gnu: Adjust package collection to Wrap using GUIX_PYTHONPATH.

This change was automated using:

$ git ls-files | grep .scm | \
  xargs sed 's/(getenv "PYTHONPATH")/(getenv "GUIX_PYTHONPATH")/' -i

$ git ls-files | grep .scm | \
  xargs sed 's/`("PYTHONPATH"/`("GUIX_PYTHONPATH"/' -i

* gnu/packages/admin.scm (nmap):
(dstat): Wrap using GUIX_PYTHONPATH.
* gnu/packages/audio.scm (jack-2):
(carla): Likewise.
* gnu/packages/benchmark.scm (fio): Likewise.
* gnu/packages/bioinformatics.scm (couger): Likewise.
(gess, find-circ, filtlong, nanopolish): Likewise.
* gnu/packages/cdrom.scm (cdemu-client): Likewise.
* gnu/packages/chemistry.scm (avogadro): Likewise.
* gnu/packages/connman.scm (econnman): Likewise.
* gnu/packages/cups.scm (hplip): Likewise.
* gnu/packages/debug.scm (scanmem): Likewise.
* gnu/packages/display-managers.scm (lightdm): Likewise.
* gnu/packages/ebook.scm (cozy): Likewise.
* gnu/packages/education.scm (anki): Likewise.
* gnu/packages/engineering.scm (kicad, volk, freecad): Likewise.
* gnu/packages/game-development.scm (renpy): Likewise.
* gnu/packages/games.scm (roguebox-adventures)
(seahorse-adventures, kajongg): Likewise.
* gnu/packages/gimp.scm (gimp, glimpse): Likewise.
* gnu/packages/glib.scm (itstool): Likewise.
* gnu/packages/gnome.scm (gnome-music, gtg, rhythmbox): Likewise.
(eolie, d-feet, gedit, caribou, gnome-shell, authenticator)
(gnome-todo, orca, passwordsafe, terminator, setzer)
(libratbag, komikku): Likewise.
* gnu/packages/gps.scm (gpsd): Likewise.
* gnu/packages/gtk.scm (gtk-doc): Likewise.
* gnu/packages/ibus.scm (ibus, ibus-libpinyin, ibus-anthy)
(ibus-libhangul): Likewise.
* gnu/packages/inkscape.scm (inkscape-1.0): Likewise.
* gnu/packages/linux.scm (bcc): Likewise.
* gnu/packages/mail.scm (notifymuch): Likewise.
* gnu/packages/maths.scm (units): Likewise.
* gnu/packages/music.scm (solfege): Likewise.
* gnu/packages/networking.scm (blueman): Likewise.
* gnu/packages/patchutils.scm (patchwork): Likewise.
* gnu/packages/photo.scm (rapid-photo-downloader, entangle): Likewise.
* gnu/packages/plotutils.scm (asymptote): Likewise.
* gnu/packages/presentation.scm (presentty): Likewise.
* gnu/packages/screen.scm (byobu): Likewise.
* gnu/packages/storage.scm (ceph): Likewise.
* gnu/packages/syndication.scm (liferea): Likewise.
* gnu/packages/task-management.scm (blanket): Likewise.
* gnu/packages/text-editors.scm (manuskript): Likewise.
* gnu/packages/version-control.scm (gitless, cgit, git-when-merged)
(git-imerge): Likewise.
* gnu/packages/video.scm (pitivi): Likewise.
* gnu/packages/virtualization.scm (criu): Likewise.
* gnu/packages/xfce.scm (catfish): Likewise.

1 files changed, 8 insertions, 8 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a6eda0c280..86270ecc75 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2263,9 +2263,9 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
           (lambda* (#:key inputs outputs #:allow-other-keys)
             ;; Make sure 'couger' runs with the correct PYTHONPATH.
             (let* ((out (assoc-ref outputs "out"))
-                   (path (getenv "PYTHONPATH")))
+                   (path (getenv "GUIX_PYTHONPATH")))
               (wrap-program (string-append out "/bin/couger")
-                `("PYTHONPATH" ":" prefix (,path))))
+                `("GUIX_PYTHONPATH" ":" prefix (,path))))
             #t)))))
     (inputs
      `(("python" ,python-2)
@@ -10696,7 +10696,7 @@ matplotlib.use('Agg')
 " line)))
                ;; Make sure GESS has all modules in its path
                (wrap-script (string-append target "GESS.py")
-                 `("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
+                 `("GUIX_PYTHONPATH" ":" = (,target ,(getenv "GUIX_PYTHONPATH"))))
                (mkdir-p bin)
                (symlink (string-append target "GESS.py")
                         (string-append bin "GESS.py"))
@@ -12871,11 +12871,11 @@ conversions, region filtering, FASTA sequence extraction and more.")
              (lambda* (#:key outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
                       (bin (string-append out "/bin"))
-                      (path (getenv "PYTHONPATH")))
+                      (path (getenv "GUIX_PYTHONPATH")))
                  (for-each (lambda (script)
                              (install-file script bin)
                              (wrap-program (string-append bin "/" script)
-                               `("PYTHONPATH" ":" prefix (,path))))
+                               `("GUIX_PYTHONPATH" ":" prefix (,path))))
                            '("cmp_bed.py"
                              "find_circ.py"
                              "maxlength.py"
@@ -13817,10 +13817,10 @@ datasets.")
            (add-after 'install 'wrap-program
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((out (assoc-ref outputs "out"))
-                      (path (getenv "PYTHONPATH")))
+                      (path (getenv "GUIX_PYTHONPATH")))
                  (wrap-program (string-append out
                                               "/share/filtlong/scripts/histogram.py")
-                   `("PYTHONPATH" ":" prefix (,path))))
+                   `("GUIX_PYTHONPATH" ":" prefix (,path))))
                #t))
            (add-before 'check 'patch-tests
              (lambda _
@@ -13894,7 +13894,7 @@ choosing which reads pass the filter.")
            (add-after 'install 'wrap-programs
              (lambda* (#:key outputs #:allow-other-keys)
                (for-each (lambda (file)
-                           (wrap-program file `("PYTHONPATH" ":" prefix (,path))))
+                           (wrap-program file `("GUIX_PYTHONPATH" ":" prefix (,path))))
                          (find-files "/share/nanopolish/scripts" "\\.py"))
                (for-each (lambda (file)
                            (wrap-program file `("PERL5LIB" ":" prefix (,path))))