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40292 Commits

Author SHA1 Message Date
Ludovic Courtès
584a3ca3a4 gnu: guile-json: Define 'guile-json-1'. 
* gnu/packages/guile.scm (guile-json-1): New variable.
 2019-07-25 00:18:45 +02:00
Ludovic Courtès
81c3dc3224 maint: Switch to Guile-JSON 3.x. 
Guile-JSON 3.x is incompatible with Guile-JSON 1.x, which we relied on
until now: it maps JSON dictionaries to alists (instead of hash tables),
and JSON arrays to vectors (instead of lists).  This commit is about
adjusting all the existing code to this new mapping.

* m4/guix.m4 (GUIX_CHECK_GUILE_JSON): New macro.
* configure.ac: Use it.
* doc/guix.texi (Requirements): Mention the Guile-JSON version.
* guix/git-download.scm (git-fetch)[guile-json]: Use GUILE-JSON-3.
* guix/import/cpan.scm (string->license): Expect vectors instead of
lists.
(module->dist-name): Use 'json-fetch' instead of 'json-fetch-alist'.
(cpan-fetch): Likewise.
* guix/import/crate.scm (crate-fetch): Likewise, and call 'vector->list'
for DEPS.
* guix/import/gem.scm (rubygems-fetch): Likewise.
* guix/import/json.scm (json-fetch-alist): Remove.
* guix/import/pypi.scm (pypi-fetch): Use 'json-fetch' instead of
'json-fetch-alist'.
(latest-source-release, latest-wheel-release): Call 'vector->list' on
RELEASES.
* guix/import/stackage.scm (stackage-lts-info-fetch): Use 'json-fetch'
instead of 'json-fetch-alist'.
(lts-package-version): Use 'vector->list'.
* guix/import/utils.scm (hash-table->alist): Remove.
(alist->package): Pass 'vector->list' on the inputs fields, and default
to the empty vector.
* guix/scripts/import/json.scm (guix-import-json): Remove call to
'hash-table->alist'.
* guix/swh.scm (define-json-reader): Expect pair? or null? instead of
hash-table?.
[extract-field]: Use 'assoc-ref' instead of 'hash-ref'.
(json->branches): Use 'map' instead of 'hash-map->list'.
(json->checksums): Likewise.
(json->directory-entries, origin-visits): Call 'vector->list' on the
result of 'json->scm'.
* tests/import-utils.scm ("alist->package with dependencies"): New test.
* gnu/installer.scm (build-compiled-file)[builder]: Use GUILE-JSON-3.
* gnu/installer.scm (installer-program)[installer-builder]: Likewise.
* gnu/installer/locale.scm (iso639->iso639-languages): Use 'assoc-ref'
instead of 'hash-ref', and pass vectors through 'vector->list'.
(iso3166->iso3166-territories): Likewise.
* gnu/system/vm.scm (system-docker-image)[build]: Use GUILE-JSON-3.
* guix/docker.scm (manifest, config): Adjust for Guile-JSON 3.
* guix/scripts/pack.scm (docker-image)[build]: Use GUILE-JSON-3.
* guix/import/github.scm (fetch-releases-or-tags): Update docstring.
(latest-released-version): Use 'assoc-ref' instead of 'hash-ref'.  Pass
the result of 'fetch-releases-or-tags' to 'vector->list'.
* guix/import/launchpad.scm (latest-released-version): Likewise.
 2019-07-25 00:16:41 +02:00
zimoun
a0efa069a1 gnu: Add r-depecher. 
* gnu/packages/bioconductor.scm (r-depecher): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
1adb9cbc5e gnu: Add r-mixomics. 
* gnu/packages/bioconductor.scm (r-mixomics): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
1502751b32 gnu: Add r-flowsom. 
* gnu/packages/bioconductor.scm (r-flowsom): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
e0cb053edb gnu: Add r-flowmeans. 
* gnu/packages/bioconductor.scm (r-flowmeans): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
ed6f49fc41 gnu: Add r-consensusclusterplus. 
* gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
a0422d18f1 gnu: Add r-flowutils. 
* gnu/packages/bioconductor.scm (r-flowutils): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
a6fedf1f37 gnu: Add r-flowcore. 
* gnu/packages/bioconductor.scm (r-flowcore): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
ad8f46c69e gnu: Add r-all. 
* gnu/packages/bioconductor.scm (r-all): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:39 +02:00
zimoun
6deb08a359 gnu: Add r-kableextra. 
* gnu/packages/cran.scm (r-kableextra): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:38 +02:00
zimoun
1c0b2e7483 gnu: Add r-umap. 
* gnu/packages/cran.scm (r-umap): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2019-07-24 23:05:38 +02:00
Jelle Licht
97bc8c47bb gnu: emacs-gitpatch: Update to 0.5.1. 
* gnu/packages/emacs-xyz.scm (emacs-gitpatch): Update to 0.5.1.
 2019-07-24 22:23:19 +02:00
Tobias Geerinckx-Rice
8126142baf gnu: terminator: Propagate gsettings-desktop-schemas. 
* gnu/packages/gnome.scm (terminator)[propagated-inputs]: Add gsettings-desktop-schemas.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice
4f20e0a2f6 gnu: spice-gtk: Update to 0.37. 
* gnu/packages/spice.scm (spice-gtk): Update to 0.37.
[propagated-inputs]: Use latest spice-protocol.
(spice-protocol-0.12): Remove unused variable.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice
7e2c050a88 gnu: libvirt-glib: Propagate pkg-config requirements. 
* gnu/packages/virtualization.scm (libvirt-glib)[inputs]: Move glib,
libvirt, libxml2, and gobject-introspection…
[native-inputs]: …here.
 2019-07-24 21:29:10 +02:00
Tobias Geerinckx-Rice
7dfda55ba2 gnu: libvirt-glib: Update to 2.0.0. 
* gnu/packages/virtualization.scm (libvirt-glib): Update to 2.0.0.
[arguments]: Remove ‘fix-tests’ phase.
 2019-07-24 21:29:09 +02:00
Ricardo Wurmus
d350d5e714 gnu: texlive-amsfonts: Build .ins file instead of installing fonts twice. 
* gnu/packages/tex.scm (texlive-amsfonts)[arguments]: Override build targets;
rename font build directory to avoid installing it a second time.
 2019-07-24 18:25:12 +02:00
Ricardo Wurmus
a6405e0333 gnu: Rename references to obsolete "texlive-fonts-cm". 
* gnu/packages/tex.scm (texlive-amsfonts, texlive-fonts-latex, texlive-etex,
texlive-hyph-utf8, texlive-base, texlive-fonts-ec,
texlive-fonts-rsfs)[native-inputs]: Rename texlive-fonts-cm to texlive-cm.
[arguments]: Adjust.
 2019-07-24 12:19:54 +02:00
Ricardo Wurmus
fdb8841fa6 gnu: texlive-base: Include texlive-tetex. 
* gnu/packages/tex.scm (texlive-base)[default-packages]: Add texlive-tetex.
 2019-07-24 12:13:44 +02:00
Ricardo Wurmus
192ad4d16f gnu: Add texlive-tetex. 
* gnu/packages/tex.scm (texlive-tetex): New variable.
 2019-07-24 12:13:23 +02:00
Ricardo Wurmus
81ca46147d gnu: Add texlive-beamer. 
* gnu/packages/tex.scm (texlive-beamer): New variable.
(texlive-latex-beamer): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
b7d779db34 gnu: Add texlive-cm. 
* gnu/packages/tex.scm (texlive-cm): New variable.
(texlive-fonts-cm): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
df19dc2f86 gnu: Add texlive-zapfding. 
* gnu/packages/tex.scm (texlive-zapfding): New variable.
(texlive-fonts-adobe-zapfding): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
57bee3cc91 gnu: Add texlive-palatino. 
* gnu/packages/tex.scm (texlive-palatino): New variable.
(texlive-fonts-adobe-palatino): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
1aaa117c0c gnu: Add texlive-times. 
* gnu/packages/tex.scm (texlive-times): New variable.
(texlive-fonts-adobe-times): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
1f50ae6346 gnu: Add texlive-charter. 
* gnu/packages/tex.scm (texlive-charter): New variable.
(texlive-fonts-charter): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
8fee5067b2 gnu: texlive-tex-plain: Simplify. 
* gnu/packages/tex.scm (texlive-tex-plain): Implement with
SIMPLE-TEXLIVE-PACKAGE.
[description]: Use full sentences.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
8bc9afeb9e gnu: Add texlive-xypic. 
* gnu/packages/tex.scm (texlive-xypic): New variable.
(texlive-fonts-xypic, texlive-generic-xypic): Deprecate them.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
0901f1b042 gnu: Add texlive-txfonts. 
* gnu/packages/tex.scm (texlive-txfonts): New variable.
(texlive-fonts-txfonts): Deprecate package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
6a4fe83b5e gnu: Add texlive-ae. 
* gnu/packages/tex.scm (texlive-ae): New variable.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
4253358ab0 gnu: texlive-fonts-ec: Update license URL. 
* gnu/packages/tex.scm (texlive-fonts-ec)[license]: Update URL.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
f75aa97f95 gnu: Replace uses of texlive-*-amsfonts. 
* gnu/packages/algebra.scm (pari-gp)[native-inputs]: Replace
texlive-fonts-amsfonts and texlive-latex-amsfonts with texlive-amsfonts in
texlive-union.
* gnu/packages/docbook.scm (dblatex)[inputs]: Same.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Same.
* gnu/packages/python-xyz.scm (python-numpy-documentation,
python-matplotlib-documentation, python-ipython-documentation)
[native-inputs]: Same.
* gnu/packages/statistics.scm (r-with-tests)[native-inputs]: Same.
* gnu/packages/tex.scm (teximpatient)[native-inputs]: Same.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
82ff725df9 gnu: Add texlive-amsfonts. 
* gnu/packages/tex.scm (texlive-fonts-amsfonts, texlive-latex-amsfonts):
Deprecate and merge...
(texlive-amsfonts): ...to this new package.
 2019-07-24 09:46:49 +02:00
Ricardo Wurmus
e976d3618d gnu: texlive-latex-base: Simplify. 
* gnu/packages/tex.scm (texlive-latex-base)[source]: Use TEXLIVE-ORIGIN.
[arguments]: Simplify build phase by running fmtutil-sys; adjust install
phase.
[native-inputs]: Remove texlive-generic-unicode-data,
texlive-generic-dehyph-exptl, texlive-generic-tex-ini-files,
texlive-latex-latexconfig, texlive-generic-hyphen, texlive-generic-ruhyphen,
texlive-generic-ukrhyph, texlive-generic-config, and
texlive-latex-base-support-files; add texlive-tex-ini-files, texlive-kpathsea,
and texlive-luatexconfig.
[propagated-inputs]: Add texlive-etex, texlive-hyph-utf8, texlive-hyphen-base,
texlive-hyphen-afrikaans, texlive-hyphen-ancientgreek,
texlive-hyphen-armenian, texlive-hyphen-basque, texlive-hyphen-belarusian,
texlive-hyphen-bulgarian, texlive-hyphen-catalan, texlive-hyphen-chinese,
texlive-hyphen-churchslavonic, texlive-hyphen-coptic, texlive-hyphen-croatian,
texlive-hyphen-czech, texlive-hyphen-danish, texlive-hyphen-dutch,
texlive-hyphen-english, texlive-hyphen-esperanto, texlive-hyphen-estonian,
texlive-hyphen-ethiopic, texlive-hyphen-finnish, texlive-hyphen-french,
texlive-hyphen-friulan, texlive-hyphen-galician, texlive-hyphen-georgian,
texlive-hyphen-german, texlive-hyphen-greek, texlive-hyphen-hungarian,
texlive-hyphen-icelandic, texlive-hyphen-indic, texlive-hyphen-indonesian,
texlive-hyphen-interlingua, texlive-hyphen-irish, texlive-hyphen-italian,
texlive-hyphen-kurmanji, texlive-hyphen-latin, texlive-hyphen-latvian,
texlive-hyphen-lithuanian, texlive-hyphen-mongolian, texlive-hyphen-norwegian,
texlive-hyphen-occitan, texlive-hyphen-piedmontese, texlive-hyphen-polish,
texlive-hyphen-portuguese, texlive-hyphen-romanian, texlive-hyphen-romansh,
texlive-hyphen-russian, texlive-hyphen-sanskrit, texlive-hyphen-serbian,
texlive-hyphen-slovak, texlive-hyphen-slovenian, texlive-hyphen-spanish,
texlive-hyphen-swedish, texlive-hyphen-thai, texlive-hyphen-turkish,
texlive-hyphen-turkmen, texlive-hyphen-ukrainian, texlive-hyphen-uppersorbian,
texlive-hyphen-welsh, texlive-unicode-data, texlive-ukrhyph, texlive-ruhyphen,
and texlive-latexconfig.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
b93d9dac24 gnu: texlive-dvips: Update source files. 
* gnu/packages/tex.scm (texlive-dvips): Include source files from the TeX Live
SVN repository according to texlive.tlpdb.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
dfdc002c9b gnu: texlive-bin: Include scripts. 
* gnu/packages/tex.scm (texlive-bin)[inputs]: Add texlive-scripts.
[arguments]: Let fmtutil.pl reference scripts directory.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
2b25469476 gnu: Add texlive-kpathsea. 
* gnu/packages/tex.scm (texlive-kpathsea): New variable.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
346354a18e gnu: Add texlive-etoolbox. 
* gnu/packages/tex.scm (texlive-etoolbox): New variable.
(texlive-latex-etoolbox): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
fb01a2965a gnu: Add texlive-doi. 
* gnu/packages/tex.scm (texlive-doi): New variable.
(texlive-latex-doi): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
a72058b950 gnu: Add texlive-seminar. 
* gnu/packages/tex.scm (texlive-seminar): New variable.
(texlive-latex-seminar): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
6090b6c474 gnu: Add texlive-pstool. 
* gnu/packages/tex.scm (texlive-pstool): New variable.
(texlive-latex-pstool): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
1333198da8 gnu: Add texlive-filemod. 
* gnu/packages/tex.scm (texlive-filemod): New variable.
(texlive-latex-filemod): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
c97d1a9123 gnu: Add texlive-url. 
* gnu/packages/tex.scm (texlive-url): New variable.
(texlive-latex-url): Deprecate package.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
152950d494 gnu: texlive-latex-graphics: Simplify. 
* gnu/packages/tex.scm (texlive-latex-graphics)[arguments]: Remove custom
phases.
[native-inputs]: Remove.
[propagated-inputs]: Add texlive-graphics-cfg and texlive-graphics-def.
[license]: Update.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
83a5c6171b gnu: Add texlive-graphics-cfg. 
* gnu/packages/tex.scm (texlive-graphics-cfg): New variable.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
f1b0939dbc gnu: Add texlive-graphics-def. 
* gnu/packages/tex.scm (texlive-graphics-def): New variable.
 2019-07-24 09:46:48 +02:00
Ricardo Wurmus
f104ff618a gnu: Add texlive-epsf. 
* gnu/packages/tex.scm (texlive-epsf): New variable.
(texlive-generic-epsf): Deprecate package.
 2019-07-24 09:46:47 +02:00
Ricardo Wurmus
114a5d85aa gnu: Add texlive-lm. 
* gnu/packages/tex.scm (texlive-lm): New variable.
(texlive-fonts-lm): Deprecate package.
 2019-07-24 09:46:47 +02:00
Ricardo Wurmus
14a87760fa gnu: texlive-fontname: Simplify. 
* gnu/packages/tex.scm (texlive-fontname): Implement with
SIMPLE-TEXLIVE-PACKAGE.
 2019-07-24 09:46:47 +02:00