpbm)               ;for pngtopnm
        ("texlive" ,(texlive-updmap.cfg (list texlive-metapost
-                                        texlive-generic-epsf
+                                        texlive-epsf
                                         texlive-lh
                                         texlive-latex-cyrillic)))
        ("texinfo" ,texinfo)
diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index ada52b291e..9a36185ecb 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -7380,7 +7380,7 @@ browsers and Node.js.")
      `(("which" ,which)
        ("texlive" ,(texlive-updmap.cfg
                     (list texlive-fonts-ec texlive-preprint
-                          texlive-latex-hyperref texlive-bibtex)))))
+                          texlive-hyperref texlive-bibtex)))))
     (propagated-inputs
      `(("hevea" ,hevea)))
     (home-page "https://www.lri.fr/~filliatr/bibtex2html/")
diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm
index 0b2c24c743..cb6ac63005 100644
--- a/gnu/packages/plotutils.scm
+++ b/gnu/packages/plotutils.scm
@@ -230,7 +230,7 @@ colors, styles, options and details.")
                                         texlive-latex-base
                                         texlive-latex-geometry
                                         texlive-latex-graphics
-                                        texlive-latex-oberdiek ; for ifluatex
+                                        texlive-oberdiek ;for ifluatex
                                         texlive-latex-parskip
                                         texlive-tex-texinfo)))))
     (inputs
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index acc7910f32..9801a3caf8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5287,16 +5287,16 @@ color scales, and color space conversion easy.  It has support for:
        ("pkg-config" ,pkg-config)
        ("python-sphinx" ,python-sphinx)
        ("python-numpydoc" ,python-numpydoc)
-       ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-cm-super
+       ("texlive" ,(texlive-updmap.cfg (list texlive-cm-super
                                         texlive-fonts-ec
-                                        texlive-generic-ifxetex
-                                        texlive-generic-pdftex
+                                        texlive-generic-iftex
+                                        texlive-pdftex
                                         texlive-amsfonts
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
                                         texlive-latex-eqparbox
-                                        texlive-latex-etoolbox
+                                        texlive-etoolbox
                                         texlive-latex-expdlist
                                         texlive-latex-fancyhdr
                                         texlive-latex-fancyvrb
@@ -5305,11 +5305,11 @@ color scales, and color space conversion easy.  It has support for:
                                         texlive-latex-framed
                                         texlive-latex-geometry
                                         texlive-latex-graphics
-                                        texlive-latex-hyperref
+                                        texlive-hyperref
                                         texlive-latex-mdwtools
                                         texlive-latex-multirow
                                         texlive-latex-needspace
-                                        texlive-latex-oberdiek
+                                        texlive-oberdiek
                                         texlive-latex-parskip
                                         texlive-latex-preview
                                         texlive-latex-tabulary
@@ -5318,7 +5318,7 @@ color scales, and color space conversion easy.  It has support for:
                                         texlive-latex-trimspaces
                                         texlive-latex-ucs
                                         texlive-latex-upquote
-                                        texlive-latex-url
+                                        texlive-url
                                         texlive-latex-varwidth
                                         texlive-latex-wrapfig)))
        ("texinfo" ,texinfo)
@@ -5842,11 +5842,11 @@ toolkits.")
                                         texlive-latex-type1cm
                                         texlive-latex-ucs
 
-                                        texlive-generic-pdftex
+                                        texlive-pdftex
 
                                         texlive-fonts-ec
-                                        texlive-fonts-adobe-times
-                                        texlive-fonts-txfonts)))
+                                        texlive-times
+                                        texlive-txfonts)))
        ("texinfo" ,texinfo)
        ,@(package-native-inputs python-matplotlib)))
     (arguments
@@ -8134,13 +8134,13 @@ computing.")
        ;; FIXME: It's possible that a smaller union would work just as well.
        ("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts
                                         texlive-fonts-ec
-                                        texlive-generic-ifxetex
+                                        texlive-generic-iftex
                                         texlive-pdftex
                                         texlive-latex-capt-of
                                         texlive-latex-cmap
                                         texlive-latex-environ
                                         texlive-latex-eqparbox
-                                        texlive-latex-etoolbox
+                                        texlive-etoolbox
                                         texlive-latex-expdlist
                                         texlive-latex-fancyhdr
                                         texlive-latex-fancyvrb
@@ -8149,11 +8149,11 @@ computing.")
                                         texlive-latex-framed
                                         texlive-latex-geometry
                                         texlive-latex-graphics
-                                        texlive-latex-hyperref
+                                        texlive-hyperref
                                         texlive-latex-mdwtools
                                         texlive-latex-multirow
                                         texlive-latex-needspace
-                                        texlive-latex-oberdiek
+                                        texlive-oberdiek
                                         texlive-latex-parskip
                                         texlive-latex-preview
                                         texlive-latex-tabulary
@@ -8162,7 +8162,7 @@ computing.")
                                         texlive-latex-trimspaces
                                         texlive-latex-ucs
                                         texlive-latex-upquote
-                                        texlive-latex-url
+                                        texlive-url
                                         texlive-latex-varwidth
                                         texlive-latex-wrapfig)))
        ("texinfo" ,texinfo)))))
@@ -11198,18 +11198,18 @@ time.")
                                         texlive-eurosym
                                         texlive-fonts-rsfs
                                         texlive-generic-ulem
-                                        texlive-iftex
+                                        texlive-generic-iftex
                                         texlive-jknappen
                                         texlive-latex-amsmath
                                         texlive-latex-enumitem
                                         texlive-latex-fancyvrb
                                         texlive-latex-float
-                                        texlive-latex-fontspec
+                                        texlive-fontspec
                                         texlive-latex-geometry
-                                        texlive-latex-hyperref
+                                        texlive-hyperref
                                         texlive-latex-jknapltx
                                         texlive-latex-ms
-                                        texlive-latex-oberdiek
+                                        texlive-oberdiek
                                         texlive-latex-parskip
                                         texlive-latex-trimspaces
                                         texlive-latex-upquote
@@ -24948,8 +24948,8 @@ By default it uses the open Python vulnerability database Safety DB.")
     (native-inputs
      `(("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts
                                         texlive-fonts-ec
-                                        texlive-latex-hyperref
-                                        texlive-latex-oberdiek
+                                        texlive-hyperref
+                                        texlive-oberdiek
                                         texlive-lm
                                         texlive-xcolor)))))
     (arguments
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 804e2e6a8c..05ce641374 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -349,11 +349,11 @@ as.POSIXct(if (\"\" != Sys.getenv(\"SOURCE_DATE_EPOCH\")) {\
                                         texlive-latex-base
                                         texlive-latex-fancyvrb
                                         texlive-latex-graphics
-                                        texlive-latex-hyperref
-                                        texlive-latex-oberdiek
+                                        texlive-hyperref
+                                        texlive-oberdiek
                                         texlive-latex-tools
                                         texlive-latex-upquote
-                                        texlive-latex-url
+                                        texlive-url
                                         texlive-latex-xkeyval)))
        ("tzdata" ,tzdata-for-tests)
        ("xz" ,xz)))
diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm
index c2846793b2..58732462ae 100644
--- a/gnu/packages/tex.scm
+++ b/gnu/packages/tex.scm
@@ -4563,7 +4563,7 @@ rotated.")
               #:trivial? #t))
     (propagated-inputs
      `(("texlive-latex-bigfoot" ,texlive-latex-bigfoot) ; for suffix
-       ("texlive-latex-filemod" ,texlive-latex-filemod)
+       ("texlive-filemod" ,texlive-filemod)
        ("texlive-latex-graphics" ,texlive-latex-graphics)
        ("texlive-latex-ifplatform" ,texlive-latex-ifplatform)
        ("texlive-latex-l3kernel" ,texlive-latex-l3kernel) ; for expl3
@@ -7134,10 +7134,10 @@ develop documents with LaTeX, in a single application.")
              #t)))))
     (native-inputs
      `(("texlive" ,(texlive-updmap.cfg (list texlive-amsfonts
-                                        texlive-fonts-adobe-palatino
-                                        texlive-fonts-adobe-zapfding
+                                        texlive-palatino
+                                        texlive-zapfding
                                         texlive-knuth-lib
-                                        texlive-fonts-mflogo-font
+                                        texlive-mflogo-font
                                         texlive-pdftex)))
        ("automake" ,automake)))
     (home-page "https://www.gnu.org/software/teximpatient/")
@@ -7487,7 +7487,7 @@ striking out (line through words) and crossing out (/// over words).")
             (base32
              "05zdq7y3am109m5534ahqqp9x5iar3ha68v1r4zkrdly2mijxz2j"))))))
     (propagated-inputs
-     `(("texlive-latex-xcolor" ,texlive-latex-xcolor)))
+     `(("texlive-xcolor" ,texlive-xcolor)))
     (arguments
      `(#:modules ((guix build utils))
        #:builder
@@ -8119,9 +8119,9 @@ for a wealth of support information.")
                "091n27n4l3iac911bvmpp735ffryyzaq46mkclgn3q9jsvc4ngiv")
               #:trivial? #t))
     (propagated-inputs
-     `(("texlive-latex-hyperref" ,texlive-latex-hyperref)
+     `(("texlive-hyperref" ,texlive-hyperref)
        ("texlive-oberdiek" ,texlive-oberdiek)
-       ("texlive-latex-etoolbox" ,texlive-latex-etoolbox)
+       ("texlive-etoolbox" ,texlive-etoolbox)
        ("texlive-latex-pgf" ,texlive-latex-pgf)))
     (home-page "https://www.ctan.org/pkg/beamer")
     (synopsis "LaTeX class for producing presentations and slides")
-- 
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