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Fixes <https://issues.guix.gnu.org/39562>.
* gnu/packages/machine-learning.scm (python-keras)[phases]{check}: Apply
upstream fix to test_topology.py. Skip the failing test_selu test.
Reported-by: Pierre Neidhardt <mail@ambrevar.xyz>
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It was failing on a /bin/sh occurrence patched twice in the configure script:
sh: ./configure:/gnu/store/...-bash-minimal-5.0.16/gnu/store/...-bash-minimal-5.0.1:bad
interpreter: No such file or directory
* gnu/packages/machine-learning.scm (ocaml-mcl)[phases]{patch-paths}: Do not
patch the configure script.
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* gnu/packages/machine-learning.scm (r-adaptivesparsity): Move from here...
* gnu/packages/cran.scm (r-adaptivesparsity): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/machine-learning.scm (vowpal-wabbit)[arguments]: Add
'install-more-headers phase to install more headers.
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Reported by Hamzeh Nasajpour <h.nasajpour@pantherx.org>.
* gnu/packages/machine-learning.scm (dlib)[arguments]: Add
configure-flag to build shared library. Remove custom
'delete-static-library phase.
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* gnu/packages/machine-learning.scm (openfst): Update to 1.7.9.
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* gnu/packages/machine-learning.scm (python-onnx): New variable.
* gnu/packages/patches/python-onnx-use-system-googletest.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
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Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs. Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
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Move the 3 lisp libraries that are not in lisp-xyz.scm with the others.
* gnu/packages/machine-learning.scm (sbcl-cl-libsvm-format, cl-libsvm-format,
ecl-cl-libsvm-format, sbcl-cl-online-learning, cl-online-learning,
ecl-cl-online-learning, sbcl-cl-random-forest, cl-random-forest,
ecl-cl-random-forest): Move to ...
* gnu/packages/lisp-xyz.scm (sbcl-cl-libsvm-format, cl-libsvm-format,
ecl-cl-libsvm-format, sbcl-cl-online-learning, cl-online-learning,
ecl-cl-online-learning, sbcl-cl-random-forest, cl-random-forest,
ecl-cl-random-forest): ... here.
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* gnu/packages/machine-learning.scm (lightgbm)[source]: Download using
git-fetch.
[arguments]: Adjust custom 'check phase accordingly.
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This prevents conflicting variants of python-prompt-toolkit from being
installed, which prevented jupyter from being installed.
* gnu/packages/python-xyz.scm (python-ipython)[propagated-inputs]: Replace
python-prompt-toolkit with python-prompt-toolkit-2.
(python-widgetsnbextension)[propagated-inputs]: Do not use
prompt-toolkit-2-instead-of-prompt-toolkit on python-ipykernel.
(python-ipywidgets)[propagated-inputs]: Do not use
prompt-toolkit-2-instead-of-prompt-toolkit on python-ipython.
(python-jupyter-console)[propagated-inputs]: Do not use
prompt-toolkit-2-instead-of-prompt-toolkit on python-ipykernel.
(prompt-toolkit-2-instead-of-prompt-toolkit): Remove variable.
* gnu/packages/machine-learning.scm (python-iml)[propagated-inputs]: Do not
use prompt-toolkit-2-instead-of-prompt-toolkit on python-ipython.
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* gnu/packages/machine-learning.scm (dlib): Update to 19.20.
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* gnu/packages/machine-learning.scm (sbcl-cl-random-forest)[arguments]: Remove
'add-sb-cltl2-dependency' phase.
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* gnu/packages/machine-learning.scm (python-iml)[propagated-inputs]: Pin
implicit python-prompt-toolkit dependency to version 2.
* gnu/packages/python-xyz.scm (python-widgetsnbextension)[propagated-inputs]:
Pin implicit python-prompt-toolkit dependency to version 2.
(python-ipywidgets)[propagated-inputs]: Pin implicit python-prompt-toolkit
dependency to version 2.
(python-jupyter-console)[propagated-inputs]: Pin explicit
python-prompt-toolkit dependency to version 2.
(python-prompt-toolkit): Update to version 3.0.5.
[propagated-inputs]: Remove PYTHON-SIX and PYTHON-PYGMENTS.
[home-page]: Adjust to current.
(python-prompt-toolkit-2): New variable.
(prompt-toolkit-2-instead-of-prompt-toolkit): New variable.
(python2-prompt-toolkit): Keep at version 2.
(python-prompt-toolkit-1): Inherit from version 2.
Signed-off-by: Marius Bakke <marius@gnu.org>
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* gnu/packages/machine-learning.scm (python-iml)[propagated-inputs]: Move
PYTHON-NOSE ...
[native-inputs]: ... here.
Signed-off-by: Marius Bakke <marius@gnu.org>
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* gnu/packages/machine-learning.scm (python-iml)[home-page]: s/http/https/
Signed-off-by: Marius Bakke <marius@gnu.org>
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* gnu/packages/machine-learning.scm (tensorflow)[arguments]: Also import
python-version from python-build-system. Adjust 'python3.7-compatibility
to also add python-3.8 compatibility. Adjust 'install-python to not
hardcode the python version.
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Conflicts:
gnu/local.mk
gnu/packages/backup.scm
gnu/packages/emacs-xyz.scm
gnu/packages/guile.scm
gnu/packages/lisp.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/web.scm
gnu/packages/xorg.scm
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* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[arguments]: Patch
master_server.py before build.
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* gnu/packages/machine-learning.scm (kaldi-gstreamer-server)[inputs]: Replace
python-tornado with python-tornado-6.
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* gnu/packages/machine-learning.scm (kaldi-gstreamer-server): Update to
0-2.f68cab4.
[inputs]: Replace python-2 with python-wrapper, python2-pygobject with
python-pygobject, python2-pyyaml with python-pyyaml, and python2-tornado with
python-tornado; remove python2-ws4py-for-kaldi-gstreamer-server and
python2-futures.
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* gnu/packages/machine-learning.scm (python-scikit-learn)
[native-inputs]: Move 'python-joblib' to ...
[propagated-inputs]: ... here.
Signed-off-by: Mathieu Othacehe <m.othacehe@gmail.com>
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* gnu/packages/machine-learning.scm (gst-kaldi-nnet2-online): Update to
0-2.cb227ef.
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* gnu/packages/machine-learning.scm (kaldi): Update to 0-2.d4791c0.
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* gnu/packages/machine-learning.scm (python-scikit-rebate): New variable.
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* gnu/packages/machine-learning (shogun): Fix grammar.
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Conflicts:
gnu/packages/admin.scm
gnu/packages/commencement.scm
gnu/packages/guile.scm
gnu/packages/linux.scm
gnu/packages/package-management.scm
gnu/packages/pulseaudio.scm
gnu/packages/web.scm
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* gnu/packages/machine-learning.scm (vowpal-wabbit)[source]: Download
using git-fetch.
[arguments]: Add custom 'make-files-writable phase.
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* gnu/packages/machine-learning.scm (python-scikit-learn)[home-page]: Use HTTPS.
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* gnu/packages/machine-learning.scm (tensorflow)[native-inputs]: Move
GRPC:STATIC ...
[inputs]: ... here.
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* gnu/packages/rpc.scm (grpc): Update to 1.27.3.
[arguments]: Add "-DgRPC_ABSL_PROVIDER=package" in #:configure-flags.
[inputs]: Add ABSEIL-CPP.
(grpc-1.16.1): New public variable.
* gnu/packages/hyperledger.scm (hyperledger-iroha)[inputs]: Change from GRPC
to GRPC-1.16.
* gnu/packages/machine-learning.scm (tensorflow)[native-inputs, inputs]: Likewise.
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* gnu/packages/machine-learning.scm (grpc): Move to ...
* gnu/packages/rpc.scm: ... here. New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Adjust accordingly.
* gnu/packages/hyperledger.scm: Adjust module imports.
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* gnu/packages/machine-learning.scm (shogun)[home-page]: Use HTTPS.
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This is a follow-up to commit 546893c2965c8114e4d7cfe1de46c46664ec4b9e.
* gnu/packages/machine-learning.scm (python-scikit-learn)[properties]: New field.
(python2-scikit-learn)[version, source]: New fields.
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* gnu/packages/machine-learning.scm (grpc)[outputs]: Add static.
[arguments]: Copy configure-flags from cmake-build-system. Add custom
phases 'configure-shared, 'install-shared-libraries and 'move-static-libs
to build shared libs and move static libs to their own output.
(tensorflow)[native-inputs]: Add grpc:static.
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* gnu/packages/machine-learning.scm (python-umap-learn): Add python-joblib to
run the test suite.
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* gnu/packages/machine-learning.scm (python-scikit-learn): Update to 0.22.1;
Add python-joblib to native-inputs to run the test suite.
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* gnu/packages/machine-learning.scm (libsvm)[home-page]: Use HTTPS.
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This is a follow-up to commit 9c2563a80b6f1d8fb8677f5314e6180ea9916aa5.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Add #:modules.
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* gnu/packages/abiword.scm (abiword)[inputs]: Change from LIBJPEG to
LIBJPEG-TURBO.
* gnu/packages/admin.scm (testdisk)[inputs]: Likewise.
* gnu/packages/algebra.scm (giac)[inputs]: Likewise.
* gnu/packages/animation.scm (synfig)[inputs]: Likewise.
* gnu/packages/astronomy.scm (gnuastro, celestia)[inputs]: Likewise.
* gnu/packages/cdrom.scm (dvdstyler)[inputs]: Likewise.
* gnu/packages/cran.scm (r-jpeg, r-tiff, r-readbitmap)[inputs]: Likewise.
* gnu/packages/cups.scm (cups-filters, hplip)[inputs]: Likewise.
* gnu/packages/display-managers.scm (slim)[inputs]: Likewise.
* gnu/packages/ebook.scm (fbreader)[inputs]: Likewise.
* gnu/packages/emacs.scm (emacs)[inputs]: Likewise.
* gnu/packages/enlightenment.scm (efl)[propagated-inputs]: Likewise.
* gnu/packages/fltk.scm (fltk, ntk)[inputs]: Likewise.
* gnu/packages/fontutils.scm (fontforge)[inputs]: Likewise.
* gnu/packages/freedesktop.scm (weston)[inputs]: Likewise.
* gnu/packages/game-development.scm (sfml, allegro, aseprite, python-pygame,
eureka, ioquake3)[inputs]: Likewise.
* gnu/packages/games.scm (adanaxisgpl, freedroidrpg, irrlicht, minetest,
fizmo, supertuxkart, gzdoom, xmoto, xonotic)[inputs]: Likewise.
* gnu/packages/gd.scm (gd, perl-gd)[inputs]: Likewise.
* gnu/packages/ghostscript.scm (lcms)[inputs]: Likewise.
(ghostscript)[inputs, native-inputs]: Likewise.
* gnu/packages/gimp.scm (gegl, gimp)[inputs]: Likewise.
* gnu/packages/gnome.scm (libgnomeui, eog, tracker-miners, gthumb)[inputs]: Likewise.
* gnu/packages/gnunet.scm (libextractor)[inputs]: Likewise.
* gnu/packages/gnustep.scm (windowmaker)[inputs]: Likewise.
* gnu/packages/graphics.scm (blender, blender-2.79, openimageio,
openscenegraph, openscenegraph-3.4, povray, fgallery)[inputs]: Likewise.
* gnu/packages/graphviz.scm (graphviz)[inputs]: Likewise.
* gnu/packages/gstreamer.scm (gst-plugins-good)[inputs]: Likewise.
* gnu/packages/gtk.scm (gdk-pixbuf)[inputs]: Likewise.
* gnu/packages/image-processing.scm (dcmtk, mia, vtk, opencv, vips, nip2, vxl,
insight-toolkit)[inputs]: Likewise.
* gnu/packages/image-viewers.scm (gpicview, luminance-hdr)[inputs]: Likewise.
* gnu/packages/image.scm (jpegoptim, libtiff, leptonica, imlib2, freeimage,
vigra, libwebp, libmng, jasper, steghide, jp2a)[inputs]: Likewise.
* gnu/packages/imagemagick.scm (imagemagick, graphicsmagick)[inputs]: Likewise.
* gnu/packages/java.scm (icedtea-6, icedtea-7, openjdk9, openjdk11,
openjdk12)[inputs]: Likewise.
* gnu/packages/kde-frameworks.scm (khtml)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[inputs]: Likewise.
* gnu/packages/machine-learning.scm (dlib, tensorflow)[inputs]: Likewise.
* gnu/packages/mate.scm (atril, eom)[inputs]: Likewise.
* gnu/packages/maths.scm (hdf4, hdf-java, hdf-eos2, netcdf)[inputs]: Likewise.
* gnu/packages/netpbm.scm (netpbm)[inputs]: Likewise.
* gnu/packages/pdf.scm (zathura-pdf-mupdf, podofo, mupdf, fbida)[inputs]: Likewise.
* gnu/packages/photo.scm (libraw, libpano13, enblend-enfuse, darktable, hugin,
rawtherapee)[inputs]: Likewise.
* gnu/packages/prolog.scm (swi-prolog)[native-inputs]: Likewise.
* gnu/packages/python-xyz.scm (python-hdf4, python-pillow)[inputs]: Likewise.
* gnu/packages/qt.scm (qtbase, qtwebkit)[inputs]: Likewise.
* gnu/packages/rdesktop.scm (freerdp)[inputs]: Likewise.
* gnu/packages/scanner.scm (sane-backends, xsane)[inputs]: Likewise.
* gnu/packages/scheme.scm (racket)[inputs]: Likewise.
* gnu/packages/scribus.scm (scribus)[inputs]: Likewise.
* gnu/packages/sdl.scm (sdl-image)[propagated-inputs]: Likewise.
(guile-sdl)[native-inputs]: Likewise.
* gnu/packages/spice.scm (spice-gtk)[inputs]: Likewise.
* gnu/packages/statistics.scm (r-with-tests)[inputs]: Likewise.
* gnu/packages/tcl.scm (perl-tk)[inputs]: Likewise.
* gnu/packages/upnp.scm (readymedia)[inputs]: Likewise.
* gnu/packages/video.scm (mplayer, mpv, v4l-utils, motion)[inputs]: Likewise.
* gnu/packages/web-browsers.scm (dillo, links)[inputs]: Likewise.
* gnu/packages/web.scm (netsurf)[inputs]: Likewise.
* gnu/packages/webkit.scm (webkitgtk)[inputs]: Likewise.
* gnu/packages/wine.scm (wine)[inputs]: Likewise.
* gnu/packages/wv.scm (wv)[inputs]: Likewise.
* gnu/packages/wxwidgets.scm (wxwidgets, wxwidgets-2)[inputs]: Likewise.
* gnu/packages/xdisorg.scm (xscreensaver)[inputs]: Likewise.
* gnu/packages/xfce.scm (tumbler)[inputs]: Likewise.
* gnu/packages/xfig.scm (xfig, transfig)[inputs]: Likewise.
* gnu/packages/xorg.scm (xpra)[inputs]: Likewise.
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* gnu/packages/machine-learning.scm (python-umap-learn): New variable.
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stumpwm to wm.
* gnu/local.mk: Include lisp-xyz.scm.
* gnu/packages/lisp-xyz.scm: New file.
* gnu/packages/lisp.scm: Move all lisp libraries to lisp-xyz.scm, uglify-js to
javascript.scm and stumpwm to wm.scm.
* gnu/packages/javascript.scm: Add uglify-js.
* gnu/packages/wm.scm: Add stumpwm.
* gnu/packages/bioinformatics.scm: Find uglify-js in javascript.scm.
* gnu/packages/machine-learning.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* gnu/packages/web.scm: Find uglify-js in javascript.scm.
* gnu/packages/web-browsers.scm: Depend on lisp-xyz.scm instead of lisp.scm.
* guix/build-system/minify.scm (default-uglify-js): Find uglify-js in
javascript module instead of lisp.
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javascript and stumpwm to wm."
This reverts commit ac1ee30f4f7f9d0ae2a655676b0e8b9eb90a35dd, which
still breaks ‘guix pull’.
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