Merge branch 'staging' into core-updates

doc/contributing.fr.texi

@@ -25,6 +25,7 @@ quel nom ou pseudonyme de leur choix.
 * Construire depuis Git::    toujours le plus récent.
 * Lancer Guix avant qu'il ne soit installé::  Astuces pour les hackers.
 * La configuration parfaite::  Les bons outils.
+* Consignes d'empaquetage::  Faire grandir la distribution.
 * Style de code::            Hygiène du contributeur.
 * Envoyer des correctifs::   Partager votre travail.
 @end menu
@@ -99,7 +100,7 @@ valeur @code{localstatedir} utilisée par votre installation actuelle
 Finalement, vous devez invoquer @code{make check} pour lancer les tests
 (@pxref{Lancer la suite de tests}).  Si quelque chose échoue, jetez un œil
 aux instructions d'installation (@pxref{Installation}) ou envoyez un message
-à la list @email{guix-devel@@gnu.org}.
+à la liste @email{guix-devel@@gnu.org}.
 
 
 @node Lancer Guix avant qu'il ne soit installé
@@ -169,12 +170,15 @@ arborescence des source locale.
 @node La configuration parfaite
 @section La configuration parfaite
 
-La configuration parfaite pour travailler sur Guix est simplement la
+The Perfect Setup to hack on Guix is basically the perfect setup used for
-configuration parfaite pour travailler en Guile (@pxref{Using Guile in
+Guile hacking (@pxref{Using Guile in Emacs,,, guile, Guile Reference
-Emacs,,, guile, Guile Reference Manual}).  Tout d'abord, vous avez besoin de
+Manual}).  First, you need more than an editor, you need
-mieux qu'un éditeur de texte, vous avez besoin de
+@url{http://www.gnu.org/software/emacs, Emacs}, empowered by the wonderful
-@url{http://www.gnu.org/software/emacs, Emacs}, amélioré par le superbe
+@url{http://nongnu.org/geiser/, Geiser}.  To set that up, run:
-@url{http://nongnu.org/geiser/, Geiser}.
+
+@example
+guix package -i emacs guile emacs-geiser
+@end example
 
 Geiser permet le développement interactif et incrémental depuis Emacs : la
 compilation du code et son évaluation depuis les buffers, l'accès à la
@@ -229,6 +233,461 @@ déclenchement @code{origin…}, qui peut aussi être étendue.  L'extrait
 finissent sur @code{…}, qui peuvent aussi être étendues.
 
 
+@node Consignes d'empaquetage
+@section Consignes d'empaquetage
+
+@cindex paquets, création
+The GNU distribution is nascent and may well lack some of your favorite
+packages.  This section describes how you can help make the distribution
+grow.
+
+Les paquets de logiciels libres sont habituellement distribués sous forme
+@dfn{d'archives de sources} — typiquement des fichiers @file{.tar.gz}
+contenant tous les fichiers sources.  Ajouter un paquet à la distribution
+signifie essentiellement deux choses : ajouter une @dfn{recette} qui décrit
+comment construire le paquet, avec une liste d'autres paquets requis pour le
+construire, et ajouter des @dfn{métadonnées de paquet} avec la recette,
+comme une description et une licence.
+
+Dans Guix, toutes ces informations sont incorporées dans les
+@dfn{définitions de paquets}.  Les définitions de paquets fournissent une
+vue de haut-niveau du paquet.  Elles sont écrites avec la syntaxe du langage
+de programmation Scheme ; en fait, pour chaque paquet nous définissons une
+variable liée à la définition et exportons cette variable à partir d'un
+module (@pxref{Modules de paquets}).  Cependant, il n'est @emph{pas} nécessaire
+d'avoir une connaissance approfondie du Scheme pour créer des paquets.  Pour
+plus d'informations sur les définitions des paquets, @pxref{Définition des paquets}.
+
+Une fois une définition de paquet en place, stocké dans un fichier de
+l'arborescence des sources de Guix, il peut être testé avec la commande
+@command{guix build} (@pxref{Invoquer guix build}).  Par exemple, en
+supposant que le nouveau paquet s'appelle @code{gnew}, vous pouvez lancer
+cette commande depuis l'arborescence de construction de Guix (@pxref{Lancer Guix avant qu'il ne soit installé}) :
+
+@example
+./pre-inst-env guix build gnew --keep-failed
+@end example
+
+Utiliser @code{--keep-failed} rend facile le débogage des échecs car il
+fournit l'accès à l'arborescence de construction qui a échouée.  Une autre
+sous-commande utile pour le débogage est @code{--log-file}, pour accéder au
+journal de construction.
+
+Si le paquet n'est pas connu de la commande @command{guix}, il se peut que
+le fichier source ait une erreur de syntaxe, ou qu'il manque une clause
+@code{define-public} pour exporter la variable du paquet.  Pour comprendre
+cela, vous pouvez charger le module depuis Guile pour avoir plus
+d'informations sur la véritable erreur :
+
+@example
+./pre-inst-env guile -c '(use-modules (gnu packages gnew))'
+@end example
+
+Once your package builds correctly, please send us a patch
+(@pxref{Envoyer des correctifs}).  Well, if you need help, we will be happy to
+help you too.  Once the patch is committed in the Guix repository, the new
+package automatically gets built on the supported platforms by
+@url{http://hydra.gnu.org/jobset/gnu/master, our continuous integration
+system}.
+
+@cindex substitution
+Users can obtain the new package definition simply by running @command{guix
+pull} (@pxref{Invoquer guix pull}).  When @code{@value{SUBSTITUTE-SERVER}}
+is done building the package, installing the package automatically downloads
+binaries from there (@pxref{Substituts}).  The only place where human
+intervention is needed is to review and apply the patch.
+
+
+@menu
+* Liberté logiciel::        Ce que la distribution peut contenir.
+* Conventions de nommage::   Qu'est-ce qu'un bon nom ?
+* Numéros de version::      Lorsque le nom n'est pas suffisant.
+* Synopsis et descriptions::  Aider les utilisateurs à trouver le bon 
+                                paquet.
+* Modules python::           Un peu de comédie anglaise.
+* Modules perl::             Petites perles.
+* Paquets java::             Pause café.
+* Polices de caractères::   À fond les fontes.
+@end menu
+
+@node Liberté logiciel
+@subsection Liberté logiciel
+
+@c ===========================================================================
+@c
+@c This file was generated with po4a. Translate the source file.
+@c
+@c ===========================================================================
+@c Adapted from http://www.gnu.org/philosophy/philosophy.html.
+@cindex logiciel libre
+Le système d'exploitation GNU a été développé pour que les utilisateurs
+puissent utiliser leur ordinateur en toute liberté.  GNU est un
+@dfn{logiciel libre}, ce qui signifie que les utilisateur ont les
+@url{http://www.gnu.org/philosophy/free-sw.fr.html,quatre libertés
+essentielles} : exécuter le programmer, étudier et modifier le programme
+sous sa forme source, redistribuer des copies exactes et distribuer les
+versions modifiées.  Les paquets qui se trouvent dans la distribution GNU ne
+fournissent que des logiciels qui respectent ces quatre libertés.
+
+En plus, la distribution GNU suit les
+@url{http://www.gnu.org/distros/free-system-distribution-guidelines.html,recommandations
+pour les distributions systèmes libres}.  Entre autres choses, ces
+recommandations rejettent les microgiciels non libres, les recommandations
+de logiciels non libres et discute des façon de gérer les marques et les
+brevets.
+
+Certaines sources amont autrement parfaitement libres contiennent une petite
+partie facultative qui viole les recommandations ci-dessus, par exemple car
+cette partie est du code non-libre.  Lorsque cela arrive, les éléments en
+question sont supprimés avec des correctifs ou des bouts de codes appropriés
+dans la forme @code{origin} du paquet (@pxref{Définition des paquets}).  De cette
+manière, @code{guix build --source} renvoie la source « libérée » plutôt que
+la source amont sans modification.
+
+
+@node Conventions de nommage
+@subsection Conventions de nommage
+
+@cindex nom du paquet
+Un paquet a en fait deux noms qui lui sont associés : d'abord il y a le nom
+de la @emph{variable Scheme}, celui qui suit @code{define-public}.  Par ce
+nom, le paquet peut se faire connaître par le code Scheme, par exemple comme
+entrée d'un autre paquet.  Deuxièmement, il y a la chaîne dans le champ
+@code{name} d'une définition de paquet.  Ce nom est utilisé par les
+commandes de gestion des paquets comme @command{guix package} et
+@command{guix build}.
+
+Les deux sont habituellement les mêmes et correspondent à la conversion en
+minuscule du nom du projet choisi en amont, où les underscores sont
+remplacés par des tirets.  Par exemple, GNUnet est disponible en tant que
+@code{gnunet} et SDL_net en tant que @code{sdl-net}.
+
+Nous n'ajoutons pas de préfixe @code{lib} au bibliothèques de paquets, à
+moins qu'il ne fasse partie du nom officiel du projet.  Mais @pxref{Modules python} et @ref{Modules perl}  pour des règles spéciales concernant les
+modules pour les langages Python et Perl.
+
+Les noms de paquets de polices sont gérés différemment, @pxref{Polices de caractères}.
+
+
+@node Numéros de version
+@subsection Numéros de version
+
+@cindex version du paquet
+Nous n'incluons en général que la dernière version d'un projet de logiciel
+libre donné.  Mais parfois, par exemple pour des versions incompatibles de
+bibliothèques, deux (ou plus) versions du même paquet sont requises.  Elles
+ont besoin d'un nom de variable Scheme différent.  Nous utilisons le nom
+défini dans @ref{Conventions de nommage} pour la version la plus récente ; les
+versions précédentes utilisent le même nom, suffixé par @code{-} et le plus
+petit préfixe du numéro de version qui permet de distinguer deux versions.
+
+Le nom dans la définition du paquet est le même pour toutes les versions
+d'un paquet et ne contient pas de numéro de version.
+
+Par exemple, les version 2.24.20 et 3.9.12 de GTK+ peuvent être inclus de
+cette manière :
+
+@example
+(define-public gtk+
+  (package
+    (name "gtk+")
+    (version "3.9.12")
+    ...))
+(define-public gtk+-2
+  (package
+    (name "gtk+")
+    (version "2.24.20")
+    ...))
+@end example
+Si nous voulons aussi GTK+ 3.8.2, cela serait inclus de cette manière :
+@example
+(define-public gtk+-3.8
+  (package
+    (name "gtk+")
+    (version "3.8.2")
+    ...))
+@end example
+
+@c See <https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00425.html>,
+@c for a discussion of what follows.
+@cindex numéro de version, pour les instantanés des systèmes de contrôle de version
+Parfois, nous incluons des paquets provenant d'instantanés de systèmes de
+contrôle de version (VCS) au lieu de versions publiées formellement.  Cela
+devrait rester exceptionnel, car c'est le rôle des développeurs amont de
+spécifier quel est la version stable.  Cependant, c'est parfois nécessaire.
+Donc, que faut-il mettre dans le champ @code{version} ?
+
+Clairement, nous devons rendre l'identifiant de commit de l'instantané du
+VCS visible dans la version, mais nous devons aussi nous assurer que la
+version augmente de manière monotone pour que @command{guix package
+--upgrade} puisse déterminer quelle version est la plus récente.  Comme les
+identifiants de commits, notamment avec Git, n'augmentent pas, nous ajoutons
+un numéro de révision qui nous augmentons à chaque fois que nous mettons à
+jour vers un nouvel instantané.  La chaîne qui en résulte ressemble à cela :
+
+@example
+2.0.11-3.cabba9e
+  ^    ^    ^
+  |    |    `-- ID du commit en amont
+  |    |
+  |    `--- révision du paquet Guix
+  |
+dernière version en amont
+@end example
+
+C'est une bonne idée de tronquer les identifiants dans le champ
+@code{version} à disons 7 caractères.  Cela évite un problème esthétique (en
+supposant que l'esthétique ait un rôle à jouer ici) et des problèmes avec
+les limites de l'OS comme la longueur maximale d'un shebang (127 octets pour
+le noyau Linux).  Il vaut mieux utilise l'identifiant de commit complet dans
+@code{origin} cependant, pour éviter les ambiguïtés.  Une définition de
+paquet peut ressembler à ceci :
+
+@example
+(define my-package
+  (let ((commit "c3f29bc928d5900971f65965feaae59e1272a3f7")
+        (revision "1"))          ;révision du paquet Guix
+    (package
+      (version (git-version "0.9" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "git://example.org/my-package.git")
+                      (commit commit)))
+                (sha256 (base32 "1mbikn@dots{}"))
+                (file-name (git-file-name name version))))
+      ;; @dots{}
+      )))
+@end example
+
+@node Synopsis et descriptions
+@subsection Synopsis et descriptions
+
+@cindex description du paquet
+@cindex résumé du paquet
+Comme nous l'avons vu avant, chaque paquet dans GNU@tie{}Guix contient un
+résumé et une description (@pxref{Définition des paquets}).  Les résumés et les
+descriptions sont importants : ce sont eux que recherche @command{guix
+package --search}, et c'est une source d'informations cruciale pour aider
+les utilisateurs à déterminer si un paquet donner correspond à leurs
+besoins.  En conséquence, les mainteneurs doivent prêter attention à leur
+contenu.
+
+Les résumés doivent commencer par une lettre capitale et ne doit pas finir
+par un point.  Ils ne doivent pas commencer par « a » ou « the » (« un » ou
+« le/la »), ce qui n'apporte généralement rien ; par exemple, préférez «
+File-frobbing tool » (« Outil de frobage de fichier ») à « A tool that frobs
+file » (« Un outil qui frobe les fichiers »).  Le résumé devrait dire ce que
+le paquet est — p.@: ex.@: « Utilitaire du cœur de GNU (fichier, text,
+shell) » — ou ce à quoi il sert — p.@: ex.@: le résumé de grep est « Affiche
+des lignes correspondant à un motif ».
+
+Gardez à l'esprit que le résumé doit avoir un sens pour une large audience.
+Par exemple « Manipulation d'alignements au format SAM » peut avoir du sens
+pour un bioinformaticien chevronné, mais n'aidera pas ou pourra perdre une
+audience de non-spécialistes.  C'est une bonne idée de créer un résumé qui
+donne une idée du domaine d'application du paquet.  Dans cet exemple, cela
+donnerait « Manipulation d'alignements de séquences de nucléotides », ce qui
+devrait donner une meilleure idée à l'utilisateur pour savoir si c'est ce
+qu'il recherche.
+
+Les descriptions devraient faire entre cinq et dix lignes.  Utilisez des
+phrases complètes, et évitez d'utiliser des acronymes sans les introduire
+d'abord.  Évitez les phrases marketings comme « world-leading », «
+industrial-strength » et « next-generation » et évitez les superlatifs comme
+« the most advanced » — ils ne sont pas utiles pour les utilisateurs qui
+cherchent un paquet et semblent même un peu suspects.  À la place, essayez
+d'être factuels, en mentionnant les cas d'utilisation et les
+fonctionnalités.
+
+@cindex balisage texinfo, dans les descriptions de paquets
+Les descriptions peuvent inclure du balisage Texinfo, ce qui est utile pour
+introduire des ornements comme @code{@@code} ou @code{@@dfn}, des listes à
+points ou des hyperliens (@pxref{Overview,,, texinfo, GNU Texinfo}).
+Cependant soyez prudents lorsque vous utilisez certains symboles, par
+exemple @samp{@@} et les accolades qui sont les caractères spéciaux de base
+en Texinfo (@pxref{Special Characters,,, texinfo, GNU Texinfo}).  Les
+interfaces utilisateurs comme @command{guix package --show} prennent en
+charge le rendu.
+
+Les résumés et les descriptions sont traduits par des volontaires
+@uref{http://translationproject.org/domain/guix-packages.html, sur le projet
+de traduction} pour que le plus d'utilisateurs possible puissent les lire
+dans leur langue natale.  Les interfaces utilisateurs les recherchent et les
+affichent dans la langue spécifiée par le paramètre de régionalisation
+actuel.
+
+Pour permettre à @command{xgettext} de les extraire comme des chaînes
+traduisibles, les résumés et les descriptions @emph{doivent être des chaînes
+litérales}.  Cela signifie que vous ne pouvez pas utiliser
+@code{string-append} ou @code{format} pour construire ces chaînes :
+
+@lisp
+(package
+  ;; @dots{}
+  (synopsis "Ceci est traduisible")
+  (description (string-append "Ceci n'est " "*pas*" " traduisible.")))
+@end lisp
+
+La traduction demande beaucoup de travail, donc en tant que packageur,
+faîtes encore plus attention à vos résumés et descriptions car chaque
+changement peut demander d'autant plus de travail de la part des
+traducteurs.  Pour les aider, il est possible de donner des recommandations
+ou des instructions qu'ils pourront voir en insérant des commentaires
+spéciaux comme ceci (@pxref{xgettext Invocation,,, gettext, GNU Gettext}) :
+
+@example
+;; TRANSLATORS: "X11 resize-and-rotate" should not be translated.
+(description "ARandR is designed to provide a simple visual front end
+for the X11 resize-and-rotate (RandR) extension. @dots{}")
+@end example
+
+
+@node Modules python
+@subsection Modules python
+
+@cindex python
+Nous incluons actuellement Python 2 et Python 3, sous les noms de variables
+Scheme @code{python-2} et @code{python} comme expliqué dans @ref{Numéros de version}.  Pour éviter la confusion et les problèmes de noms avec d'autres
+langages de programmation, il semble désirable que le nom d'un paquet pour
+un module Python contienne le mot @code{python}.
+
+Certains modules ne sont compatibles qu'avec une version de Python, d'autres
+avec les deux.  Si le paquet Foo ne compile qu'avec Ptyhon 3, on le nomme
+@code{python-foo} ; s'il ne compile qu'avec Python 2, on le nome
+@code{python2-foo}.  S'il est compatible avec les deux versions, nous créons
+deux paquets avec les noms correspondant.
+
+If a project already contains the word @code{python}, we drop this; for
+instance, the module python-dateutil is packaged under the names
+@code{python-dateutil} and @code{python2-dateutil}.  If the project name
+starts with @code{py} (e.g.@: @code{pytz}), we keep it and prefix it as
+described above.
+
+@subsubsection Spécifier les dépendances
+@cindex entrées, pour les paquets Python
+
+Les informations de dépendances pour les paquets Python se trouvent
+généralement dans l'arborescence des source du paquet, avec plus ou moins de
+précision : dans le fichier @file{setup.py}, dans @file{requirements.txt} ou
+dans @file{tox.ini}.
+
+Votre mission, lorsque vous écrivez une recette pour un paquet Python, est
+de faire correspondre ces dépendances au bon type « d'entrée »
+(@pxref{Référence de paquet, inputs}).  Bien que l'importeur @code{pypi} fasse
+du bon boulot (@pxref{Invoquer guix import}), vous devriez vérifier la liste
+suivant pour déterminer où va telle dépendance.
+
+@itemize
+
+@item
+Nous empaquetons Python 2 avec @code{setuptools} et @code{pip} installé
+comme Python 3.4 par défaut.  Ainsi, vous n'avez pas à spécifié ces
+entrées.  @command{guix lint} vous avertira si vous faîtes cela.
+
+@item
+Les dépendances Python requises à l'exécutions vont dans
+@code{propagated-inputs}.  Elles sont typiquement définies dans le mot-clef
+@code{install_requires} dans @file{setup.py} ou dans le fichier
+@file{requirements.txt}.
+
+@item
+Les paquets Python requis uniquement à la construction — p.@: ex.@: ceux
+listés dans le mot-clef @code{setup_requires} de @file{setup.py} — ou
+seulement pour les tests — p.@: ex.@: ceux dans @code{tests_require} — vont
+dans @code{native-inputs}.  La raison est qu'ils n'ont pas besoin d'être
+propagés car ils ne sont pas requis à l'exécution et dans le cas d'une
+compilation croisée, c'est l'entrée « native » qu'il nous faut.
+
+Les cadriciels de tests @code{pytest}, @code{mock} et @code{nose} sont des
+exemples.  Bien sûr si l'un de ces paquets est aussi requis à l'exécution,
+il doit aller dans @code{propagated-inputs}.
+
+@item
+Tout ce qui ne tombe pas dans les catégories précédentes va dans
+@code{inputs}, par exemple des programmes pour des bibliothèques C requises
+pour construire des paquets Python avec des extensions C.
+
+@item
+Si un paquet Python a des dépendances facultatives (@code{extras_require}),
+c'est à vous de décider de les ajouter ou non, en fonction du ratio entre
+utilité et complexité (@pxref{Envoyer des correctifs, @command{guix size}}).
+
+@end itemize
+
+
+@node Modules perl
+@subsection Modules perl
+
+@cindex perl
+Les programmes Perl utiles en soit sont nommés comme les autres paquets,
+avec le nom amont en minuscule.  Pour les paquets Perl contenant une seule
+classe, nous utilisons le nom de la classe en minuscule, en remplaçant les
+occurrences de @code{::} par des tirets et en préfixant le tout par
+@code{perl-}.  Donc la classe @code{XML::Parser} devient
+@code{perl-xml-parser}.  Les modules contenant plusieurs classes gardent
+leur nom amont en minuscule et sont aussi préfixés par @code{perl-}.  Ces
+modules tendent à avoir le mot @code{perl} quelque part dans leur nom, que
+nous supprimons en faveur du préfixe.  Par exemple, @code{libwww-perl}
+devient @code{perl-libwww}.
+
+
+@node Paquets java
+@subsection Paquets java
+
+@cindex java
+Le programmes Java utiles en soit sont nommés comme les autres paquets, avec
+le nom amont en minuscule.
+
+Pour éviter les confusions et les problèmes de nom avec d'autres langages de
+programmation, il est désirable que le nom d'un paquet Java soit préfixé par
+@code{java-}.  Si un projet contient déjà le mot @code{java}, nous le
+supprimons, par exemple le paquet @code{ngsjava} est empaqueté sous le nom
+@code{java-ngs}.
+
+Pour les paquets java contenant une seul classe ou une petite hiérarchie de
+classes, nous utilisons le nom de la classe en minuscule, en remplaçant les
+occurrences de @code{.} par des tirets et en préfixant le tout par
+@code{java-}.  Donc la classe @code{apache.commons.cli} devient
+@code{java-apache-commons-cli}.
+
+
+@node Polices de caractères
+@subsection Polices de caractères
+
+@cindex polices
+Pour les polices qui n esont en général par installées par un utilisateurs
+pour du traitement de texte, ou qui sont distribuées en tant que partie d'un
+paquet logiciel plus gros, nous nous appuyons sur les règles générales pour
+les logiciels ; par exemple, cela s'applique aux polices livrées avec le
+système X.Org ou les polices qui font partie de TeX Live.
+
+Pour rendre plus facile la recherche par l'utilisateur, les noms des autres
+paquets contenant seulement des polices sont construits ainsi,
+indépendamment du nom du paquet en amont.
+
+Le nom d'un paquet contenant une unique famille de polices commence par
+@code{font-} ; il est suivi du nom du fondeur et d'un tiret @code{-} si le
+fondeur est connu, et du nom de la police, dont les espaces sont remplacés
+par des tirets (et comme d'habitude, toutes les lettres majuscules sont
+transformées en minuscules).  Par exemple, la famille de polices Gentium de
+SIL est empaqueté sous le nom @code{font-sil-gentium}.
+
+Pour un paquet contenant plusieurs familles de polices, le nom de la
+collection est utilisée à la place du nom de la famille.  Par exemple les
+polices Liberation consistent en trois familles, Liberation Sans, Liberation
+Serif et Liberation Mono.  Elles pourraient être empaquetées séparément sous
+les noms @code{font-liberation-sans} etc, mais comme elles sont distribuées
+ensemble sous un nom commun, nous préférons les empaqueter ensemble en tant
+que @code{font-liberation}.
+
+Dans le cas où plusieurs formats de la même famille ou collection sont
+empaquetés séparément, une forme courte du format, préfixé d'un tiret est
+ajouté au nom du paquet.  Nous utilisont @code{-ttf} pour les polices
+TrueType, @code{-otf} pour les polices OpenType et @code{-type1} pour les
+polices Type 1 de PostScript.
+
+
 @node Style de code
 @section Style de code
 
@@ -323,9 +782,8 @@ vous l'entrez.  En plus,
 @code{paredit.vim}} peut vous aider à gérer toutes ces parenthèses.
 
 Nous demandons que toutes les procédure de premier niveau contiennent une
-chaîne de documentation.  Ce pré-requis peut être relâché pour les
+chaîne de documentation.  Ce prérequis peut être relâché pour les procédures
-procédures privées simples dans l'espace de nom @code{(guix build @dots{})}
+privées simples dans l'espace de nom @code{(guix build @dots{})} cependant.
-cependant.
 
 Les procédures ne devraient pas avoir plus de quatre paramètres
 positionnés. Utilisez des paramètres par mot-clefs pour les procédures qui
@@ -375,6 +833,33 @@ paquet ou du paquet modifié, et corrigez les erreurs qu'il rapporte
 Assurez-vous que le paquet se construise sur votre plate-forme avec
 @code{guix build @var{paquet}}.
 
+@item
+We recommend you also try building the package on other supported
+platforms.  As you may not have access to actual hardware platforms, we
+recommend using the @code{qemu-binfmt-service-type} to emulate them.  In
+order to enable it, add the following service to the list of services in
+your @code{operating-system} configuration:
+
+@example
+(service qemu-binfmt-service-type
+ (qemu-binfmt-configuration
+   (platforms (lookup-qemu-platforms "arm" "aarch64" "ppc" "mips64el"))
+   (guix-support? #t)))
+@end example
+
+Then reconfigure your system.
+
+You can then build packages for different platforms by specifying the
+@code{--system} option.  For example, to build the "hello" package for the
+armhf, aarch64, powerpc, or mips64 architectures, you would run the
+following commands, respectively:
+@example
+guix build --system=armhf-linux --rounds=2 hello
+guix build --system=aarch64-linux --rounds=2 hello
+guix build --system=powerpc-linux --rounds=2 hello
+guix build --system=mips64el-linux --rounds=2 hello
+@end example
+
 @item
 @cindex construction groupée
 Assurez-vous que le paquet n'utilise pas de copie groupée d'un logiciel déjà
@@ -391,21 +876,18 @@ depuis un unique emplacement et qu'ils affectent tout le système, ce
 qu'empêchent les copies groupées.
 
 @item
-Regardez le profile rapporté par @command{guix size} (@pxref{Invoquer guix size}).  Cela vous permettra de remarquer des références à d'autres paquets
+Take a look at the profile reported by @command{guix size} (@pxref{Invoquer guix size}).  This will allow you to notice references to other packages
-qui ont été retenus.  Il peut aussi aider à déterminer s'il faut découper le
+unwillingly retained.  It may also help determine whether to split the
-paquet (@pxref{Des paquets avec plusieurs résultats}) et quelle dépendance
+package (@pxref{Des paquets avec plusieurs résultats}), and which optional
-facultative utiliser.
+dependencies should be used.  In particular, avoid adding @code{texlive} as
+a dependency: because of its extreme size, use @code{texlive-tiny} or
+@code{texlive-union} instead.
 
 @item
 Pour les changements important, vérifiez que les paquets qui en dépendent
 (s'ils existent) ne sont pas affectés par le changement ; @code{guix refresh
 --list-dependant @var{paquet}} vous aidera (@pxref{Invoquer guix refresh}).
 
-@c ===========================================================================
-@c
-@c This file was generated with po4a. Translate the source file.
-@c
-@c ===========================================================================
 @c See <https://lists.gnu.org/archive/html/guix-devel/2016-10/msg00933.html>.
 @cindex stratégie de branche
 @cindex stratégie de planification des reconstructions
@@ -418,7 +900,7 @@ principes :
 branche @code{master} (changements non-disruptifs).
 
 @item entre 300 et 1 200 paquets dépendants
-branche @code{staging} (changemets non-disruptifs).  Cette branche devrait
+branche @code{staging} (changements non-disruptifs).  Cette branche devrait
 être fusionnées dans @code{master} tous les 3 semaines.  Les changements par
 thèmes (par exemple une mise à jour de la pile GNOME) peuvent aller dans une
 branche spécifique (disons, @code{gnome-updates}).
@@ -460,15 +942,14 @@ Cela est suffisant pour trouver une classe de non-déterminisme commune,
 comme l'horodatage ou des sorties générées aléatoirement dans le résultat de
 la construction.
 
-Une autre option consiste à utiliser @command{guix challenge}
+Another option is to use @command{guix challenge} (@pxref{Invoquer guix challenge}).  You may run it once the package has been committed and built
-(@pxref{Invoquer guix challenge}).  Vous pouvez lancer la commande une fois
+by @code{@value{SUBSTITUTE-SERVER}} to check whether it obtains the same
-que les paquets ont été commités et construits par @code{hydra.gnu.org} pour
+result as you did.  Better yet: Find another machine that can build it and
-vérifier s'il obtient le même résultat que vous.  Mieux encore : trouvez une
+run @command{guix publish}.  Since the remote build machine is likely
-autre machine qui peut le construire et lancez @command{guix publish}.  Puis
+different from yours, this can catch non-determinism issues related to the
-la machine distante est sûrement différente de la vôtre, cela peut trouver
+hardware---e.g., use of different instruction set extensions---or to the
-des problèmes de non-déterminisme liés au matériel — par exemple utiliser
+operating system kernel---e.g., reliance on @code{uname} or @file{/proc}
-une extension du jeu d'instruction — ou du noyau du système d'exploitation —
+files.
-par exemple se reposer sur @code{uname} ou les fichiers de @file{/proc}.
 
 @item
 Lorsque vous écrivez de la documentation, utilisez une formulation au genre

doc/guix.texi

@@ -4456,17 +4456,18 @@ that will be added to the environment directly.
 
 @item --pure
 Unset existing environment variables when building the new environment, except
-those specified with @option{--inherit} (see below.)  This has the effect of
+those specified with @option{--preserve} (see below.)  This has the effect of
 creating an environment in which search paths only contain package inputs.
 
-@item --inherit=@var{regexp}
+@item --preserve=@var{regexp}
-When used alongside @option{--pure}, inherit all the environment variables
+@itemx -E @var{regexp}
+When used alongside @option{--pure}, preserve the environment variables
 matching @var{regexp}---in other words, put them on a ``white list'' of
 environment variables that must be preserved.  This option can be repeated
 several times.
 
 @example
-guix environment --pure --inherit=^SLURM --ad-hoc openmpi @dots{} \
+guix environment --pure --preserve=^SLURM --ad-hoc openmpi @dots{} \
   -- mpirun @dots{}
 @end example
 
@@ -10695,6 +10696,7 @@ account.  System accounts are sometimes treated specially; for instance,
 graphical login managers do not list them.
 
 @anchor{user-account-password}
+@cindex password, for user accounts
 @item @code{password} (default: @code{#f})
 You would normally leave this field to @code{#f}, initialize user
 passwords as @code{root} with the @command{passwd} command, and then let
@@ -10702,11 +10704,29 @@ users change it with @command{passwd}.  Passwords set with
 @command{passwd} are of course preserved across reboot and
 reconfiguration.
 
-If you @emph{do} want to have a preset password for an account, then
+If you @emph{do} want to set an initial password for an account, then
-this field must contain the encrypted password, as a string.
+this field must contain the encrypted password, as a string.  You can use the
-@xref{crypt,,, libc, The GNU C Library Reference Manual}, for more information
+@code{crypt} procedure for this purpose:
-on password encryption, and @ref{Encryption,,, guile, GNU Guile Reference
+
-Manual}, for information on Guile's @code{crypt} procedure.
+@example
+(user-account
+  (name "charlie")
+  (home-directory "/home/charlie")
+  (group "users")
+
+  ;; Specify a SHA-512-hashed initial password.
+  (password (crypt "InitialPassword!" "$6$abc")))
+@end example
+
+@quotation Note
+The hash of this initial password will be available in a file in
+@file{/gnu/store}, readable by all the users, so this method must be used with
+care.
+@end quotation
+
+@xref{Passphrase Storage,,, libc, The GNU C Library Reference Manual}, for
+more information on password encryption, and @ref{Encryption,,, guile, GNU
+Guile Reference Manual}, for information on Guile's @code{crypt} procedure.
 
 @end table
 @end deftp

gnu/build/activation.scm

@@ -298,9 +298,9 @@ they already exist."
                 (gid (passwd:gid pw)))
            (mkdir-p home)
            (chown home uid gid)
-           (unless system?
+           (chmod home #o700)
-             (copy-account-skeletons home
+           (copy-account-skeletons home
-                                     #:uid uid #:gid gid)))))))
+                                   #:uid uid #:gid gid))))))
 
   (for-each ensure-user-home users))
 

gnu/local.mk

@@ -65,6 +65,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/antivirus.scm			\
   %D%/packages/apl.scm				\
   %D%/packages/apr.scm				\
+  %D%/packages/arcan.scm			\
   %D%/packages/aspell.scm			\
   %D%/packages/assembly.scm			\
   %D%/packages/astronomy.scm			\
@@ -250,6 +251,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/iso-codes.scm			\
   %D%/packages/java.scm				\
   %D%/packages/java-compression.scm		\
+  %D%/packages/java-maths.scm			\
   %D%/packages/javascript.scm			\
   %D%/packages/jemalloc.scm			\
   %D%/packages/jrnl.scm				\
@@ -978,6 +980,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libffi-3.2.1-complex-alpha.patch		\
   %D%/packages/patches/libjxr-fix-function-signature.patch	\
   %D%/packages/patches/libjxr-fix-typos.patch			\
+  %D%/packages/patches/libopenshot-fixup-tests.patch		\
   %D%/packages/patches/libopenshot-tests-with-system-libs.patch	\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
   %D%/packages/patches/libmad-armv7-thumb-pt1.patch		\
@@ -1030,7 +1033,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/luminance-hdr-qt-printer.patch		\
   %D%/packages/patches/lvm2-static-link.patch			\
   %D%/packages/patches/lxsession-use-gapplication.patch         \
-  %D%/packages/patches/lyx-2.2.3-fix-test.patch			\
   %D%/packages/patches/make-glibc-compat.patch			\
   %D%/packages/patches/make-impure-dirs.patch			\
   %D%/packages/patches/mariadb-client-test-32bit.patch		\
@@ -1278,6 +1280,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/texi2html-document-encoding.patch	\
   %D%/packages/patches/texi2html-i18n.patch			\
   %D%/packages/patches/thefuck-test-environ.patch		\
+  %D%/packages/patches/thermald-make-int-max32-visible.patch	\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
   %D%/packages/patches/tinyxml-use-stl.patch			\
   %D%/packages/patches/tipp10-fix-compiling.patch		\

gnu/packages/admin.scm

@@ -1284,7 +1284,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
 (define-public acpica
   (package
     (name "acpica")
-    (version "20180810")
+    (version "20190215")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1292,7 +1292,7 @@ module slots, and the list of I/O ports (e.g. serial, parallel, USB).")
                     version ".tar.gz"))
               (sha256
                (base32
-                "01drf32h0v1s8yd414rgc9bavb52yffrwpnbzfxd9sk1lwssr6v7"))))
+                "1iy2zwi8aicq0b5a0phfacvk1f9z1d89cx43adcf0qh82gb9m4wg"))))
     (build-system gnu-build-system)
     (native-inputs `(("flex" ,flex)
                      ("bison" ,bison)))
@@ -1856,13 +1856,13 @@ platform-specific methods.")
   (package
     (name "audit")
     (home-page "https://people.redhat.com/sgrubb/audit/")
-    (version "2.8.4")
+    (version "2.8.5")
     (source (origin
               (method url-fetch)
               (uri (string-append home-page "audit-" version ".tar.gz"))
               (sha256
                (base32
-                "0f4ci6ffznnmgblwgv7ich9mjfk3p6y5l6m6h3chhmzw156nj454"))))
+                "1dzcwb2q78q7x41shcachn7f4aksxbxd470yk38zh03fch1l2p8f"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags (list "--with-python=no"
@@ -2523,7 +2523,7 @@ make it a perfect utility on modern distros.")
 (define-public thermald
   (package
     (name "thermald")
-    (version "1.7.2")
+    (version "1.8")
     (source
      (origin
       (method git-fetch)
@@ -2532,8 +2532,9 @@ make it a perfect utility on modern distros.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-       (base32
+       (base32 "1g1l7k8yxj8bl1ysdx8v6anv1s7xk9j072y44gwki70dy48n7j92"))
-        "1cs2pq8xvfnsvrhg2bxawk4kn3z1qmfrnpnhs178pvfbglzh15hc"))))
+      (patches
+       (search-patches "thermald-make-int-max32-visible.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags

gnu/packages/arcan.scm

@@ -0,0 +1,179 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 L  p R n  d n <guix@lprndn.info>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages arcan)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix git-download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (gnu packages apr)
+  #:use-module (gnu packages audio)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages fontutils)
+  #:use-module (gnu packages gl)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages image)
+  #:use-module (gnu packages libusb)
+  #:use-module (gnu packages lua)
+  #:use-module (gnu packages ocr)
+  #:use-module (gnu packages pcre)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages ruby)
+  #:use-module (gnu packages sdl)
+  #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages video)
+  #:use-module (gnu packages xdisorg)
+  #:use-module (srfi srfi-1))
+
+(define-public arcan
+  (let ((commit "b4dd1fbd1938492ff4b269189d3c8524be7450a9")
+        (revision "1"))
+    (package
+      (name "arcan")
+      (version (git-version "0.5.5.2" revision commit))
+      (source (origin
+                (method git-fetch)
+                (file-name (git-file-name name version))
+                (uri (git-reference
+                      (url "https://github.com/letoram/arcan.git")
+                      (commit commit)))
+                (sha256
+                 (base32 "1pd0avlzc2rig1hd37zbhc7r2s6fjzdhshfg9l9cfzibl7caclyw"))))
+      (build-system cmake-build-system)
+      (arguments
+       `(#:configure-flags '("-DVIDEO_PLATFORM=egl-dri" "-DBUILTIN_LUA=off"
+                             "-DSTATIC_OPENAL=off""-DENABLE_LWA=on"
+                             "-DSTATIC_SQLITE3=off" "-DSTATIC_FREETYPE=off"
+                             "-DSHMIF_TUI_ACCEL=on")
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-cmake-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* "src/platform/cmake/modules/FindGBMKMS.cmake"
+                 (("/usr/local/include/libdrm")
+                  (string-append (assoc-ref inputs "libdrm")
+                                 "/include/libdrm")))
+               (substitute* "src/platform/cmake/modules/FindAPR.cmake"
+                 (("/usr/local/apr/include/apr-1")
+                  (string-append (assoc-ref inputs "apr")
+                                 "/include/apr-1")))
+               #t))
+           ;; Normally, it tries to fetch patched openal with git
+           ;; but copying files manually in the right place seems to work too.
+           (add-after 'unpack 'prepare-static-openal
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((arcan-openal (assoc-ref inputs "arcan-openal")))
+                 (copy-recursively arcan-openal "external/git/openal"))
+               #t))
+           (add-after 'prepare-static-openal 'generate-man
+             (lambda _
+               (with-directory-excursion "doc"
+                 (invoke "ruby" "docgen.rb" "mangen"))
+               #t))
+           (add-before 'configure 'chdir
+             (lambda _
+               (chdir "src")
+               #t))
+           (add-after 'install 'wrap-program
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (wrap-program (string-append out "/bin/arcan")
+                   `("ARCAN_RESOURCEPATH" ":" suffix
+                     (,(string-append out "/share/arcan/resources")))
+                   `("ARCAN_STATEBASEPATH" ":" =
+                     ("$HOME/.arcan/resources/savestates"))
+                   `("ARCAN_STATEPATH" ":" =
+                     ("$HOME/.arcan/resources/savestates"))
+                   `("ARCAN_BINPATH" ":" =
+                     (,(string-append out "/bin/arcan_frameserver")))))
+               #t)))
+         #:tests? #f))
+      (native-search-paths
+       (list (search-path-specification
+              (variable "ARCAN_APPLBASEPATH")
+              (separator #f)
+              (files '("share/arcan/appl")))
+             (search-path-specification
+              (variable "ARCAN_SCRIPTPATH")
+              (separator #f)
+              (files '("share/arcan/scripts")))))
+      (inputs
+       `(("apr" ,apr)
+         ("ffmpeg" ,ffmpeg)
+         ("freetype" ,freetype)
+         ("glib" ,glib)
+         ("glu" ,glu)
+         ("harfbuzz" ,harfbuzz)
+         ("libdrm" ,libdrm)
+         ("libusb" ,libusb)
+         ("libxkbcommon" ,libxkbcommon)
+         ("lua" ,luajit)
+         ("lzip" ,lzip)
+         ("openal" ,openal)
+         ("pcre" ,pcre)
+         ("sqlite" ,sqlite)
+         ("tesseract-ocr" ,tesseract-ocr)
+         ("leptonica" ,leptonica)
+         ("vlc" ,vlc)
+         ;;  To build arcan_lwa, we need a patched version of openal.
+         ;; https://github.com/letoram/arcan/wiki/packaging
+         ("arcan-openal" ,(origin
+                            (method git-fetch)
+                            (file-name "arcan-openal-0.5.4")
+                            (uri (git-reference
+                                  (url "https://github.com/letoram/openal.git")
+                                  (commit "1c7302c580964fee9ee9e1d89ff56d24f934bdef")))
+                            (sha256
+                             (base32
+                              "0dcxcnqjkyyqdr2yk84mprvkncy5g172kfs6vc4zrkklsbkr8yi2"))))))
+      (native-inputs
+       `(("pkg-config" ,pkg-config)
+         ("ruby" ,ruby)))               ; For documentation and testing
+      (home-page "https://arcan-fe.com")
+      (synopsis "Display server, multimedia framework and game engine (egl-dri)")
+      (description "Arcan is a development framework for creating virtually
+anything from user interfaces for specialized embedded applications
+all the way to full-blown desktop environments.  At its heart lies a multimedia
+engine programmable using Lua.")
+      ;; https://github.com/letoram/arcan/blob/master/COPYING
+      (license (list license:gpl2+
+                     license:lgpl2.0
+                     license:lgpl2.0+
+                     license:public-domain
+                     license:bsd-3)))))
+
+(define-public arcan-sdl
+  (package
+    (inherit arcan)
+    (name "arcan-sdl")
+    (inputs
+     `(("sdl" ,sdl)
+       ,@(fold alist-delete (package-inputs arcan)
+               '("libdrm"))))
+    (arguments
+     `(,@(ensure-keyword-arguments
+          (package-arguments arcan)
+          '(#:configure-flags
+            '("-DVIDEO_PLATFORM=sdl" "-DBUILTIN_LUA=off"
+              "-DSTATIC_OPENAL=off" "-DDISABLE_JIT=off"
+              "-DENABLE_LWA=on" "-DSTATIC_SQLITE3=off"
+              "-DSTATIC_FREETYPE=off" "-DSHMIF_TUI_ACCEL=on")))))
+    (synopsis "Combined display server, multimedia framework and game engine (SDL)")))

gnu/packages/audio.scm

@@ -20,6 +20,7 @@
 ;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
 ;;; Copyright © 2019 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2019 Rutger Helling <rhelling@mykolab.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -87,6 +88,7 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages telephony)
   #:use-module (gnu packages tls)
@@ -1739,14 +1741,14 @@ essential distortions.")
 (define-public liblo
   (package
     (name "liblo")
-    (version "0.29")
+    (version "0.30")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/liblo/liblo/" version
                                  "/liblo-" version ".tar.gz"))
              (sha256
               (base32
-               "0sn0ckc1d0845mhsaa62wf7f9v0c0ykiq796a30ja5096kib9qdc"))))
+               "06wdjzxjdshr6hyl4c94yvg3jixiylap8yjs8brdfpm297gck9rh"))))
     (build-system gnu-build-system)
     (arguments
      `(;; liblo test FAILED
@@ -3673,3 +3675,29 @@ surround).")
 high-quality editing and playback of audio, and is based on the JUCE
 library.")
     (license license:lgpl3+)))
+
+(define-public faudio
+  (package
+    (name "faudio")
+    (version "19.03")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FNA-XNA/FAudio.git")
+             (commit version)))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32 "0v5l67ixr5kd9jz5sza8xgzxamqnlgn3gs1q8gg6ir60g0jvzbd4"))))
+    (arguments
+     '(#:tests? #f                      ; No tests.
+       #:configure-flags '("-DFFMPEG=ON")))
+    (build-system cmake-build-system)
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs `(("ffmpeg" ,ffmpeg)
+              ("sdl2" ,sdl2)))
+    (home-page "https://github.com/FNA-XNA/FAudio")
+    (synopsis "XAudio reimplementation")
+    (description "FAudio is an XAudio reimplementation that focuses solely on
+developing fully accurate DirectX Audio runtime libraries.")
+    (license license:zlib)))

gnu/packages/bioconductor.scm

@@ -1199,3 +1199,32 @@ sequencing data.")
 algorithm to segment DNA copy number data and identify genomic regions with
 abnormal copy number.")
     (license license:gpl2+)))
+
+;; This is a CRAN package, but it uncharacteristically depends on a
+;; Bioconductor package.
+(define-public r-htscluster
+  (package
+    (name "r-htscluster")
+    (version "2.0.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "HTSCluster" version))
+       (sha256
+        (base32
+         "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
+    (properties `((upstream-name . "HTSCluster")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-capushe" ,r-capushe)
+       ("r-edger" ,r-edger)
+       ("r-plotrix" ,r-plotrix)))
+    (home-page "https://cran.r-project.org/web/packages/HTSCluster")
+    (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
+    (description
+     "This package provides a Poisson mixture model is implemented to cluster
+genes from high-throughput transcriptome sequencing (RNA-seq) data.  Parameter
+estimation is performed using either the EM or CEM algorithm, and the slope
+heuristics are used for model selection (i.e., to choose the number of
+clusters).")
+    (license license:gpl3+)))

gnu/packages/bioinformatics.scm

@@ -12902,7 +12902,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.21")
+    (version "0.0.31")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -12910,7 +12910,7 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "0psgdzlnx5xwhlhpss5yvmnl7yv19y9742l97m04f7awd8w74gxs"))))
+                "0l3vd9xwqzap3mmyj8xwqp84kj7scbq308diqnwg2albphl75xqs"))))
     (build-system gnu-build-system)
     ;; parts of the tests rely on access to the network
     (arguments '(#:tests? #f))

gnu/packages/calcurse.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2015, 2017 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,15 +30,14 @@
 (define-public calcurse
   (package
     (name "calcurse")
-    (version "4.3.0")
+    (version "4.4.0")
     (source
      (origin
-      (method url-fetch)
+       (method url-fetch)
-      (uri (string-append "https://calcurse.org/files/calcurse-"
+       (uri (string-append "https://calcurse.org/files/calcurse-"
-                          version ".tar.gz"))
+                           version ".tar.gz"))
-      (sha256
+       (sha256
-       (base32
+        (base32 "0vw2xi6a2lrhrb8n55zq9lv4mzxhby4xdf3hmi1vlfpyrpdwkjzd"))))
-        "16jzg0nasnxdlz23i121x41pq5kbxmjzk52c5d863rg117fc7v1i"))))
     (build-system gnu-build-system)
     (inputs `(("ncurses" ,ncurses)))
     (native-inputs `(("tzdata" ,tzdata-for-tests)))
@@ -46,15 +45,25 @@
      ;; The ical tests all want to create a ".calcurse" directory, and may
      ;; fail with "cannot create directory '.calcurse': File exists" if run
      ;; concurently.
-     `(#:parallel-tests? #f
+     `(#:configure-flags
+       (list (string-append "--docdir=" (assoc-ref %outputs "out")
+                            "/share/doc/" ,name "-" ,version))
+       #:parallel-tests? #f
        ;; Since this tzdata is only used for tests and not referenced by the
        ;; built package, used the "fixed" obsolete version of tzdata and ensure
        ;; it does not sneak in to the closure.
        #:disallowed-references (,tzdata-for-tests)
        #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'respect-docdir
+                    ;; doc/Makefile disregards ./configure's --docdir option.
+                    (lambda _
+                      (substitute* "doc/Makefile.in"
+                        (("(docdir =) .*" _ match)
+                         (format "~a @docdir@\n" match)))
+                      #t))
                   (add-before 'check 'check-setup
                     (lambda* (#:key inputs #:allow-other-keys)
-                      (setenv "TZDIR"   ;for test/ical-007.sh
+                      (setenv "TZDIR"   ; for test/ical-007.sh
                               (string-append (assoc-ref inputs "tzdata")
                                              "/share/zoneinfo")))))))
     (home-page "https://www.calcurse.org")

gnu/packages/chromium.scm

@@ -224,7 +224,7 @@ from forcing GEXP-PROMISE."
                       #:system system
                       #:guile-for-build guile)))
 
-(define %chromium-version "72.0.3626.119")
+(define %chromium-version "72.0.3626.121")
 (define %ungoogled-revision "a80839c418de8843dfcd6c13a557f12d26a0a17a")
 (define package-revision "0")
 
@@ -245,7 +245,7 @@ from forcing GEXP-PROMISE."
                                 %chromium-version ".tar.xz"))
             (sha256
              (base32
-              "0ylig933xzn6c0018nxq95xhl0wkxcm95fdiy2c7s4a4h3hkr5dk"))))
+              "07xwmlvmzfga61nrimqmzl7s29jb4kc94nkzwwlb7sh6nr55a7jc"))))
          (ungoogled-source
           (origin
             (method git-fetch)

gnu/packages/coq.scm

@@ -184,15 +184,15 @@ provers.")
 (define-public coq-flocq
   (package
     (name "coq-flocq")
-    (version "2.6.1")
+    (version "3.1.0")
     (source (origin
               (method url-fetch)
               ;; Use the ‘Latest version’ link for a stable URI across releases.
               (uri (string-append "https://gforge.inria.fr/frs/download.php/"
-                                  "file/37454/flocq-" version ".tar.gz"))
+                                  "file/37901/flocq-" version ".tar.gz"))
               (sha256
                (base32
-                "06msp1fwpqv6p98a3i1nnkj7ch9rcq3rm916yxq8dxf51lkghrin"))))
+                "02szrgz9m0ac51la1lqpiv6i2g0zbgx9gz5rp0q1g00ajldyna5c"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -327,14 +327,14 @@ part of the distribution.")
 (define-public coq-coquelicot
   (package
     (name "coq-coquelicot")
-    (version "3.0.1")
+    (version "3.0.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gforge.inria.fr/frs/download.php/"
-                                  "file/37045/coquelicot-" version ".tar.gz"))
+                                  "file/37523/coquelicot-" version ".tar.gz"))
               (sha256
                (base32
-                "0hsyhsy2lwqxxx2r8xgi5csmirss42lp9bkb9yy35mnya0w78c8r"))))
+                "1biia7nfqf7vaqq5gmykl4rwjyvrcwss6r2jdf0in5pvp2rnrj2w"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)
@@ -348,12 +348,6 @@ part of the distribution.")
                             "/lib/coq/user-contrib/Coquelicot"))
        #:phases
        (modify-phases %standard-phases
-         (add-before 'configure 'fix-coq8.8
-           (lambda _
-             ; appcontext has been removed from coq 8.8
-             (substitute* "theories/AutoDerive.v"
-               (("appcontext") "context"))
-             #t))
          (add-before 'configure 'fix-remake
            (lambda _
              (substitute* "remake.cpp"
@@ -413,14 +407,14 @@ provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
 (define-public coq-interval
   (package
     (name "coq-interval")
-    (version "3.3.0")
+    (version "3.4.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gforge.inria.fr/frs/download.php/"
-                                  "file/37077/interval-" version ".tar.gz"))
+                                  "file/37524/interval-" version ".tar.gz"))
               (sha256
                (base32
-                "08fdcf3hbwqphglvwprvqzgkg0qbimpyhnqsgv3gac4y1ap0f903"))))
+                "023j9sd64brqvjdidqkn5m8d7a93zd9r86ggh573z9nkjm2m7vvg"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("ocaml" ,ocaml)

gnu/packages/cran.scm

@@ -10681,3 +10681,24 @@ functions are provided.")
 help you to better understand object oriented programming in R, particularly
 using @code{S3}.")
     (license license:gpl3)))
+
+(define-public r-capushe
+  (package
+    (name "r-capushe")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "capushe" version))
+       (sha256
+        (base32
+         "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-mass" ,r-mass)))
+    (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
+    (synopsis "Calibrating penalities using slope heuristics")
+    (description
+     "This package provides tools for the calibration of penalized criteria
+for model selection.  The calibration methods available are based on the slope
+heuristics.")
+    (license license:gpl2+)))

gnu/packages/databases.scm

@@ -837,7 +837,7 @@ types are supported, as is encryption.")
 (define-public rocksdb
   (package
     (name "rocksdb")
-    (version "5.15.10")
+    (version "5.18.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -846,7 +846,7 @@ types are supported, as is encryption.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0q26frbj9pykarcfa0yxgwncxlvsqhjkby0jrbfs1a8srja688r4"))
+                "1v2slmmr1dsgf8z0qcfg1y9x1al96859rg48b66p9nsawczd5zv9"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -1031,14 +1031,14 @@ changes.")
 (define-public tdb
   (package
     (name "tdb")
-    (version "1.3.16")
+    (version "1.3.18")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/tdb/tdb-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1ibcz466xwk1x6xvzlgzd5va4lyrjzm3rnjak29kkwk7cmhw4gva"))))
+                "1drnsdh1w0px35r0y7l7g59yvyr67mvcsdrli4wab0mwi07b8mn1"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -1055,7 +1055,8 @@ changes.")
        ;; ("docbook-xsl" ,docbook-xsl)
        ;; ("libxml2" ,libxml2)
        ;; ("libxslt" ,libxslt)
-       ("python" ,python-2)))                     ;for the Waf build system
+       ("python" ,python)                         ;for the Waf build system
+       ("which" ,which)))
     (home-page "https://tdb.samba.org/")
     (synopsis "Trivial database")
     (description
@@ -2478,13 +2479,13 @@ reasonable substitute.")
 (define-public python-redis
   (package
     (name "python-redis")
-    (version "2.10.6")
+    (version "3.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "redis" version))
        (sha256
-        (base32 "03vcgklykny0g0wpvqmy8p6azi2s078317wgb2xjv5m2rs9sjb52"))))
+        (base32 "0m1b88wg1w6xdwg0siky5k86x8sh6smhbr42ixz41ra81lv34jbj"))))
     (build-system python-build-system)
     ;; Tests require a running Redis server
     (arguments '(#:tests? #f))
@@ -2503,13 +2504,13 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "0.12.0")
+    (version "0.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "rq" version))
        (sha256
-        (base32 "16d8kni57xlnah2hawy4xgw21xrv3f64j5q5shyp3zxx4yd9iibs"))))
+        (base32 "0xvapd2bxnyq480i48bdkddzlqmv2axbsq85rlfy8k3al8zxxxrf"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-click" ,python-click)

gnu/packages/django.scm

@@ -218,14 +218,14 @@ them do this.")
 (define-public python-django-allauth
   (package
     (name "python-django-allauth")
-    (version "0.30.0")
+    (version "0.39.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "django-allauth" version))
        (sha256
         (base32
-         "1fslqc5qqb0b66yscvkyjwfv8cnbfx5nlkpnwimyb3pf1nc1w7r3"))))
+         "17l0acpr3cihdndzccjhgv58f9z170v2qwx7w0b8w6235x646i24"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -234,19 +234,20 @@ them do this.")
          (add-before 'check 'skip-test-requiring-network-access
            (lambda _
              (substitute* "allauth/socialaccount/providers/openid/tests.py"
+               (("import override_settings") "import tag, override_settings")
                (("def test_login")
-                "from django.test import tag
+                "@tag('requires-web')
-    @tag('requires-web')
     def test_login"))))
          (replace 'check
            (lambda _
+             ;; TODO: investigate why this test fails
+             (delete-file "allauth/socialaccount/providers/cern/tests.py")
              (setenv "DJANGO_SETTINGS_MODULE" "test_settings")
-             (zero? (system*
+             (invoke "django-admin"
-                     "django-admin"
                      "test"
                      "allauth"
                      "--verbosity=2"
-                     "--exclude-tag=requires-web")))))))
+                     "--exclude-tag=requires-web"))))))
     (propagated-inputs
      `(("python-openid" ,python-openid)
        ("python-requests" ,python-requests)
@@ -638,22 +639,22 @@ support, and optional data-URI image and font embedding.")
 (define-public python-django-redis
   (package
     (name "python-django-redis")
-    (version "4.7.0")
+    (version "4.10.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-redis" version))
               (sha256
                (base32
-                "0yyyxv8n9l9dhs893jsqwg2cxqkkc79g719n9dzzzqgkzialv1c1"))))
+                "1rxcwnv9ik0swkwvfqdi9i9baw6n8if5pj6q63fjh4p9chw3j2xg"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (and (zero? (system* "redis-server" "--daemonize" "yes"))
+             (invoke "redis-server" "--daemonize" "yes")
-                  (with-directory-excursion "tests"
+             (with-directory-excursion "tests"
-                    (zero? (system* "python" "runtests.py")))))))))
+               (invoke "python" "runtests.py")))))))
     (native-inputs
      `(("python-fakeredis" ,python-fakeredis)
        ("python-hiredis" ,python-hiredis)
@@ -675,25 +676,26 @@ support, and optional data-URI image and font embedding.")
 (define-public python-django-rq
   (package
     (name "python-django-rq")
-    (version "0.9.4")
+    (version "1.3.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-rq" version))
               (sha256
                (base32
-                "04v8ilfdp10bk31fxgh4cn083gsn5m06342cnpm5d10nd8hc0vky"))))
+                "0xh6qa7i779vh58lwwv6yk0wx8bi38mvmpz79grnl2cl8531r928"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          (replace 'check
            (lambda _
-             (and (zero? (system* "redis-server" "--daemonize" "yes"))
+             (invoke "redis-server" "--daemonize" "yes")
-                  (zero? (system* "django-admin.py" "test" "django_rq"
+             (invoke "django-admin.py" "test" "django_rq"
-                                  "--settings=django_rq.test_settings"
+                     "--settings=django_rq.tests.settings"
-                                  "--pythonpath="))))))))
+                     "--pythonpath="))))))
     (native-inputs
-     `(("redis" ,redis)))
+     `(("python-mock" ,python-mock)
+       ("redis" ,redis)))
     (propagated-inputs
      `(("python-django" ,python-django)
        ("python-rq" ,python-rq)))
@@ -788,14 +790,14 @@ static files.")
 (define-public pootle
   (package
     (name "pootle")
-    (version "2.8.0rc5")
+    (version "2.8.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "Pootle" version ".tar.bz2"))
         (sha256
          (base32
-          "0m6qcpkcy22dk3ad5y2k8851kqg2w6vrkywgy4vabwbacd7r1mvn"))))
+          "1ng8igq0alsqzasgxdh3fb23581anyzp121h9041pwdzzv98kn4m"))))
     (build-system python-build-system)
     (arguments
      `(; pootle supports only python2.

gnu/packages/emacs-xyz.scm

@@ -43,6 +43,7 @@
 ;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
 ;;; Copyright © 2019 Dimakakos Dimos <bendersteed@teknik.io>
+;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -253,16 +254,16 @@ on stdout instead of using a socket as the Emacsclient does.")
 (define-public emacs-magit
   (package
     (name "emacs-magit")
-    (version "2.13.1")
+    (version "2.90.1")
     (source (origin
              (method git-fetch)
              (uri (git-reference
                     (url "https://github.com/magit/magit")
-                    (commit version)))
+                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
-               "1kmjjcvhcb21qi6kmrlhf92ync8va5l41n9ban8kj25h7dbqyiym"))))
+               "1kw94sdczswsyzn1zlk5s5aplpdv4qd7qcqc5zfxsmsfwm3jacl4"))))
     (build-system gnu-build-system)
     (native-inputs `(("texinfo" ,texinfo)
                      ("emacs" ,emacs-minimal)))
@@ -11131,6 +11132,29 @@ my_thing reload} all the time.  It offers a consistent UI over different init
 systems.")
     (license license:gpl3+)))
 
+(define-public emacs-isearch+
+  (let ((commit "95e49af9dbf0254e095a11f115e101b52659520a")
+        (revision "1"))
+    (package
+      (name "emacs-isearch+")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/emacsmirror/isearch-plus.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "0xhd9zgknf4lvzyf4apirpd7spb1hbpzkvys00a7pkmd0vvahk0v"))))
+      (build-system emacs-build-system)
+      (home-page "https://www.emacswiki.org/emacs/isearch+.el")
+      (synopsis "Extensions to @code{isearch.el}")
+      (description "This package extends @code{isearch} with advice, dynamic
+filters, highlighting of regexp group levels, and more.")
+      (license license:gpl2+))))
+
 (define-public emacs-esh-autosuggest
   (package
     (name "emacs-esh-autosuggest")
@@ -11161,29 +11185,30 @@ autosuggestions with:
     (license license:gpl3+)))
 
 (define-public emacs-desktop-environment
-  (package
+  (let ((commit "a9eba14f2b5b8070f78dca839ca8259736e346a6"))
-    (name "emacs-desktop-environment")
+    (package
-    (version "0.2.0")
+      (name "emacs-desktop-environment")
-    (source
+      (version (git-version "0.2.0" "1" commit))
-     (origin
+      (source
-       (method git-fetch)
+       (origin
-       (uri (git-reference
+         (method git-fetch)
-             (url "https://github.com/DamienCassou/desktop-environment.git")
+         (uri (git-reference
-             (commit (string-append "v" version))))
+               (url "https://gitlab.petton.fr/DamienCassou/desktop-environment")
-       (file-name (string-append name "-" version "-checkout"))
+               (commit commit)))
-       (sha256
+         (file-name (string-append name "-" version "-checkout"))
-        (base32
+         (sha256
-         "1fal3yfmqg10cb53qsf5gsq2gvyz9w16wmlpnpjwjzwnjfn6l73r"))))
+          (base32
-    (build-system emacs-build-system)
+           "0x73x5hy7w55jrzy3xvqhk90rrsznmxjqvsvwhh21qznv5w269xz"))))
-    (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment")
+      (build-system emacs-build-system)
-    (synopsis "Control your GNU/Linux desktop environment from Emacs")
+      (home-page "https://gitlab.petton.fr/DamienCassou/desktop-environment")
-    (description
+      (synopsis "Control your GNU/Linux desktop environment from Emacs")
-     "This package helps you control your GNU/Linux desktop from Emacs.
+      (description
+       "This package helps you control your GNU/Linux desktop from Emacs.
 With @code{desktop-environment}, you can control the brightness and volume as
 well as take screenshots and lock your screen.  The package depends on the
 availability of shell commands to do the hard work for us.  These commands can
 be changed by customizing the appropriate variables.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-org-caldav
   (package
@@ -11239,10 +11264,10 @@ Org-mode file, and citations of Zotero items in Pandoc Markdown files.")
   (deprecated-package "emacs-evil-ediff" emacs-evil-collection))
 
 (define-public emacs-evil-magit
-  (let ((commit "dbf5a646a7ce1c35c229dfdc423bd5ecd927a3a8"))
+  (let ((commit "e2fec5877994c0c19f0c25fa01f3d22cb0ab38ba"))
     (package
       (name "emacs-evil-magit")
-      (version (git-version "0.4.2" "1" commit))
+      (version (git-version "0.4.2" "2" commit))
       (source
        (origin
          (method git-fetch)
@@ -11252,7 +11277,7 @@ Org-mode file, and citations of Zotero items in Pandoc Markdown files.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "0ya0dkviq4pi92ab69a4j674y5r1hc1x3x7r7hlm97ag3a6zfkav"))))
+           "134v7s03jvbhm70mavwab85r09i68g2a5bvriirh0chz1av2y16v"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-evil" ,emacs-evil)
@@ -11508,10 +11533,10 @@ you searched for and execute it, or view its documentation.")
     (license license:gpl3+))))
 
 (define-public emacs-helm-emms
-  (let ((commit "d3f9bdef8ff0d093eaf6e26af50ea905ab53fdec"))
+  (let ((commit "b785cb845a98a643eba9d5d53c9c0b4e6810a3cd"))
     (package
       (name "emacs-helm-emms")
-      (version (git-version "1.3" "1" commit))
+      (version (git-version "1.3" "2" commit))
       (source
        (origin
          (method git-fetch)
@@ -11521,7 +11546,7 @@ you searched for and execute it, or view its documentation.")
          (file-name (string-append name "-" version "-checkout"))
          (sha256
           (base32
-           "0bdb8xp0yp3gijpa9i2rc17gfzjhzlm92vdzw93i10qpd1xhj4aa"))))
+           "1595r09y3rmwd46nnhvjja3hb8j2ila295ijxv61cg52ws4wginh"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-helm" ,emacs-helm)
@@ -12125,7 +12150,7 @@ buffers – other modes on the TODO list).
 (define-public emacs-magit-todos
   (package
     (name "emacs-magit-todos")
-    (version "1.1")
+    (version "1.1.7")
     (source
      (origin
        (method git-fetch)
@@ -12135,7 +12160,7 @@ buffers – other modes on the TODO list).
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1mvzbxshr6zjdim3jd368ar1hy5l7n22i03cpvzdmrw83kkwdyhd"))))
+         "0qagdxpik64n4rw9scy451ws5sw00v64ri9g2dcw7b66bx2c6c6w"))))
     (build-system emacs-build-system)
     (propagated-inputs
      `(("emacs-async" ,emacs-async)
@@ -13161,10 +13186,10 @@ recursively.  The results are cached for speed.")
     (license license:gpl3+)))
 
 (define-public emacs-orgit
-  (let ((commit "ddb830c38cb71e5cf86db7fa62d6ee88ab3962d5"))
+  (let ((commit "2456436a7e64d26bcf455b3890a586acaa3e7f93"))
     (package
       (name "emacs-orgit")
-      (version (git-version "1.5.1" "1" commit))
+      (version (git-version "1.5.1" "2" commit))
       (home-page "https://github.com/magit/orgit")
       (source (origin
                 (method git-fetch)
@@ -13174,7 +13199,7 @@ recursively.  The results are cached for speed.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0fy4n71yskfkjl6w9mzrw3pfd5lp8f48g2c9bxiwg7mwzsmsb9nb"))))
+                  "1i52dq2ynddb1irgigr5mdwfbfd3bvm1f29jnzd7nlc0nk186nvh"))))
       (build-system emacs-build-system)
       (propagated-inputs
        `(("emacs-dash" ,emacs-dash)

gnu/packages/emacs.scm

@@ -115,6 +115,7 @@
     (build-system glib-or-gtk-build-system)
     (arguments
      `(#:tests? #f  ; no check target
+       #:configure-flags (list "--with-modules")
        #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'fix-/bin/pwd
@@ -201,11 +202,11 @@ languages.")
     (synopsis "The extensible text editor (used only for byte-compilation)")
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags (list "--with-gnutls=no")
+     `(,@(substitute-keyword-arguments (package-arguments emacs)
-       ,@(substitute-keyword-arguments (package-arguments emacs)
            ((#:phases phases)
             `(modify-phases ,phases
-               (delete 'install-site-start))))))
+               (delete 'install-site-start))))
+        #:configure-flags (list "--with-gnutls=no")))
     (inputs
      `(("ncurses" ,ncurses)))
     (native-inputs

gnu/packages/glib.scm

@@ -793,7 +793,7 @@ programming langauage.  It also contains the utility
 (define-public appstream-glib
   (package
     (name "appstream-glib")
-    (version "0.7.14")
+    (version "0.7.15")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://people.freedesktop.org/~hughsient/"
@@ -801,7 +801,7 @@ programming langauage.  It also contains the utility
                                   "appstream-glib-" version ".tar.xz"))
               (sha256
                (base32
-                "0n0s99jmx2sx5895lcvmfjwa9r0f06i71495dpn9v9frz4asvk3d"))))
+                "17ram4j3cvs78si0gi1labarr91pw68zn8kam41cqbvlwdyr89vy"))))
     (build-system meson-build-system)
     (native-inputs
      `(("gettext" ,gettext-minimal)

gnu/packages/gnome.scm

@@ -2706,7 +2706,7 @@ and the GLib main loop, to integrate well with GNOME applications.")
 (define-public libsecret
   (package
     (name "libsecret")
-    (version "0.18.7")
+    (version "0.18.8")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2715,7 +2715,7 @@ and the GLib main loop, to integrate well with GNOME applications.")
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "11ylmcfx6ff7xd1gpi58i2nbma83lz2xg0g2dq23w6snqhgzwrhd"))))
+                "058x64689k55wxfkdp4svhnwvv8jmqm7z5mrynybl38f4sfqiyiv"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -4214,15 +4214,15 @@ work and the interface is well tested.")
 (define-public eolie
   (package
     (name "eolie")
-    (version "0.9.45")
+    (version "0.9.52")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gitlab.gnome.org/World/eolie/"
-                                  "uploads/020f3f686e2b938731752a1d9f5bfa7e/"
+                                  "uploads/d95bf72958276c80dfaca8cce0e4e92c/"
                                   "eolie-" version ".tar.xz"))
               (sha256
                (base32
-                "0371p7g13r0b7zjc48fdcil43ddwpmyvkd2a4vv6ifsqmny6kl42"))))
+                "1s3b0rkm8sxmhzzi624snzqvz61i1rja5wxyzw6jg2kcdjcylwln"))))
     (build-system meson-build-system)
     (arguments
      `(#:glib-or-gtk? #t

gnu/packages/java-maths.scm

@@ -0,0 +1,89 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2019 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages java-maths)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system ant)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages ruby))
+
+(define-public java-jblas
+  (package
+    (name "java-jblas")
+    (version "1.2.4")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/mikiobraun/jblas.git")
+                    (commit (string-append "jblas-" version))))
+              (sha256
+               (base32
+                "0afh48hq8i8li5z11x415c8slwsfrlib0w1xjfbg186mximqvv3g"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f                      ; there are none
+       #:configure-flags
+       (list (string-append "--libpath="
+                            (assoc-ref %build-inputs "openblas")
+                            "/lib")
+             "--build-type=openblas")
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-writable
+           (lambda _
+             (map make-file-writable
+                  (find-files "." ".*"))
+             #t))
+         (add-before 'build 'setenv-JAVA_HOME
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
+             #t))
+         (add-after 'build 'build-jar
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (setenv "M2_HOME" (assoc-ref outputs "out"))
+             (invoke "ant" "jar" (string-append "-Dversion=" ,version))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((target (string-append (assoc-ref outputs "out")
+                                          "/share/java")))
+               (mkdir-p target)
+               (install-file (string-append "jblas-" ,version ".jar") target))
+             #t)))))
+    (inputs
+     `(("openblas" ,openblas)))
+    (native-inputs
+     `(("ant" ,ant)
+       ("ruby" ,ruby)                   ; for configure script
+       ("gfortran" ,gfortran)
+       ("jdk" ,icedtea "jdk")))
+    (home-page "http://jblas.org")
+    (synopsis "Linear algebra for Java")
+    (description
+     "jblas is a fast linear algebra library for Java.  jblas is based on BLAS
+and LAPACK, the de-facto industry standard for matrix computations, and uses
+state-of-the-art implementations for all its computational routines, making
+jBLAS very fast.")
+    (license license:bsd-3)))

gnu/packages/java.scm

@@ -10622,12 +10622,14 @@ and reporting) project dependencies.  It is characterized by the following:
     (name "java-eclipse-sisu-inject")
     (version "0.3.3")
     (source (origin
-              (method url-fetch)
+              (method git-fetch)
-              (uri (string-append "https://github.com/eclipse/sisu.inject/"
+              (uri (git-reference
-                                  "archive/releases/" version ".tar.gz"))
+                     (url "https://github.com/eclipse/sisu.inject/")
+                     (commit "releases/0.3.3")))
+              (file-name (git-file-name name version))
               (sha256
                (base32
-                "11rg6yw5nl13i65xsp4jxxgr341qcnnaan48p767h28kb07s0ajn"))))
+                "0gibc9x0bw0f4ls086fx73610fcspz9g2as7kcpcfhvl5znysvg7"))))
     (build-system ant-build-system)
     (arguments
      `(#:jar-name "eclipse-sisu-inject.jar"

gnu/packages/mail.scm

@@ -2017,7 +2017,7 @@ transfer protocols.")
        (modify-phases %standard-phases
          ;; Fix some incorrectly hard-coded external tool file names.
          (add-after 'unpack 'patch-FHS-file-names
-           (lambda* (#:key inputs #:allow-other-keys)
+           (lambda _
              (substitute* "smtpd/smtpctl.c"
                (("/bin/cat") (which "cat"))
                (("/bin/sh") (which "sh")))

gnu/packages/music.scm

@@ -3637,7 +3637,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
 (define-public musescore
   (package
     (name "musescore")
-    (version "3.0.3")
+    (version "3.0.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3646,7 +3646,7 @@ audio samples and various soft sythesizers.  It can receive input from a MIDI ke
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1drgmivqs2c5xck7dy5y9xf41wfnnj7n84069h273q96b783cx3f"))
+                "05cn4j5f7xr438lgl0by3lrc7wckdgicdn4jrvxfqic8hv81sca7"))
               (modules '((guix build utils)))
               (snippet
                ;; Un-bundle OpenSSL and remove unused libraries.

gnu/packages/networking.scm

@@ -912,7 +912,7 @@ private (reserved).")
 (define-public perl-net-dns
  (package
   (name "perl-net-dns")
-  (version "1.18")
+  (version "1.19")
   (source
     (origin
       (method url-fetch)
@@ -923,8 +923,7 @@ private (reserved).")
         (string-append "mirror://cpan/authors/id/N/NL/NLNETLABS/Net-DNS-"
                        version ".tar.gz")))
       (sha256
-        (base32
+       (base32 "1myc23vz0m42yyg8iw7bf1pdrmx9ql6fhl2vwk1vwf55v6yphqi0"))))
-          "1lx902cbvlfl63bqfdrnyavmfwbjvrfdnwgdc1dgs1wpzja19kjj"))))
   (build-system perl-build-system)
   (inputs
     `(("perl-digest-hmac" ,perl-digest-hmac)))

gnu/packages/patches/libopenshot-fixup-tests.patch

@@ -0,0 +1,148 @@
+From 691536f2f8a9ed7322fedb24d489db08c70705b9 Mon Sep 17 00:00:00 2001
+From: "Dr. Tobias Quathamer" <toddy@debian.org>
+Date: Sat, 18 Nov 2017 13:54:22 +0100
+Subject: [PATCH] This the combination of two patches:
+ https://sources.debian.org/data/main/libo/libopenshot/0.2.2+dfsg1-1/debian/patches/0003-Fix-failing-tests-by-using-a-fault-tolerance.patch
+ https://sources.debian.org/data/main/libo/libopenshot/0.2.2+dfsg1-1/debian/patches/0004-Add-some-more-fault-tolerance-for-arm64.patch
+
+Together they should fix the test suite on all architectures
+---
+ tests/FFmpegReader_Tests.cpp |  9 ++++-----
+ tests/ImageWriter_Tests.cpp  |  8 ++++----
+ tests/Timeline_Tests.cpp     | 28 ++++++++++++++--------------
+ 3 files changed, 22 insertions(+), 23 deletions(-)
+
+diff --git a/tests/FFmpegReader_Tests.cpp b/tests/FFmpegReader_Tests.cpp
+index 53563ca..07fc41e 100644
+--- a/tests/FFmpegReader_Tests.cpp
++++ b/tests/FFmpegReader_Tests.cpp
+@@ -95,8 +95,8 @@ TEST(FFmpegReader_Check_Video_File)
+ 	int pixel_index = 112 * 4; // pixel 112 (4 bytes per pixel)
+ 
+ 	// Check image properties on scanline 10, pixel 112
+-	CHECK_EQUAL(21, (int)pixels[pixel_index]);
+-	CHECK_EQUAL(191, (int)pixels[pixel_index + 1]);
++	CHECK_CLOSE(21, (int)pixels[pixel_index], 1);
++	CHECK_CLOSE(191, (int)pixels[pixel_index + 1], 2);
+ 	CHECK_EQUAL(0, (int)pixels[pixel_index + 2]);
+ 	CHECK_EQUAL(255, (int)pixels[pixel_index + 3]);
+ 
+@@ -109,8 +109,8 @@ TEST(FFmpegReader_Check_Video_File)
+ 
+ 	// Check image properties on scanline 10, pixel 112
+ 	CHECK_EQUAL(0, (int)pixels[pixel_index]);
+-	CHECK_EQUAL(96, (int)pixels[pixel_index + 1]);
+-	CHECK_EQUAL(188, (int)pixels[pixel_index + 2]);
++	CHECK_CLOSE(96, (int)pixels[pixel_index + 1], 1);
++	CHECK_CLOSE(188, (int)pixels[pixel_index + 2], 1);
+ 	CHECK_EQUAL(255, (int)pixels[pixel_index + 3]);
+ 
+ 	// Close reader
+@@ -209,4 +209,3 @@ TEST(FFmpegReader_Multiple_Open_and_Close)
+ 	// Close reader
+ 	r.Close();
+ }
+-
+diff --git a/tests/ImageWriter_Tests.cpp b/tests/ImageWriter_Tests.cpp
+index 107ee39..d10c8bd 100644
+--- a/tests/ImageWriter_Tests.cpp
++++ b/tests/ImageWriter_Tests.cpp
+@@ -73,9 +73,9 @@ TEST(ImageWriter_Test_Gif)
+ 	int pixel_index = 230 * 4; // pixel 230 (4 bytes per pixel)
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(20, (int)pixels[pixel_index]);
+-	CHECK_EQUAL(18, (int)pixels[pixel_index + 1]);
+-	CHECK_EQUAL(11, (int)pixels[pixel_index + 2]);
++	CHECK_CLOSE(20, (int)pixels[pixel_index], 5);
++	CHECK_CLOSE(18, (int)pixels[pixel_index + 1], 2);
++	CHECK_CLOSE(11, (int)pixels[pixel_index + 2], 2);
+ 	CHECK_EQUAL(255, (int)pixels[pixel_index + 3]);
+ }
+-#endif
+\ No newline at end of file
++#endif
+diff --git a/tests/Timeline_Tests.cpp b/tests/Timeline_Tests.cpp
+index 8c81579..4d861a6 100644
+--- a/tests/Timeline_Tests.cpp
++++ b/tests/Timeline_Tests.cpp
+@@ -119,8 +119,8 @@ TEST(Timeline_Check_Two_Track_Video)
+ 	int pixel_index = 230 * 4; // pixel 230 (4 bytes per pixel)
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(21, (int)f->GetPixels(pixel_row)[pixel_index]);
+-	CHECK_EQUAL(191, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
++	CHECK_CLOSE(21, (int)f->GetPixels(pixel_row)[pixel_index], 2);
++	CHECK_CLOSE(191, (int)f->GetPixels(pixel_row)[pixel_index + 1], 2);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+@@ -128,17 +128,17 @@ TEST(Timeline_Check_Two_Track_Video)
+ 	f = t.GetFrame(2);
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(176, (int)f->GetPixels(pixel_row)[pixel_index]);
++	CHECK_CLOSE(176, (int)f->GetPixels(pixel_row)[pixel_index], 1);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
+-	CHECK_EQUAL(186, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
++	CHECK_CLOSE(186, (int)f->GetPixels(pixel_row)[pixel_index + 2], 1);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+ 	// Get frame
+ 	f = t.GetFrame(3);
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(23, (int)f->GetPixels(pixel_row)[pixel_index]);
+-	CHECK_EQUAL(190, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
++	CHECK_CLOSE(23, (int)f->GetPixels(pixel_row)[pixel_index], 1);
++	CHECK_CLOSE(190, (int)f->GetPixels(pixel_row)[pixel_index + 1], 2);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+@@ -146,8 +146,8 @@ TEST(Timeline_Check_Two_Track_Video)
+ 	f = t.GetFrame(24);
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(186, (int)f->GetPixels(pixel_row)[pixel_index]);
+-	CHECK_EQUAL(106, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
++	CHECK_CLOSE(186, (int)f->GetPixels(pixel_row)[pixel_index], 1);
++	CHECK_CLOSE(106, (int)f->GetPixels(pixel_row)[pixel_index + 1], 1);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+@@ -155,8 +155,8 @@ TEST(Timeline_Check_Two_Track_Video)
+ 	f = t.GetFrame(5);
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(23, (int)f->GetPixels(pixel_row)[pixel_index]);
+-	CHECK_EQUAL(190, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
++	CHECK_CLOSE(23, (int)f->GetPixels(pixel_row)[pixel_index], 1);
++	CHECK_CLOSE(190, (int)f->GetPixels(pixel_row)[pixel_index + 1], 2);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+@@ -165,17 +165,17 @@ TEST(Timeline_Check_Two_Track_Video)
+ 
+ 	// Check image properties
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index]);
+-	CHECK_EQUAL(94, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
+-	CHECK_EQUAL(186, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
++	CHECK_CLOSE(94, (int)f->GetPixels(pixel_row)[pixel_index + 1], 1);
++	CHECK_CLOSE(186, (int)f->GetPixels(pixel_row)[pixel_index + 2], 1);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+ 	// Get frame
+ 	f = t.GetFrame(4);
+ 
+ 	// Check image properties
+-	CHECK_EQUAL(176, (int)f->GetPixels(pixel_row)[pixel_index]);
++	CHECK_CLOSE(176, (int)f->GetPixels(pixel_row)[pixel_index], 1);
+ 	CHECK_EQUAL(0, (int)f->GetPixels(pixel_row)[pixel_index + 1]);
+-	CHECK_EQUAL(186, (int)f->GetPixels(pixel_row)[pixel_index + 2]);
++	CHECK_CLOSE(186, (int)f->GetPixels(pixel_row)[pixel_index + 2], 1);
+ 	CHECK_EQUAL(255, (int)f->GetPixels(pixel_row)[pixel_index + 3]);
+ 
+ 	// Close reader
+-- 
+2.21.0
+

gnu/packages/patches/lyx-2.2.3-fix-test.patch

@@ -1,13 +0,0 @@
-See https://www.lyx.org/trac/ticket/10800#comment:17
-diff --git a/src/tex2lyx/test/test-structure.lyx.lyx b/src/tex2lyx/test/test-structure.lyx.lyx
-index feff755cd2..2c7f2ace5c 100644
---- a/src/tex2lyx/test/test-structure.lyx.lyx
-+++ b/src/tex2lyx/test/test-structure.lyx.lyx
-@@ -212,7 +212,7 @@ This causes the
- \begin_inset Flex Flex:Strong
- status collapsed
- 
--\begin_layout Standard
-+\begin_layout Plain Layout
- logikalmkup
- \end_layout

gnu/packages/patches/thermald-make-int-max32-visible.patch

@@ -0,0 +1,24 @@
+From 5fb947886bf1e40475edf930fb2b284c24c8cb9a Mon Sep 17 00:00:00 2001
+From: Sanel Zukan <karijes@users.sourceforge.net>
+Date: Sun, 23 Dec 2018 00:04:34 +0100
+Subject: [PATCH] Make sure INT_MAX32 is visible.
+
+---
+ src/thd_trip_point.h | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/src/thd_trip_point.h b/src/thd_trip_point.h
+index 0eedc95..89eb083 100644
+--- a/src/thd_trip_point.h
++++ b/src/thd_trip_point.h
+@@ -29,6 +29,10 @@
+ #include "thd_sys_fs.h"
+ #include "thd_preference.h"
+ #include "thd_cdev.h"
++
++#define __STDC_LIMIT_MACROS
++#include <stdint.h>
++
+ #include <time.h>
+ #include <vector>
+ #include <algorithm>    // std::sort

gnu/packages/python-web.scm

@@ -600,7 +600,9 @@ for clients and servers.")
     (build-system python-build-system)
     (arguments
      ;; Python 3 support is in `python3-openid`, a separate package.
-     `(#:python ,python-2))
+     `(#:python ,python-2
+       ;; Tests aren't initialized correctly.
+       #:tests? #f))
     (home-page "https://github.com/openid/python-openid")
     (synopsis "OpenID support for servers and consumers")
     (description "This library provides OpenID authentication for Python, both

gnu/packages/python-xyz.scm

@@ -2802,14 +2802,14 @@ and is very extensible.")
 (define-public python-cython
   (package
     (name "python-cython")
-    (version "0.29.5")
+    (version "0.29.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Cython" version))
        (sha256
         (base32
-         "1wfb68g115gmf3mv23w0hh972b0ll85gpb92ci28x6h997br0llx"))))
+         "1bp7cn0pp5qy63k9hbp4ka34fm01kvysh478phpkhr68npqk6pbc"))))
     (build-system python-build-system)
     ;; we need the full python package and not just the python-wrapper
     ;; because we need libpython3.3m.so
@@ -2841,9 +2841,6 @@ and is very extensible.")
 
          (replace 'check
            (lambda _
-             ;; The "with_outer_raising" test fails with Python 3.7.  See
-             ;; https://github.com/cython/cython/issues/2454
-             (delete-file "tests/run/generators_py.py")
              (invoke "python" "runtests.py" "-vv"))))))
     (home-page "http://cython.org/")
     (synopsis "C extensions for Python")
@@ -3262,13 +3259,13 @@ library, libgit2 implements Git plumbing.")
 (define-public python-pyparsing
   (package
     (name "python-pyparsing")
-    (version "2.2.1")
+    (version "2.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32 "06dgd0iilvf8m0ssmfpcbh8l6jf0zkp8adbb84llksg17crfx4zl"))))
+        (base32 "0yk6xl885b91dmlhlsap7x78hk2rdr879fln9anbq6k4ca42djb6"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (arguments
@@ -3537,9 +3534,24 @@ toolkits.")
        ("python-sphinx-gallery" ,python-sphinx-gallery)
        ("python-numpydoc" ,python-numpydoc)
        ("python-ipython" ,python-ipython)
+       ("python-ipykernel" ,python-ipykernel)
        ("python-mock" ,python-mock)
        ("graphviz" ,graphviz)
-       ("texlive" ,texlive)
+       ("texlive" ,(texlive-union (list texlive-latex-amsfonts
+                                        texlive-latex-amsmath
+                                        texlive-latex-enumitem
+                                        texlive-latex-expdlist
+                                        texlive-latex-geometry
+                                        texlive-latex-preview
+                                        texlive-latex-type1cm
+                                        texlive-latex-ucs
+
+                                        texlive-generic-pdftex
+
+                                        texlive-fonts-amsfonts
+                                        texlive-fonts-ec
+                                        texlive-fonts-adobe-times
+                                        texlive-fonts-txfonts)))
        ("texinfo" ,texinfo)
        ,@(package-native-inputs python-matplotlib)))
     (arguments
@@ -3549,15 +3561,24 @@ toolkits.")
          (replace 'build
            (lambda _
              (chdir "doc")
-             ;; Produce pdf in 'A4' format.
+             (setenv "PYTHONPATH"
+                     (string-append (getenv "PYTHONPATH")
+                                    ":" (getcwd) "/../examples/units"))
              (substitute* "conf.py"
-               (("latex_paper_size = 'letter'") "")
+               ;; Don't use git.
-               ;; latex_paper_size is deprecated -> set paper size using
+               (("^SHA = check_output.*")
-               ;; latex_elements
+                (string-append "SHA = \"" ,version "\"\n"))
-               (("latex_elements\\['pointsize'\\] = '11pt'" match)
+               ;; Don't fetch intersphinx files from the Internet
-                ;; insert at a point where latex_elements{} is defined:
+               (("^explicit_order_folders" m)
-                (string-append match "\nlatex_elements['papersize'] = 'a4paper'")))
+                (string-append "intersphinx_mapping = {}\n" m))
-             (invoke "make" "SPHINXBUILD=sphinx-build" "html" "latex" "texinfo")))
+               (("'sphinx.ext.intersphinx',") "")
+               ;; Disable URL embedding which requires internet access.
+               (("'https://docs.scipy.org/doc/numpy'") "None")
+               (("'https://docs.scipy.org/doc/scipy/reference'") "None"))
+             (invoke "make"
+                     "SPHINXBUILD=sphinx-build"
+                     "SPHINXOPTS=" ; don't abort on warnings
+                     "html" "texinfo")))
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((data (string-append (assoc-ref outputs "out") "/share"))
@@ -3575,12 +3596,9 @@ toolkits.")
                     (string-append "@image{matplotlib-figures/" file)))
                  (symlink (string-append html "/_images")
                           "./matplotlib-figures")
-                 (system* "makeinfo" "--no-split"
+                 (invoke "makeinfo" "--no-split"
-                          "-o" "matplotlib.info" "matplotlib.texi"))
+                         "-o" "matplotlib.info" "matplotlib.texi"))
-               (copy-file "build/texinfo/matplotlib.info"
+               (install-file "build/texinfo/matplotlib.info" info))
-                          (string-append info "/matplotlib.info"))
-               (copy-file "build/latex/Matplotlib.pdf"
-                          (string-append doc "/Matplotlib.pdf")))
              #t)))))
     (home-page (package-home-page python-matplotlib))
     (synopsis "Documentation for the python-matplotlib package")
@@ -14643,14 +14661,14 @@ append on old values.  Partd excels at shuffling operations.")
 (define-public python-dask
   (package
     (name "python-dask")
-    (version "1.0.0")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dask" version))
        (sha256
         (base32
-         "1xwz8h020ipwav2p5gcq9pskya1cvzd6hjyvd06dvr3w5lxlmym1"))))
+         "03ykmq46q2hh7mn68vcxkgylybjaj3r0kfspaiymdmqmjzpjivr5"))))
     (build-system python-build-system)
     ;; A single test out of 5000+ fails.  This test is marked as xfail when
     ;; pytest-xdist is used.

gnu/packages/rails.scm

@@ -413,6 +413,34 @@ application bootup, plugins, generators, and Rake tasks.")
     "https://github.com/rails/sprockets-rails")
    (license license:expat)))
 
+(define-public ruby-with-advisory-lock
+  (package
+    (name "ruby-with-advisory-lock")
+    (version "4.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "with_advisory_lock" version))
+       (sha256
+        (base32
+         "1k37hxgmaqgsd54gplm5xim9nw3ghvqsbzaw7q4q64ha1nbd9a41"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; TODO Tests require a running MySQL service
+    (propagated-inputs
+     `(("ruby-activerecord" ,ruby-activerecord)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-yard" ,ruby-yard)
+       ("ruby-mysql2" ,ruby-mysql2)))
+    (synopsis "Advisory locking for ActiveRecord")
+    (description
+     "The With advisory lock gem adds advisory locking to ActiveRecord for
+PostgreSQL and MySQL.  SQLite is also supported, but this uses the filesystem
+for locks.")
+    (home-page "https://closuretree.github.io/with_advisory_lock/")
+    (license license:expat)))
+
 (define-public ruby-rails
   (package
    (name "ruby-rails")

gnu/packages/ruby.scm

@@ -10,6 +10,7 @@
 ;;; Copyright © 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2017, 2018, 2019 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2018 Alex Vong <alexvong1995@gmail.com>
 ;;;
@@ -34,6 +35,7 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dbm)
   #:use-module (gnu packages rails)
@@ -645,13 +647,13 @@ expectations and mocks frameworks.")
 (define-public bundler
   (package
     (name "bundler")
-    (version "1.15.4")
+    (version "1.17.3")
     (source (origin
               (method url-fetch)
               (uri (rubygems-uri "bundler" version))
               (sha256
                (base32
-                "0wl4r7wbwdq68xidfv4hhzfb1spb6lmhbspwlzrg4pf1l6ipxlgs"))))
+                "0ln3gnk7cls81gwsbxvrmlidsfd78s6b2hzlm4d4a9wbaidzfjxw"))))
     (build-system ruby-build-system)
     (arguments
      '(#:tests? #f)) ; avoid dependency cycles
@@ -1172,6 +1174,133 @@ complexity.")
     (home-page "https://github.com/ThoughtWorksStudios/saikuro_treemap")
     (license license:expat)))
 
+(define-public ruby-oauth2
+  (package
+    (name "ruby-oauth2")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "oauth2" version))
+       (sha256
+        (base32
+         "0av6nlb5y2sm6m8fx669ywrqa9858yqaqfqzny75nqp3anag89qh"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (propagated-inputs
+     `(("ruby-faraday" ,ruby-faraday)
+       ("ruby-jwt" ,ruby-jwt)
+       ("ruby-multi-json" ,ruby-multi-json)
+       ("ruby-multi-xml" ,ruby-multi-xml)
+       ("ruby-rack" ,ruby-rack)))
+    (synopsis "Ruby wrapper for the OAuth 2.0")
+    (description
+     "This package provides a Ruby wrapper for the OAuth 2.0 protocol built
+with a similar style to the original OAuth spec.")
+    (home-page "https://github.com/oauth-xx/oauth2")
+    (license license:expat)))
+
+(define-public ruby-omniauth
+  (package
+    (name "ruby-omniauth")
+    (version "1.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "omniauth" version))
+       (sha256
+        (base32
+         "1p16h1rp8by05k8gfw17xjhgwp60dk8qmj1xalv1n23kmxfsxb1x"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (propagated-inputs
+     `(("ruby-hashie" ,ruby-hashie)
+       ("ruby-rack" ,ruby-rack)))
+    (synopsis "Generalized Rack framework for multiple-provider authentication")
+    (description
+     "This package provides a generalized Rack framework for multiple-provider
+authentication.")
+    (home-page "https://github.com/omniauth/omniauth")
+    (license license:expat)))
+
+(define-public ruby-omniauth-oauth2
+  (package
+    (name "ruby-omniauth-oauth2")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "omniauth-oauth2" version))
+       (sha256
+        (base32
+         "11mi36l9d97r77q99jnafdc1yaa0a9wahhpp7dj7ank8q52g7g79"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-unnecessary-dependencies
+           (lambda _
+             ;; The coveralls gem submits coverage information to an online
+             ;; service, and is unnecessary when running the tests
+             (substitute* "Gemfile"
+               ((".*coveralls\"") ""))
+             (substitute* "spec/helper.rb"
+               (("require \"coveralls\"") "")
+               (("Coveralls::SimpleCov::Formatter") ""))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-oauth2" ,ruby-oauth2)
+       ("ruby-omniauth" ,ruby-omniauth)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)
+       ("ruby-simplecov" ,ruby-simplecov)
+       ("ruby-rack-test" ,ruby-rack-test)
+       ("ruby-webmock" ,ruby-webmock-2)))
+    (synopsis "Abstract OAuth2 strategy for OmniAuth")
+    (description
+     "This library provides a generic OAuth2 strategy for OmniAuth.  It
+doesn't provide a way to gather user information, so should be used as a
+building block for authentication strategies.")
+    (home-page "https://github.com/omniauth/omniauth-oauth2")
+    (license license:expat)))
+
+(define-public ruby-open4
+  (package
+  (name "ruby-open4")
+  (version "1.3.4")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (rubygems-uri "open4" version))
+      (sha256
+        (base32
+          "1cgls3f9dlrpil846q0w7h66vsc33jqn84nql4gcqkk221rh7px1"))))
+  (build-system ruby-build-system)
+  (arguments
+   '(#:phases
+     (modify-phases %standard-phases
+       (add-after 'unpack 'patch
+         (lambda _
+           (substitute* "rakefile"
+             ;; Update the Rakefile so it works
+             (("-rubygems") "-rrubygems")
+             (("Config") "RbConfig"))
+           #t))
+       (add-before 'check 'set-LIB
+         (lambda _
+           ;; This is used in the rakefile when running the tests
+           (setenv "LIB" "open4")
+           #t)))))
+  (synopsis "Open child processes from Ruby and manage them easily")
+  (description
+    "@code{Open4} is a Ruby library to run child processes and manage their
+input and output.")
+  (home-page "https://github.com/ahoward/open4")
+  (license license:ruby)))
+
 (define-public ruby-options
   (package
     (name "ruby-options")
@@ -1291,6 +1420,31 @@ the GNOME Libxml2 XML toolkit.")
     (home-page "https://xml4r.github.com/libxml-ruby")
     (license license:expat)))
 
+(define-public ruby-lino
+  (package
+    (name "ruby-lino")
+    (version "1.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "lino" version))
+       (sha256
+        (base32
+         "11d29g0fk372b9fcpyr0k6hxm2b4j4igpysmi542hgbbgqgp9cd3"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (propagated-inputs
+     `(("ruby-hamster" ,ruby-hamster)
+       ("ruby-open4" ,ruby-open4)))
+    (synopsis "Build and execute commands in Ruby")
+    (description
+     "@code{Lino} provides an interface to run external commands.  It provides
+an interface to add options as well as managing the standard input, output and
+error streams.")
+    (home-page "https://github.com/tobyclemson/lino")
+    (license license:expat)))
+
 (define-public ruby-xml-simple
   (package
     (name "ruby-xml-simple")
@@ -1353,6 +1507,63 @@ same log file.")
     (home-page "https://github.com/bdurand/lumberjack")
     (license license:expat)))
 
+(define-public ruby-rbnacl
+  (package
+    (name "ruby-rbnacl")
+    (version "6.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "rbnacl" version))
+       (sha256
+        (base32
+         "0ajxy5kj2jw09wdsla3jmha8w07vj5l14288xr9djpl327g3lzhn"))))
+    (build-system ruby-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-unnecessary-dependencies
+           (lambda _
+             ;; Coveralls relates to a network service, and Rubocop to code
+             ;; linting and both are unnecessary to run the tests
+             (substitute* "Gemfile"
+               ((".*rubocop.*") "\n")
+               ((".*guard-rspec.*") "\n")
+               ((".*coveralls.*") "\n"))
+             (substitute* "spec/spec_helper.rb"
+               (("require \"coveralls\"") "")
+               (("Coveralls.wear!") ""))
+             #t))
+         (add-after 'unpack 'use-libsodium-from-store
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* '("lib/rbnacl/init.rb"
+                            "lib/rbnacl/sodium.rb")
+               (("ffi_lib \\[.+\\]")
+                (string-append "ffi_lib [\""
+                               (assoc-ref inputs "libsodium") "/lib/libsodium.so"
+                               "\"]")))
+             #t))
+         ;; Run Rspec directly to avoid the Rubocop dependency in the Rakefile
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "rspec"))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-ffi" ,ruby-ffi)))
+    (inputs
+     `(("libsodium" ,libsodium)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)))
+    (synopsis "Ruby FFI binding to libsodium")
+    (description
+     "This package provides Ruby FFI bindings to the Networking and
+Cryptography (NaCl) library, also known as libsodium.  This provides a
+high-level toolkit for building cryptographic systems and protocols.")
+    (home-page "https://github.com/crypto-rb/rbnacl")
+    (license license:expat)))
+
 (define-public ruby-nenv
   (package
     (name "ruby-nenv")
@@ -1527,6 +1738,79 @@ failure.")
     (home-page "https://github.com/thekompanee/fuubar")
     (license license:expat)))
 
+(define-public ruby-haml
+  (package
+    (name "ruby-haml")
+    (version "5.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "haml" version))
+       (sha256
+        (base32
+         "1q0a9fvqh8kn6wm97fcks6qzbjd400bv8bx748w8v87m7p4klhac"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (propagated-inputs
+     `(("ruby-tilt" ,ruby-tilt)
+       ("ruby-temple" ,ruby-temple)))
+    (synopsis "Haml is a Ruby library to generate HTML documents")
+    (description
+     "@acronym{Haml, HTML Abstraction Markup Language} is a layer on top of
+HTML or XML that is designed to express the structure of documents using
+indentation rather than closing tags.  It was originally envisioned as a
+plugin for Ruby on Rails, but it can function as a stand-alone templating
+engine.")
+    (home-page "http://haml.info/")
+    (license license:expat)))
+
+(define-public ruby-hamster
+  (package
+  (name "ruby-hamster")
+  (version "3.0.0")
+  (source
+    (origin
+      (method url-fetch)
+      (uri (rubygems-uri "hamster" version))
+      (sha256
+        (base32
+          "1n1lsh96vnyc1pnzyd30f9prcsclmvmkdb3nm5aahnyizyiy6lar"))))
+  (build-system ruby-build-system)
+  (arguments
+   '(#:phases
+     (modify-phases %standard-phases
+       (add-after 'unpack 'remove-unnecessary-dependencies
+         (lambda _
+           ;; pry is a debugging tool, and is unnecessary when running the
+           ;; tests
+           (substitute* "spec/lib/hamster/vector/insert_spec.rb"
+             (("require 'pry'") ""))
+           (substitute* "spec/spec_helper.rb"
+             (("require \"pry\"") "")
+             ;; CodeClimate is an online service, and is unnecessary for
+             ;; running the tests
+             (("require \"codeclimate-test-reporter\"") "")
+             (("CodeClimate.*\n") ""))
+           #t))
+       ;; No Rakefile is included, so run rspec directly.
+       (replace 'check
+         (lambda* (#:key tests? #:allow-other-keys)
+           (when tests?
+             (invoke "rspec"))
+           #t)))))
+  (propagated-inputs
+   `(("ruby-concurrent" ,ruby-concurrent)))
+  (native-inputs
+   `(("ruby-rspec" ,ruby-rspec)))
+  (synopsis "Efficient, immutable, thread-safe collection classes for Ruby")
+  (description
+    "Hamster provides 6 persistent data structures: @code{Hash}, @code{Vector},
+@code{Set}, @code{SortedSet}, @code{List}, and @code{Deque} (which works as an
+immutable queue or stack).")
+  (home-page "https://github.com/hamstergem/hamster")
+  (license license:expat)))
+
 (define-public ruby-hashdiff
   (package
     (name "ruby-hashdiff")
@@ -1913,6 +2197,29 @@ localization.")
     (home-page "https://github.com/ruby-gettext/locale")
     (license (list license:lgpl3+ license:ruby))))
 
+(define-public ruby-temple
+  (package
+    (name "ruby-temple")
+    (version "0.8.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "temple" version))
+       (sha256
+        (base32
+         "158d7ygbwcifqnvrph219p7m78yjdjazhykv5darbkms7bxm5y09"))))
+    (build-system ruby-build-system)
+    (native-inputs
+     `(("ruby-tilt" ,ruby-tilt)
+       ("ruby-bacon" ,ruby-bacon)
+       ("ruby-erubis" ,ruby-erubis)))
+    (synopsis "Template compilation framework in Ruby")
+    (description
+     "Temple is an abstraction and framework for compiling templates to pure
+Ruby.")
+    (home-page "https://github.com/judofyr/temple")
+    (license license:expat)))
+
 (define-public ruby-text
   (package
     (name "ruby-text")
@@ -1985,6 +2292,29 @@ use GNU gettext tools for maintenance.")
     (home-page "http://ranguba.org/packnga/")
     (license license:lgpl2.0+)))
 
+(define-public ruby-test-construct
+  (package
+    (name "ruby-test-construct")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "test_construct" version))
+       (sha256
+        (base32
+         "1a2ym3l068d0pxzzr95kvqx87zpdsarxslz9ygd4qfm9frrz0kgj"))))
+    (build-system ruby-build-system)
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-mocha" ,ruby-mocha)
+       ("ruby-rspec" ,ruby-rspec)))
+    (synopsis "Creates temporary files and directories for testing")
+    (description
+     "TestConstruct is a @acronym{DSL, Domain Specific Language} for creating
+temporary files and directories during tests.")
+    (home-page "https://github.com/bhb/test_construct")
+    (license license:expat)))
+
 (define-public ruby-test-unit
   (package
     (name "ruby-test-unit")
@@ -2010,6 +2340,43 @@ It allows writing tests, checking results and automated testing in Ruby.")
     (home-page "https://test-unit.github.io/")
     (license (list license:psfl license:ruby))))
 
+(define-public ruby-markaby
+  (package
+    (name "ruby-markaby")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "markaby" version))
+       (sha256
+        (base32
+         "1j4jc31ycydbkh5h3q6zwidzpavg3g5mbb5lqyaczd3jrq78rd7i"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; Run rspec manually without using the Rakefile, as the versions of
+         ;; Rake and RSpec 2 are incompatible:
+         ;;
+         ;; NoMethodError: undefined method `last_comment'
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "rspec"))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-builder" ,ruby-builder)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec-2)))
+    (synopsis "Write HTML pages in pure Ruby")
+    (description
+     "Markaby allows writing HTML packages in pure Ruby.  This is similar to
+the functionality provided by @acronym{ERB, Embeded Ruby}, but without the
+mixture of HTML and additional ERB syntax.")
+    (home-page "http://markaby.github.io/")
+    (license license:expat)))
+
 (define-public ruby-maruku
   (package
     (name "ruby-maruku")
@@ -2562,6 +2929,40 @@ facilities supporting TDD, BDD, mocking, and benchmarking.")
              (delete-file "test/minitest/test_minitest_spec.rb")
              #t)))))))
 
+(define-public ruby-minitest-around
+  (package
+    (name "ruby-minitest-around")
+    (version "0.5.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "minitest-around" version))
+       (sha256
+        (base32
+         "15ywnqx0719jl9c25yqfshmwcir57i5f4hr1ra9v9vay9ylcwndr"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'extract-gemspec 'remove-unnecessary-dependency-versions
+           (lambda _
+             (substitute* "minitest-around.gemspec"
+               (("%q<cucumber>.*") "%q<cucumber>, [\">= 0\"])\n"))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-minitest" ,ruby-minitest)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-cucumber" ,ruby-cucumber)
+       ("ruby-bump" ,ruby-bump)
+       ("ruby-test-construct" ,ruby-test-construct)))
+    (synopsis "Run code around tests in Minitest")
+    (description
+     "This library provides a way to run code around tests in Minitest,
+written using either the unit test or spec style.")
+    (home-page "https://github.com/splattael/minitest-around")
+    (license license:expat)))
+
 (define-public ruby-minitest-sprint
   (package
     (name "ruby-minitest-sprint")
@@ -2934,6 +3335,27 @@ options and parsing command line flags.")
                (base32
                 "00w8g3j7k7kl8ri2cf1m58ckxk8rn350gp4chfscmgv6pq1spk3n"))))))
 
+(define-public ruby-multi-xml
+  (package
+    (name "ruby-multi-xml")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "multi_xml" version))
+       (sha256
+        (base32
+         "0lmd4f401mvravi1i1yq7b2qjjli0yq7dfc4p1nj5nwajp7r6hyj"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (synopsis "Swappable XML backends for Ruby")
+    (description
+     "@code{MultiXml} provides swappable XML backends utilizing either LibXML,
+Nokogiri, Ox, or REXML.")
+    (home-page "https://github.com/sferik/multi_xml")
+    (license license:expat)))
+
 (define-public ruby-multipart-post
   (package
     (name "ruby-multipart-post")
@@ -3398,6 +3820,52 @@ file or directories are modified.")
     (home-page "http://guardgem.org/")
     (license license:expat)))
 
+(define-public ruby-tilt
+  (package
+    (name "ruby-tilt")
+    (version "2.0.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "tilt" version))
+       (sha256
+        (base32
+         "0ca4k0clwf0rkvy7726x4nxpjxkpv67w043i39saxgldxd97zmwz"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-some-dependencies
+           (lambda _
+             (substitute* "Gemfile"
+               ;; TODO ronn is used for generating the manual
+               (("gem 'ronn'.*") "\n")
+               ;; ruby-haml has a runtime dependency on ruby-tilt, so don't
+               ;; pass it in as a native-input
+               (("gem 'haml'.*") "\n")
+               ;; TODO Not all of these gems are packaged for Guix yet:
+               ;; less, coffee-script, livescript, babel-transpiler,
+               ;; typescript-node
+               (("if can_execjs") "if false")
+               ;; Disable the secondary group to reduce the number of
+               ;; dependencies. None of the normal approaches work, so patch
+               ;; the Gemfile instead.
+               (("group :secondary") "[].each"))
+             #t)))))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-yard" ,ruby-yard)
+       ("ruby-builder" ,ruby-builder)
+       ("ruby-erubis" ,ruby-erubis)
+       ("ruby-markaby" ,ruby-markaby)
+       ("ruby-sassc" ,ruby-sassc)))
+    (synopsis "Generic interface to multiple Ruby template engines")
+    (description
+     "Tilt is a thin interface over a number of different Ruby template
+engines in an attempt to make their usage as generic as possible.")
+    (home-page "https://github.com/rtomayko/tilt/")
+    (license license:expat)))
+
 (define-public ruby-thread-safe
   (package
     (name "ruby-thread-safe")
@@ -3706,6 +4174,29 @@ of terminal output.")
     ;; There is no mention of the "or later" clause.
     (license license:gpl2)))
 
+(define-public ruby-terraform
+  (package
+  (name "ruby-terraform")
+  (version "0.22.0")
+  (source
+   (origin
+     (method url-fetch)
+     (uri (rubygems-uri "ruby-terraform" version))
+     (sha256
+      (base32
+       "13zjkp71cd19j2ds2h9rqwcfr1zdg5nsh63p89l6qcsc9z39z324"))))
+  (build-system ruby-build-system)
+  (arguments
+   '(#:tests? #f)) ; No included tests
+  (propagated-inputs
+   `(("ruby-lino" ,ruby-lino)))
+  (synopsis "Ruby wrapper around the Terraform command line interface")
+  (description
+   "This package provides a Ruby wrapper around the Terraform command line
+interface so that Terraform can be more easily invoked from Ruby code.")
+  (home-page "https://github.com/infrablocks/ruby_terraform")
+  (license license:expat)))
+
 (define-public ruby-pstree
   (package
     (name "ruby-pstree")
@@ -3843,6 +4334,44 @@ a native C extension.")
     (home-page "https://flori.github.com/json")
     (license license:ruby)))
 
+(define-public ruby-jwt
+  (package
+    (name "ruby-jwt")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "jwt" version))
+       (sha256
+        (base32
+         "1w0kaqrbl71cq9sbnixc20x5lqah3hs2i93xmhlfdg2y3by7yzky"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:test-target "test"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-unnecessary-dependencies
+           (lambda _
+             (substitute* "spec/spec_helper.rb"
+               (("require 'simplecov.*") "\n")
+               ;; Use [].each to disable running the SimpleCov configuration
+               ;; block
+               (("SimpleCov\\.configure") "[].each")
+               (("require 'codeclimate-test-reporter'") "")
+               (("require 'codacy-coverage'") "")
+               (("Codacy::Reporter\\.start") ""))
+             #t)))))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec)
+       ("ruby-rbnacl" ,ruby-rbnacl)))
+    (synopsis "Ruby implementation of the JSON Web Token standard")
+    (description
+     "This package provides a pure Ruby implementation of the RFC 7519 OAuth
+@acronym{JWT, JSON Web Token} standard.")
+    (home-page "https://github.com/jwt/ruby-jwt")
+    (license license:expat)))
+
 ;; Even though this package only provides bindings for a Mac OSX API it is
 ;; required by "ruby-listen" at runtime.
 (define-public ruby-rb-fsevent
@@ -5518,6 +6047,77 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} on CRuby and
     (home-page "https://github.com/knu/ruby-unf")
     (license license:bsd-2)))
 
+(define-public ruby-warden
+  (package
+    (name "ruby-warden")
+    (version "1.2.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "warden" version))
+       (sha256
+        (base32
+         "1fr9n9i9r82xb6i61fdw4xgc7zjv7fsdrr4k0njchy87iw9fl454"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (propagated-inputs
+     `(("ruby-rack" ,ruby-rack)))
+    (synopsis "Rack middleware providing authentication")
+    (description
+     "Warden is a Rack-based middleware that provides a mechanism for
+authentication in Ruby web applications.")
+    (home-page "https://github.com/wardencommunity/warden")
+    (license license:expat)))
+
+(define-public ruby-warden-oauth2
+  (package
+    (name "ruby-warden-oauth2")
+    (version "0.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "warden-oauth2" version))
+       (sha256
+        (base32
+         "1z9154lvzrnnfjbjkmirh4n811nygp6pm2fa6ikr7y1ysa4zv3cz"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:test-target "spec"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-unnecessary-dependencies
+           (lambda _
+             (substitute* "Gemfile"
+               ;; All of these gems relate to development, and are unnecessary
+               ;; when running the tests
+               (("gem 'guard-bundler'") "")
+               (("gem 'guard'") "")
+               (("gem 'guard-rspec'") "")
+               (("gem 'rb-fsevent'") "")
+               (("gem 'pry'") "")
+               (("gem 'growl'") ""))
+             #t))
+         ;; The test suite doesn't work with rspec@2, and this is incompatible
+         ;; with the current version of Rake, so invoke Rspec directly
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "bundle" "exec" "rspec"))
+             #t)))))
+    (propagated-inputs
+     `(("ruby-warden" ,ruby-warden)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-rspec" ,ruby-rspec-2)
+       ("ruby-rack-test" ,ruby-rack-test)))
+    (synopsis "OAuth 2.0 strategies for Warden")
+    (description
+     "This library extends Warden to support OAuth 2.0 authorized API
+requests.")
+    (home-page "https://github.com/opperator/warden-oauth2")
+    (license license:expat)))
+
 (define-public ruby-webmock-2
   (package
     (name "ruby-webmock")
@@ -5985,6 +6585,27 @@ requirement specifications systems like Cucumber.")
     (home-page "https://rubyworks.github.io/qed")
     (license license:bsd-2)))
 
+(define-public ruby-que
+  (package
+    (name "ruby-que")
+    (version "1.0.0.beta3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "que" version))
+       (sha256
+        (base32
+         "0gr9pb814d4qj3ds98g6cjrdk7wv0yg8aqbm7c1lmgl87jkg8q04"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:tests? #f)) ; No included tests
+    (synopsis "Job queue using PostgreSQL written in Ruby")
+    (description
+     "This package provides a job queue that uses PostgreSQL for storing jobs
+and locking between worker processes.")
+    (home-page "https://github.com/chanks/que")
+    (license license:expat)))
+
 (define-public ruby-ae
   (package
     (name "ruby-ae")
@@ -6927,6 +7548,81 @@ the @file{spec} directory.")
 features that don't exist yet like variables, nesting, mixins and inheritance.")
     (license license:expat)))
 
+(define-public ruby-sassc
+  (package
+    (name "ruby-sassc")
+    (version "2.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (rubygems-uri "sassc" version))
+       (sha256
+        (base32
+         "1sr4825rlwsrl7xrsm0sgalcpf5zgp4i56dbi3qxfa9lhs8r6zh4"))))
+    (build-system ruby-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         ;; TODO: This would be better as a snippet, but the ruby-build-system
+         ;; doesn't seem to support that
+         (add-after 'unpack 'remove-libsass
+           (lambda _
+             (delete-file-recursively "ext")
+             #t))
+         (add-after 'unpack 'dont-check-the-libsass-version
+           (lambda _
+             (substitute* "test/native_test.rb"
+               (("assert_equal.*Native\\.version") ""))
+             #t))
+         (add-after 'unpack 'remove-git-from-gemspec
+           (lambda _
+             (substitute* "sassc.gemspec"
+               (("`git ls-files -z`") "`find . -type f -print0 |sort -z`")
+               (("`git submodule --quiet foreach pwd`") "''"))
+             #t))
+         (add-after 'unpack 'remove-extensions-from-gemspec
+           (lambda _
+             (substitute* "sassc.gemspec"
+               (("\\[\"ext/Rakefile\"\\]") "[]"))
+             #t))
+         (add-after 'unpack 'fix-Rakefile
+           (lambda _
+             (substitute* "Rakefile"
+               (("test: 'libsass:compile'") ":test"))
+             #t))
+         (add-after 'unpack 'remove-unnecessary-dependencies
+           (lambda _
+             (substitute* "test/test_helper.rb"
+               (("require \"pry\"") ""))
+             #t))
+         (add-before 'build 'patch-native.rb
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "lib/sassc/native.rb"
+               ((".*gem_root = spec.gem_dir") "")
+               (("ffi_lib .*\n")
+                (string-append
+                 "ffi_lib '" (assoc-ref inputs "libsass") "/lib/libsass.so'")))
+             #t))
+         ;; The gemspec still references the libsass files, so just keep the
+         ;; one in the gem.
+         (delete 'extract-gemspec))))
+    (propagated-inputs
+     `(("ruby-ffi" ,ruby-ffi)
+       ("ruby-rake" ,ruby-rake)))
+    (inputs
+     `(("libsass" ,libsass)))
+    (native-inputs
+     `(("bundler" ,bundler)
+       ("ruby-minitest-around" ,ruby-minitest-around)
+       ("ruby-test-construct" ,ruby-test-construct)))
+    (synopsis "Use libsss from Ruby")
+    (description
+     "This library provides Ruby q@acronym{FFI, Foreign Function Interface}
+bindings to the libsass library.  This enables rendering
+@acronym{SASS,Syntactically awesome style sheets} from Ruby code.")
+    (home-page "https://github.com/sass/sassc-ruby")
+    (license license:expat)))
+
 (define-public ruby-jekyll-sass-converter
   (package
     (name "ruby-jekyll-sass-converter")

gnu/packages/samba.scm

@@ -33,6 +33,7 @@
   #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages check)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages cups)
@@ -240,14 +241,14 @@ Desktops into Active Directory environments using the winbind daemon.")
 (define-public talloc
   (package
     (name "talloc")
-    (version "2.1.14")
+    (version "2.1.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/talloc/talloc-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1kk76dyav41ip7ddbbf04yfydb4jvywzi2ps0z2vla56aqkn11di"))))
+                "1aajda08yf7njgvg6r21ccxlvkarb9bwvf4jqh8yn3871a1zcnqr"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -260,8 +261,10 @@ Desktops into Active Directory environments using the winbind daemon.")
              (let ((out (assoc-ref outputs "out")))
                (invoke "./configure"
                        (string-append "--prefix=" out))))))))
+    (native-inputs
+     `(("which" ,which)))
     (inputs
-     `(("python" ,python-2)))
+     `(("python" ,python)))
     (home-page "https://talloc.samba.org")
     (synopsis "Hierarchical, reference counted memory pool system")
     (description
@@ -288,7 +291,8 @@ destructors.  It is the core memory allocator used in Samba.")
            (replace 'build
              (lambda _
                (invoke "gcc" "-c" "-Ibin/default" "-I" "lib/replace"
-                       "-I." "-Wall" "-g" "talloc.c")
+                       "-I." "-Wall" "-g" "-D__STDC_WANT_LIB_EXT1__=1"
+                       "talloc.c")
                (invoke "ar" "rc" "libtalloc.a" "talloc.o")))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
@@ -304,14 +308,14 @@ destructors.  It is the core memory allocator used in Samba.")
 (define-public tevent
   (package
     (name "tevent")
-    (version "0.9.37")
+    (version "0.9.39")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/tevent/tevent-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1q77vbjic2bb79li2a54ffscnrnwwww55fbpry2kgh7acpnlb0qn"))))
+                "1rnln76ngd2b8lgqvfa9iscy6jizwycj85nfp9zd46b1c760z3gn"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -325,7 +329,8 @@ destructors.  It is the core memory allocator used in Samba.")
                        "--bundled-libraries=NONE")))))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
-       ("python" ,python-2)))
+       ("python" ,python)
+       ("which" ,which)))
     (propagated-inputs
      `(("talloc" ,talloc))) ; required by tevent.pc
     (synopsis "Event system library")
@@ -339,14 +344,14 @@ many event types, including timers, signals, and the classic file descriptor eve
 (define-public ldb
   (package
     (name "ldb")
-    (version "1.4.3")
+    (version "1.6.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.samba.org/ftp/ldb/ldb-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "07vacwr941y2x31yl9knsr2rpffz5pqabvqds6sbyngqxy4r785c"))
+                "1kiwlra6nfkb5n870k2db41jrm59bq9lxqmil4v7ignblgsdfdwb"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -376,7 +381,8 @@ many event types, including timers, signals, and the classic file descriptor eve
     (native-inputs
      `(("cmocka" ,cmocka)
        ("pkg-config" ,pkg-config)
-       ("python" ,python-2)))
+       ("python" ,python)
+       ("which" ,which)))
     (propagated-inputs
      ;; ldb.pc refers to all these.
      `(("talloc" ,talloc)

gnu/packages/sdl.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2015, 2017 Sou Bunnbu <iyzsong@member.fsf.org>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Kei Kebreau <kkebreau@posteo.net>
@@ -117,7 +117,8 @@ joystick, and graphics hardware.")
     (arguments
      (substitute-keyword-arguments (package-arguments sdl)
        ((#:configure-flags flags)
-        `(append '("--disable-wayland-shared")
+        `(append '("--disable-wayland-shared" "--enable-video-kmsdrm"
+                   "--disable-kmsdrm-shared")
                  ,flags))))
     (inputs
      ;; SDL2 needs to be built with ibus support otherwise some systems

gnu/packages/tex.scm

@@ -3,7 +3,7 @@
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
@@ -901,13 +901,17 @@ Computers & Typesetting series.")
                        (string-append (getcwd) ":"
                                       mf "/share/texmf-dist/metafont/base")))
              (mkdir "build")
-             (invoke "mf" "-progname=mf"
+             (for-each (lambda (font)
-                     "-output-directory=build"
+                         (format #t "building font ~a\n" font)
-                     (string-append "\\"
+                         (invoke "mf" "-progname=mf"
-                                    "mode:=ljfour; "
+                                 "-output-directory=build"
-                                    "mag:=1; "
+                                 (string-append "\\"
-                                    "batchmode; "
+                                                "mode:=ljfour; "
-                                    "input manfnt"))))
+                                                "mag:=1; "
+                                                "batchmode; "
+                                                "input " font)))
+                       (find-files "." "(manfnt|logo.+)\\.mf$"))
+             #t))
          (replace 'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
@@ -1006,6 +1010,98 @@ class), line and circle fonts (for use in the picture environment) and LaTeX
 symbol fonts.")
     (license license:lppl1.2+)))
 
+(define-public texlive-latex-mflogo
+  (package
+    (name "texlive-latex-mflogo")
+    (version (number->string %texlive-revision))
+    (source
+     (origin
+       (method svn-fetch)
+       (uri (texlive-ref "latex" "mflogo"))
+       (sha256
+        (base32
+         "15i2ib6nvhf31g1b92c6njf7n0g29znlq7hbfp9ii7qabhcwwvrj"))))
+    (build-system texlive-build-system)
+    (arguments '(#:tex-directory "latex/mflogo"))
+    (home-page "http://www.ctan.org/pkg/mflogo")
+    (synopsis "LaTeX support for Metafont logo fonts")
+    (description
+     "This package provides LaTeX and font definition files to access the
+Knuthian mflogo fonts described in The Metafontbook and to typeset Metafont
+logos in LaTeX documents.")
+    (license license:lppl)))
+
+(define-public texlive-fonts-mflogo-font
+  (package
+    (name "texlive-fonts-mflogo-font")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/fonts/type1/hoekwater/mflogo-font"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "09fsxfpiyxjljkrb52b197728bjnkcnv3bdwm4hl6hf23mbmqadf"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (ice-9 match))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let ((root (string-append (assoc-ref %outputs "out")
+                                    "/share/texmf-dist/"))
+               (pkgs '(("source"    . "fonts/type1/hoekwater/mflogo-font")
+                       ("afm"       . "fonts/afm/hoekwater/mflogo-font")
+                       ("fonts-map" . "fonts/map/dvips/mflogo-font"))))
+           (for-each (match-lambda
+                       ((pkg . dir)
+                        (let ((target (string-append root dir)))
+                          (mkdir-p target)
+                          (copy-recursively (assoc-ref %build-inputs pkg)
+                                            target))))
+                     pkgs)
+           #t))))
+    (native-inputs
+     `(("afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/hoekwater/mflogo-font"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0bx1mfhhzsk9gj1pha36q2rk0jd0y285qm62zgvdvzzzlfnk8sdb"))))
+       ("fonts-map"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/map/dvips/mflogo-font/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-fonts-map-" version "-checkout"))
+           (sha256
+            (base32
+             "044xrrpl8hnvj55cx2ql1ib1bcyr33nzanx5nkwxpai7fb7pg4y6"))))))
+    (home-page "https://www.ctan.org/pkg/mflogo-font")
+    (synopsis "Metafont logo font")
+    (description
+     "These fonts were created in METAFONT by Knuth, for his own publications.
+At some stage, the letters P and S were added, so that the METAPOST logo could
+also be expressed.  The fonts were originally issued (of course) as METAFONT
+source; they have since been autotraced and reissued in Adobe Type 1 format by
+Taco Hoekwater.")
+    (license license:knuth)))
+
 (define-public texlive-fonts-amsfonts
   (package
     (name "texlive-fonts-amsfonts")
@@ -3110,6 +3206,8 @@ BibLaTeX, and is considered experimental.")
                 "0yw6bjfgsli3s1dldsgb7mkr7lnk329cgdjbgs8z2xn59pmmdsn4"))))
     (build-system texlive-build-system)
     (arguments '(#:tex-directory "latex/geometry"))
+    (propagated-inputs
+     `(("texlive-latex-oberdiek" ,texlive-latex-oberdiek))) ;for ifpdf
     (home-page "https://www.ctan.org/pkg/geometry")
     (synopsis "Flexible and complete interface to document dimensions")
     (description
@@ -3649,6 +3747,467 @@ differs from the EC in a number of particulars.")
     (license (license:fsf-free "https://www.tug.org/svn/texlive/tags/\
 texlive-2017.1/Master/texmf-dist/doc/fonts/ec/copyrite.txt"))))
 
+(define-public texlive-fonts-adobe-times
+  (package
+    (name "texlive-fonts-adobe-times")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/fonts/type1/urw/times/"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "15vzyr7favkv1mj00qxr03s89kw78nd066fh69by93272g8p5sgd"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (ice-9 match))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let ((root (string-append (assoc-ref %outputs "out")
+                                    "/share/texmf-dist/"))
+               (pkgs '(("source"        . "fonts/type1/urw/times")
+
+                       ("times-afm"     . "fonts/afm/adobe/times")
+                       ("times-tfm"     . "fonts/tfm/adobe/times")
+                       ("times-vf"      . "fonts/vf/adobe/times")
+
+                       ("urw-afm"       . "fonts/afm/urw/times")
+                       ("urw35vf-tfm"   . "fonts/tfm/urw35vf/times")
+                       ("urw35vf-vf"    . "fonts/vf/urw35vf/times")
+
+                       ("times-tex"     . "tex/latex/times")
+                       ("dvips"         . "dvips/times")
+                       ("fonts-map"     . "fonts/map/dvips/times"))))
+           (for-each (match-lambda
+                       ((pkg . dir)
+                        (let ((target (string-append root dir)))
+                          (mkdir-p target)
+                          (copy-recursively (assoc-ref %build-inputs pkg)
+                                            target))))
+                     pkgs)
+           #t))))
+    (native-inputs
+     `(("times-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/adobe/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "1k7h6vihfc6ri2lq9ggnq2g4zq3qcgq1vd0hr486g9cqrdpys6cy"))))
+       ("times-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/adobe/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "1hbgkjnf5xyganbznwpwszvr3iyk4bzb0ys4hd8ybawp60paadrr"))))
+       ("times-vf"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/vf/adobe/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-vf-" version "-checkout"))
+           (sha256
+            (base32
+             "18rfspnwdw9r81dy18lb4w96d09b6c4g7y80azwylalkhwdf2lfp"))))
+       ("urw-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/urw/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0g0xpsyn6634g0b4rpd420v7i4gkz3zr12vcy2b8csbcscjvwri5"))))
+       ("urw35vf-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/urw35vf/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw35vf-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "0a4idlvpaqd0ypqgy1xw0rpx8q23bvssg8xq757zzn3zikj0w7pr"))))
+       ("urw35vf-vf"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/vf/urw35vf/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw35vf-vf-" version "-checkout"))
+           (sha256
+            (base32
+             "05mppwxd4c5x0yw50gca726f0ylc1rk8jf0jjkrriixq6rnw03di"))))
+       ("times-tex"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/tex/latex/times"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tex-" version "-checkout"))
+           (sha256
+            (base32
+             "1gmd0x7c3vkvfzgmrsp4866rcdbyimfk3bjr91zaadc41r1i8xrp"))))
+       ("dvips"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/dvips/times/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-dvips-" version "-checkout"))
+           (sha256
+            (base32
+             "1fvqpgqi7bp2q76nf5kmlhsdijxw65arqfy3ax3djwih3yg12mp0"))))
+       ("fonts-map"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/map/dvips/times/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-fonts-map-" version "-checkout"))
+           (sha256
+            (base32
+             "12f00gzs2zgllkm59qdhw2xxj7lvg3p256232f1l275z3pldfqqi"))))))
+    (home-page "https://ctan.org/pkg/urw-base35")
+    (synopsis "URW Base 35 font pack for LaTeX")
+    (description
+     "This package provides a drop-in replacements for the Times font from
+Adobe's basic set.")
+    ;; No license version specified.
+    (license license:gpl3+)))
+
+(define-public texlive-fonts-adobe-palatino
+  (package
+    (name "texlive-fonts-adobe-palatino")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/fonts/type1/urw/palatino/"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "18dw5260c6fy7acxaqwrg3hw04kg63ijq4lkn56q5pa2g6nyylrp"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (ice-9 match))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let ((root (string-append (assoc-ref %outputs "out")
+                                    "/share/texmf-dist/"))
+               (pkgs '(("source"        . "fonts/type1/urw/palatino")
+
+                       ("palatino-afm"  . "fonts/afm/adobe/palatino")
+                       ("palatino-tfm"  . "fonts/tfm/adobe/palatino")
+                       ("palatino-vf"   . "fonts/vf/adobe/palatino")
+
+                       ("urw-afm"       . "fonts/afm/urw/palatino")
+                       ("urw35vf-tfm"   . "fonts/tfm/urw35vf/palatino")
+                       ("urw35vf-vf"    . "fonts/vf/urw35vf/palatino")
+
+                       ("palatino-tex"  . "tex/latex/palatino")
+                       ("dvips"         . "dvips/palatino")
+                       ("fonts-map"     . "fonts/map/dvips/palatino"))))
+           (for-each (match-lambda
+                       ((pkg . dir)
+                        (let ((target (string-append root dir)))
+                          (mkdir-p target)
+                          (copy-recursively (assoc-ref %build-inputs pkg)
+                                            target))))
+                     pkgs)
+           #t))))
+    (native-inputs
+     `(("palatino-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/adobe/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0pxizay730cx7rb9y5bqq9dn1zxx3arc33rmdsn7l29pc51flmmi"))))
+       ("palatino-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/adobe/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "1w1vm0sk9kpsy14yhyf1v1q3c6b97cgbba74g578bcwjlh810mg0"))))
+       ("palatino-vf"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/vf/adobe/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-vf-" version "-checkout"))
+           (sha256
+            (base32
+             "1maqfis8hpybcn9lmm8r2b1g56620lfpsncg0742c3kkjd6dh97h"))))
+       ("urw-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/urw/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0gk0xwy1fs2si5kb1j3dzgm52c8sagv32gd9dmw88m7sgh5qkd87"))))
+       ("urw35vf-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/urw35vf/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw35vf-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "19aq3xwfg7vkf1qzjdxgcvcdqwpvpavq3l25y64xni72qx0kmppz"))))
+       ("urw35vf-vf"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/vf/urw35vf/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw35vf-vf-" version "-checkout"))
+           (sha256
+            (base32
+             "1lkn4p6zimrs0ah6mxsang4bicp8j7xzl016529a3f168an7mdmj"))))
+       ("palatino-tex"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/tex/latex/palatino"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tex-" version "-checkout"))
+           (sha256
+            (base32
+             "0ng9w7i0p1nb51amla32jj86vx6p84m6qc7asam3g4x8w5jf7s27"))))
+       ("dvips"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/dvips/palatino/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-dvips-" version "-checkout"))
+           (sha256
+            (base32
+             "1pdbkfmhx4kk3brh5lg6fyl9ad2kbjmkrhgcx84klnlhq01mfdhb"))))
+       ("fonts-map"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/map/dvips/palatino/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-fonts-map-" version "-checkout"))
+           (sha256
+            (base32
+             "0rg13hyp652hp3gnrj5pbyb84zkqmyi1qnm8c6spcyaq8pm06l0d"))))))
+    (home-page "https://ctan.org/pkg/urw-base35")
+    (synopsis "URW Base 35 font pack for LaTeX")
+    (description
+     "This package provides a drop-in replacements for the Palatino font from
+Adobe's basic set.")
+    ;; No license version specified.
+    (license license:gpl3+)))
+
+(define-public texlive-fonts-adobe-zapfding
+  (package
+    (name "texlive-fonts-adobe-zapfding")
+    (version (number->string %texlive-revision))
+    (source (origin
+              (method svn-fetch)
+              (uri (svn-reference
+                    (url (string-append "svn://www.tug.org/texlive/tags/"
+                                        %texlive-tag "/Master/texmf-dist/"
+                                        "/fonts/type1/urw/zapfding/"))
+                    (revision %texlive-revision)))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1sp3jblg3khp0yj121blvhph6ib09919kyrsk5x2lg258yypqyis"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (ice-9 match))
+       #:builder
+       (begin
+         (use-modules (guix build utils)
+                      (ice-9 match))
+         (let ((root (string-append (assoc-ref %outputs "out")
+                                    "/share/texmf-dist/"))
+               (pkgs '(("source"      . "fonts/type1/urw/zapfding")
+                       ("zapf-afm"    . "fonts/afm/adobe/zapfding")
+                       ("zapf-tfm"    . "fonts/tfm/adobe/zapfding")
+                       ("urw-afm"     . "fonts/afm/urw/zapfding")
+                       ("urw35vf-tfm" . "fonts/tfm/urw35vf/zapfding")
+
+                       ("zapf-tex"    . "tex/latex/zapfding")
+                       ("dvips"       . "dvips/zapfding")
+                       ("fonts-map"   . "fonts/map/dvips/zapfding"))))
+           (for-each (match-lambda
+                       ((pkg . dir)
+                        (let ((target (string-append root dir)))
+                          (mkdir-p target)
+                          (copy-recursively (assoc-ref %build-inputs pkg)
+                                            target))))
+                     pkgs)
+           #t))))
+    (native-inputs
+     `(("zapf-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/adobe/zapfding"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0qvl4w1bfcpiakkd8rvkism46qnvzj9w7x4r8z9m0y7mspbkblyr"))))
+       ("zapf-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/adobe/zapfding"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "1i8mh9xsl8l4cgsg3nl4ha9q6m55j122riclaxsvkc5ka83432qm"))))
+       ("urw-afm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/afm/urw/zapfding"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw-afm-" version "-checkout"))
+           (sha256
+            (base32
+             "0m4qndqh7ji723ff82c5c1q8ziqvblbaip7vx05vnl15fqbsnfx1"))))
+       ("urw35vf-tfm"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/tfm/urw35vf/zapfding"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-urw35vf-tfm-" version "-checkout"))
+           (sha256
+            (base32
+             "167g2x6mpjfqh0w1fhjbw14qcx6ridrj2zm1bd8bi0l2d7phj28m"))))
+       ("zapf-tex"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/tex/latex/zapfding"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-tex-" version "-checkout"))
+           (sha256
+            (base32
+             "0hp7i8f6nbrg7irrwc8fd7n1hrzjysa84d6iyivwlc65v9p7lmd0"))))
+       ("dvips"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/dvips/zapfding/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-dvips-" version "-checkout"))
+           (sha256
+            (base32
+             "1f18sc4qwxykd786zhn6szcrycqvpvfhlcim71aamxmwghakd7fa"))))
+       ("fonts-map"
+        ,(origin
+           (method svn-fetch)
+           (uri (svn-reference
+                 (url (string-append "svn://www.tug.org/texlive/tags/"
+                                     %texlive-tag "/Master/texmf-dist/"
+                                     "/fonts/map/dvips/zapfding/"))
+                 (revision %texlive-revision)))
+           (file-name (string-append name "-fonts-map-" version "-checkout"))
+           (sha256
+            (base32
+             "17kwxmdrgz2fb072hx57a3pidcrhbgayphx11zyld2hv9149pkyl"))))))
+    (home-page "https://ctan.org/pkg/urw-base35")
+    (synopsis "URW Base 35 font pack for LaTeX")
+    (description
+     "This package provides a drop-in replacements for the Zapfding font from
+Adobe's basic set.")
+    ;; No license version specified.
+    (license license:gpl3+)))
+
 (define-public texlive-fonts-rsfs
   (package
     (name "texlive-fonts-rsfs")
@@ -4943,13 +5502,12 @@ PDF documents.")
 develop documents with LaTeX, in a single application.")
     (license license:gpl2+)))
 
-
 (define-public teximpatient
   (package
     (name "teximpatient")
     (version "2.4")
     (source (origin
-              (method url-fetch)
+              (method url-fetch/tarbomb)
               (uri (string-append "mirror://gnu/" name "/" name "-"
                                   version ".tar.gz"))
               (sha256
@@ -4957,25 +5515,28 @@ develop documents with LaTeX, in a single application.")
                 "0h56w22d99dh4fgld4ssik8ggnmhmrrbnrn1lnxi1zr0miphn1sd"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(#:tests? #f ; there are none
+       #:phases
        (modify-phases %standard-phases
-         (delete 'check)
+         (add-after 'unpack 'fix-packaging-error
-         ;; Unfortunately some mistakes have been made in packaging.
+           (lambda* (#:key inputs #:allow-other-keys)
-         ;; Work around them here ...
+             ;; This file should have been part of the tarball.
-         (replace 'unpack
+             (install-file (car
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+                            (find-files
-             (let ((srcdir "teximpatient-2.4"))
+                             (assoc-ref inputs "automake")
-               (system* "tar" "-xzf" (assoc-ref inputs "source")
+                             "^install-sh$"))
-                        (string-append "--one-top-level=" srcdir))
+                           ".")
-               (delete-file (string-append srcdir "/book.pdf"))
+             ;; Remove generated file.
-               (install-file (car
+             (delete-file "book.pdf")
-                              (find-files
+             #t)))))
-                               (assoc-ref inputs "automake")
-                               "^install-sh$"))
-                             srcdir)
-               (chdir srcdir)))))))
     (native-inputs
-     `(("texlive" ,texlive)
+     `(("texlive" ,(texlive-union (list texlive-latex-amsfonts
+                                        texlive-fonts-amsfonts
+                                        texlive-fonts-adobe-palatino
+                                        texlive-fonts-adobe-zapfding
+                                        texlive-fonts-knuth-lib
+                                        texlive-fonts-mflogo-font
+                                        texlive-generic-pdftex)))
        ("automake" ,automake)))
     (home-page "https://www.gnu.org/software/teximpatient/")
     (synopsis "Book on TeX, plain TeX and Eplain")
@@ -4987,20 +5548,20 @@ and Karl Berry.")
 (define-public lyx
   (package
     (name "lyx")
-    (version "2.2.3")
+    (version "2.3.2-2")
     (source (origin
-             (method url-fetch)
+              (method url-fetch)
-             (uri (string-append "http://ftp.lyx.org/pub/lyx/stable/2.2.x/"
+              (uri (string-append "http://ftp.lyx.org/pub/lyx/stable/"
-                                 name "-" version ".tar.gz"))
+                                  (version-major+minor version) ".x/"
-             (sha256
+                                  name "-" version ".tar.gz"))
-              (base32
+              (sha256
-               "0xvaz0i371nn2ndinc0d3ywj76ivb62649a4sdgwbivisiahd2fj"))
+               (base32
-             (patches (search-patches "lyx-2.2.3-fix-test.patch"))
+                "0vr0qwis6rhind6azfa270hqxci7rj8qb1kk5x6lm80mc34nvrqi"))
-             (modules '((guix build utils)))
+              (modules '((guix build utils)))
-             (snippet
+              (snippet
-              '(begin
+               '(begin
-                (delete-file-recursively "3rdparty")
+                  (delete-file-recursively "3rdparty")
-                #t))))
+                  #t))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags `("-DLYX_USE_QT=QT5"
@@ -5010,56 +5571,68 @@ and Karl Berry.")
                            ,(string-append "-DLYX_INSTALL_PREFIX="
                                            (assoc-ref %outputs "out")
                                            ;; Exact name and level is necessary.
-                                           "/lyx2.2"))
+                                           "/lyx" ,(version-major+minor version)))
        #:phases
        (modify-phases %standard-phases
+         ;; See ;; https://www.lyx.org/trac/changeset/3a123b90af838b08680471d87170c38e56787df9/lyxgit
+         (add-after 'unpack 'fix-compilation-with-boost-1.69
+           (lambda _
+             (substitute* "src/support/FileName.cpp"
+               (("^template struct boost::detail::crc_table_t.*") ""))
+             #t))
          (add-after 'unpack 'patch-python
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* '("src/support/os.cpp")
-              (("\"python ")
+               (("\"python ")
-               (string-append "\""
+                (string-append "\""
-                              (assoc-ref inputs "python-2")
+                               (assoc-ref inputs "python")
-                              "/bin/python ")))
+                               "/bin/python ")))
-             #t))
-         (add-after 'patch-python 'patch-installer
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* "CMakeLists.txt"
-              (("/usr/local/man/man1")
-               (string-append (assoc-ref outputs "out")
-                              "/share/man/man1")))
              #t))
          (add-after 'patch-python 'patch-desktop-file
            (lambda* (#:key outputs #:allow-other-keys)
              (substitute* "lib/lyx.desktop.in"
-              (("Exec=")
+               (("Exec=")
-               (string-append "Exec="
+                (string-append "Exec="
-                              (assoc-ref outputs "out")
+                               (assoc-ref outputs "out")
-                              "/")))
+                               "/")))
              #t))
          (add-before 'check 'setenv-check
            (lambda _
-             (setenv "LYX_DIR_22x" (string-append (getcwd) "/../lyx-"
+             ;; Create missing file that would cause tests to fail.
-                                                  ,version "/lib"))
+             (with-output-to-file (string-append "../lyx-"
+                                                 ,version
+                                                 "/src/tests/check_layout.cmake")
+               (const #t))
+             (setenv (string-append "LYX_DIR_"
+                                    (string-join
+                                      (string-split
+                                        ,(version-major+minor version) #\-)) "x")
+                     (string-append (getcwd) "/../lyx-" ,version "/lib"))
              #t))
          (add-after 'install 'install-symlinks
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((out (assoc-ref outputs "out")))
                (mkdir-p (string-append out "/bin"))
-               (symlink "../lyx2.2/bin/lyx2.2"
+               (symlink (string-append "../lyx" ,(version-major+minor version)
-                (string-append out "/bin/lyx2.2"))
+                                       "/bin/lyx" ,(version-major+minor version))
+                        (string-append out "/bin/lyx" ,(version-major+minor version)))
                #t))))))
     (inputs
      `(("boost" ,boost)
-       ("hunspell" ,hunspell) ; Note: Could also use aspell instead.
+       ("hunspell" ,hunspell)           ; Note: Could also use aspell instead.
        ("libx11" ,libx11)
-       ("python-2" ,python-2)
+       ("mythes" ,mythes)
+       ("python" ,python-2)
        ("qtbase" ,qtbase)
        ("qtsvg" ,qtsvg)
        ("zlib" ,zlib)))
     (propagated-inputs
-     `(("texlive" ,texlive))) ; article.cls is in texmf-dist.
+     `(("texlive" ,(texlive-union (list texlive-fonts-ec)))))
+    ;; FIXME: Python 3.7.0 cannot be used because the test infrastructure
+    ;; "requires a bytes-like object, not 'str'".  This may be fixed with
+    ;; upgrades to Python.
     (native-inputs
-     `(("python-2" ,python-2)
+     `(("python" ,python-2)
        ("pkg-config" ,pkg-config)
        ("bc" ,bc)))
     (home-page "https://www.lyx.org/")

gnu/packages/tls.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 David Thompson <davet@gnu.org>
 ;;; Copyright © 2015, 2016, 2017, 2018 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2018 Nils Gillmann <ng0@n0.is>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -900,14 +900,13 @@ extensions.")
     (name "dehydrated")
     (version "0.6.2")
     (source (origin
-              (method url-fetch/tarbomb)
+              (method url-fetch)
               (uri (string-append
-                    "https://github.com/lukas2511/dehydrated/archive/v"
+                    "https://github.com/lukas2511/dehydrated/releases/download/"
-                    version ".tar.gz"))
+                    "v" version "/dehydrated-" version ".tar.gz"))
               (sha256
                (base32
-                "03p80yj6bnzjc6dkp5hb9wpplmlrla8n5src71cnzw4rj53q8cqn"))
+                "03p80yj6bnzjc6dkp5hb9wpplmlrla8n5src71cnzw4rj53q8cqn"))))
-              (file-name (string-append name "-" version ".tar.gz"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
@@ -915,15 +914,20 @@ extensions.")
        (begin
          (use-modules (guix build utils))
          (let* ((source (assoc-ref %build-inputs "source"))
+                (tar (assoc-ref %build-inputs "tar"))
+                (gz  (assoc-ref %build-inputs "gzip"))
                 (out (assoc-ref %outputs "out"))
                 (bin (string-append out "/bin"))
+                (doc (string-append out "/share/doc/"))
                 (bash (in-vicinity (assoc-ref %build-inputs "bash") "bin")))
-           (mkdir-p bin)
+
+           (setenv "PATH" (string-append gz "/bin"))
+           (invoke (string-append tar "/bin/tar") "xvf" source)
+           (chdir (string-append ,name "-" ,version))
+
+           (install-file "dehydrated" bin)
+           (install-file "LICENSE" (string-append doc ,name "-" ,version))
            (with-directory-excursion bin
-             (copy-file
-              (in-vicinity source (string-append "/dehydrated-" ,version
-                                                 "/dehydrated"))
-              (in-vicinity bin "dehydrated"))
              (patch-shebang "dehydrated" (list bash))
 
              ;; Do not try to write in the store.
@@ -954,6 +958,9 @@ extensions.")
        ("grep" ,grep)
        ("openssl" ,openssl)
        ("sed" ,sed)))
+    (native-inputs
+     `(("gzip" ,gzip)
+       ("tar" ,tar)))
     (home-page "https://dehydrated.io/")
     (synopsis "Let's Encrypt/ACME client implemented as a shell script")
     (description "Dehydrated is a client for signing certificates with an

gnu/packages/video.scm

@@ -112,6 +112,7 @@
   #:use-module (gnu packages lua)
   #:use-module (gnu packages m4)
   #:use-module (gnu packages man)
+  #:use-module (gnu packages markup)
   #:use-module (gnu packages mp3)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages networking)
@@ -119,6 +120,7 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages popt)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
@@ -316,7 +318,7 @@ H.264 (MPEG-4 AVC) video streams.")
 (define-public mkvtoolnix
   (package
     (name "mkvtoolnix")
-    (version "13.0.0")
+    (version "31.0.0")
     (source
      (origin
        (method url-fetch)
@@ -324,12 +326,13 @@ H.264 (MPEG-4 AVC) video streams.")
                            name "-" version ".tar.xz"))
        (sha256
         (base32
-         "0hknnnnx9661igm1r73dc7aqxnnrl5a8yvyvr1nhd9ymn2klwpl5"))
+         "0d8va2iamzc7y3wi71z8mk2vnqvnkgwb2p7casdfp37400x8r2pr"))
        (modules '((guix build utils)))
        (snippet '(begin
                    ;; Delete bundled libraries.
                    (for-each delete-file-recursively
-                             '("lib/libebml"
+                             '("lib/fmt"
+                               "lib/libebml"
                                "lib/libmatroska"
                                "lib/nlohmann-json"
                                "lib/pugixml"
@@ -339,15 +342,18 @@ H.264 (MPEG-4 AVC) video streams.")
     (inputs
      `(("boost" ,boost)
        ("bzip2" ,bzip2)
+       ("cmark" ,cmark)
        ("libebml" ,libebml)
-       ("flac" ,flac)
        ("file" ,file)
+       ("flac" ,flac)
+       ("fmt" ,fmt)
        ("libmatroska" ,libmatroska)
        ("libogg" ,libogg)
        ("libvorbis" ,libvorbis)
        ("lzo" ,lzo)
        ("pugixml" ,pugixml)
-       ("qt" ,qt)
+       ("qtbase" ,qtbase)
+       ("qtmultimedia" ,qtmultimedia)
        ("utfcpp" ,utfcpp)
        ("zlib" ,zlib)))
     (native-inputs
@@ -359,6 +365,7 @@ H.264 (MPEG-4 AVC) video streams.")
        ("perl" ,perl)
        ("pkg-config" ,pkg-config)
        ("po4a" ,po4a)
+       ("qttools" ,qttools)
        ("ruby" ,ruby)))
     (arguments
      `(#:configure-flags
@@ -368,16 +375,15 @@ H.264 (MPEG-4 AVC) video streams.")
                             (assoc-ref %build-inputs "docbook-xsl")
                             "/xml/xsl/docbook-xsl-"
                             ,(package-version docbook-xsl))
-             (string-append "--with-extra-includes="
+             "--enable-update-check=no"
-                            (assoc-ref %build-inputs "nlohmann-json-cpp")
+             "--enable-precompiled-headers=no")
-                            "/include/nlohmann"))
         #:phases
        (modify-phases %standard-phases
          (add-before 'configure 'add-googletest
-           (lambda _
+           (lambda* (#:key inputs #:allow-other-keys)
              (symlink
-              (string-append (assoc-ref %build-inputs "googletest")
+               (string-append (assoc-ref inputs "googletest")
-                             "/include/gtest") "lib/gtest")
+                              "/include/gtest") "lib/gtest")
              #t))
          (replace 'build
            (lambda _
@@ -1764,7 +1770,7 @@ for use with HTML5 video.")
 (define-public avidemux
   (package
     (name "avidemux")
-    (version "2.6.12")
+    (version "2.7.1")
     (source (origin
              (method url-fetch)
              (uri (string-append
@@ -1772,7 +1778,7 @@ for use with HTML5 video.")
                    name "_" version ".tar.gz"))
              (sha256
               (base32
-               "0nz52yih8sff53inndkh2dba759xjzsh4b8xjww419lcpk0qp6kn"))
+               "15g9h791qbnmycabbbl7s2b3n3xpvygm88qrfk35g2cw6957ik9w"))
              (patches (search-patches "avidemux-install-to-lib.patch"))))
     (build-system cmake-build-system)
     (native-inputs
@@ -1794,9 +1800,8 @@ for use with HTML5 video.")
        ("perl" ,perl)
        ("pulseaudio" ,pulseaudio)
        ("python" ,python-wrapper)
-       ("qt" ,qt) ; FIXME: reenable modular qt after update - requires building
+       ("qtbase" ,qtbase)
-       ;("qtbase" ,qtbase) with -std=gnu++11.
+       ("qttools" ,qttools)
-       ;("qttools" ,qttools)
        ("sdl" ,sdl)
        ("sqlite" ,sqlite)
        ("yasm" ,yasm)
@@ -1810,19 +1815,19 @@ for use with HTML5 video.")
        (add-before 'patch-source-shebangs 'unpack-ffmpeg
          (lambda _
            (with-directory-excursion "avidemux_core/ffmpeg_package"
-             (invoke "tar" "xf" "ffmpeg-2.7.6.tar.bz2")
+             (invoke "tar" "xf" "ffmpeg-3.3.7.tar.bz2")
-             (delete-file "ffmpeg-2.7.6.tar.bz2"))
+             (delete-file "ffmpeg-3.3.7.tar.bz2"))
            #t))
        (add-after 'patch-source-shebangs 'repack-ffmpeg
          (lambda _
            (with-directory-excursion "avidemux_core/ffmpeg_package"
-             (substitute* "ffmpeg-2.7.6/configure"
+             (substitute* "ffmpeg-3.3.7/configure"
                (("#! /bin/sh") (string-append "#!" (which "sh"))))
-             (invoke "tar" "cjf" "ffmpeg-2.7.6.tar.bz2" "ffmpeg-2.7.6"
+             (invoke "tar" "cjf" "ffmpeg-3.3.7.tar.bz2" "ffmpeg-3.3.7"
                      ;; avoid non-determinism in the archive
                      "--sort=name" "--mtime=@0"
                      "--owner=root:0" "--group=root:0")
-             (delete-file-recursively "ffmpeg-2.7.6"))
+             (delete-file-recursively "ffmpeg-3.3.7"))
            #t))
        (replace 'configure
          (lambda _
@@ -3225,8 +3230,10 @@ create smoother and stable videos.")
                             (("(SET\\(PYTHON_MODULE_PATH.*)\\)" _ set)
                              (string-append set " CACHE PATH "
                                             "\"Python bindings directory\")")))
+                          (delete-file-recursively "thirdparty")
                           #t))
-              (patches (search-patches "libopenshot-tests-with-system-libs.patch"))))
+              (patches (search-patches "libopenshot-fixup-tests.patch"
+                                       "libopenshot-tests-with-system-libs.patch"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)
@@ -3239,7 +3246,8 @@ create smoother and stable videos.")
        ("imagemagick" ,imagemagick)
        ("jsoncpp" ,jsoncpp)
        ("libopenshot-audio" ,libopenshot-audio)
-       ("qt" ,qt)       ;widgets, core, gui, multimedia, and multimediawidgets
+       ("qtbase" ,qtbase)
+       ("qtmultimedia" ,qtmultimedia)
        ("zeromq" ,zeromq)))
     (arguments
      `(#:configure-flags

gnu/packages/virtualization.scm

@@ -796,10 +796,10 @@ incremental backups of running QEMU virtual machines via QMP, the QEMU
 Machine Protocol.")
     (license license:gpl3+)))
 
-(define-public lookingglass
+(define-public looking-glass-client
-  (let ((commit "41f4166aedeba65892f6db4de4de467aec9a2052"))
+  (let ((commit "182c4752d57690da7f99d5e788de9b8baea33895"))
     (package
-     (name "lookingglass")
+     (name "looking-glass-client")
      (version (string-append "a12-" (string-take commit 7)))
      (source
       (origin
@@ -809,7 +809,7 @@ Machine Protocol.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1sjxf4zy7h0zprla3s6dfwsxhmkrwhlhj07svf5bk5ij20bs0dc2"))))
+         "02bq46ndmzq9cihazzn7xq1x7q5nzm7iw4l9lqzihxcxp9famkhw"))))
      (build-system cmake-build-system)
      (inputs `(("fontconfig" ,fontconfig)
                ("glu" ,glu)
@@ -847,6 +847,9 @@ monitor/GPU.")
      (supported-systems '("i686-linux" "x86_64-linux"))
      (license license:gpl2+))))
 
+(define-public lookingglass
+  (deprecated-package "lookingglass" looking-glass-client))
+
 (define-public runc
   (package
     (name "runc")

gnu/packages/vpn.scm

@@ -8,6 +8,7 @@
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
+;;; Copyright © 2019 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -449,3 +450,68 @@ The peer-to-peer VPN implements a Layer 2 (Ethernet) network between the peers
     ;; This project contains a bundled lwIP. lwIP is also released under the
     ;; 3-clause BSD license.
     (license license:bsd-3)))
+
+(define-public wireguard
+  (package
+    (name "wireguard")
+    (version "0.0.20190123")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://git.zx2c4.com/WireGuard/snapshot/"
+                                  "WireGuard-" version ".tar.xz"))
+              (sha256
+               (base32
+                "16yzzy4i0z2zslmyr3kppkvkrxryzwdil6v270w9w5mg65v3rlgd"))))
+    (build-system gnu-build-system)
+    (outputs '("out" ; The WireGuard userspace tools
+               "kernel-patch")) ; A patch to build Linux with WireGuard support
+    (arguments
+     `(#:make-flags
+       (list "CC=gcc"
+             "WITH_BASHCOMPLETION=yes"
+             ;; Build and install the helper script wg-quick(8).
+             "WITH_WGQUICK=yes"
+             (string-append "PREFIX=" (assoc-ref %outputs "out"))
+             (string-append "SYSCONFDIR=" (assoc-ref %outputs "out") "/etc"))
+       #:modules ((guix build gnu-build-system)
+                  (guix build utils)
+                  (ice-9 popen)
+                  (ice-9 textual-ports))
+       #:phases
+       (modify-phases %standard-phases
+         ;; There is no ./configure script.
+         (delete 'configure)
+         ;; Until WireGuard is added to the upstream Linux kernel, it is
+         ;; distributed as a kernel patch generated by this script.
+         (add-after 'patch-source-shebangs 'make-patch
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((output (string-append (assoc-ref outputs "kernel-patch")
+                                           "/wireguard.patch"))
+                    (patch-builder "./contrib/kernel-tree/create-patch.sh")
+                    (port (open-input-pipe patch-builder))
+                    (str (get-string-all port)))
+               (close-pipe port)
+               (mkdir-p (dirname output))
+               (call-with-output-file output
+                 (lambda (port)
+                   (format port "~a" str))))
+               #t))
+         (add-after 'make-patch 'chdir
+           (lambda _
+             (chdir "src/tools")
+             #t))
+         ;; Otherwise the 'install-license-file' phase installs nothing.
+         ;; <https://bugs.gnu.org/34703>
+         (add-after 'install 'reset-cwd
+           (lambda _
+             (chdir "../..")
+             #t)))))
+    (inputs
+     `(("libmnl" ,libmnl)))
+    (home-page "https://www.wireguard.com/")
+    (synopsis "Tools for configuring WireGuard")
+    (description "This package provides the userspace tools for setting and
+retrieving configuration of WireGuard network tunnel interfaces, and a patch
+that can be applied to a Linux kernel source tree in order to build it with
+WireGuard support.")
+    (license license:gpl2)))

gnu/packages/web.scm

@@ -24,6 +24,7 @@
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
 ;;; Copyright © 2017 Pierre Langlois <pierre.langlois@gmx.com>
 ;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2017, 2019 Christopher Baines <mail@cbaines.net>
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
@@ -1248,57 +1249,88 @@ minimum to provide high performance operation.")
     ;; bundled CuTest framework uses a different non-copyleft license.
     (license (list l:asl2.0 (l:non-copyleft "file://test/CuTest-README.txt")))))
 
+(define-public libsass
+  (package
+    (name "libsass")
+    (version "3.5.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/sass/libsass.git")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0830pjcvhzxh6yixj82x5k5r1xnadjqzi16kp53213icbly0r9ma"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'set-LIBSASS_VERSION
+           (lambda _
+             (setenv "LIBSASS_VERSION" ,version)
+             #t)))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (home-page "https://sass-lang.com/libsass")
+    (synopsis "SASS Compiler, implemented as a C/C++ library")
+    (description
+     "LibSass is a @acronym{SASS,Syntactically awesome style sheets} compiler
+library designed for portability and efficiency.  To actually compile SASS
+stylesheets, you'll need to use another program that uses this library,
+@var{sassc} for example.")
+    (license l:expat)))
+
 (define-public sassc
-  ;; libsass must be statically linked and it isn't included in the sassc
+  (package
-  ;; release tarballs, hence this odd package recipe.
+    (name "sassc")
-  (let* ((version "3.4.5")
+    (version "3.5.0")
-         (libsass
+    (source (origin
-          (origin
+              (method git-fetch)
-            (method url-fetch)
+              (uri (git-reference
-            (uri (string-append
+                    (url "https://github.com/sass/sassc.git")
-                  "https://github.com/sass/libsass/archive/"
+                    (commit  version)))
-                  version ".tar.gz"))
+              (file-name (git-file-name name version))
-            (file-name (string-append "libsass-" version ".tar.gz"))
+              (sha256
-            (sha256
+               (base32
-             (base32
+                "0jsfz1zg4gwk0dq8i92ll12axs3s70wsdsmdyi71zx8zmvib5nl6"))))
-              "1j22138l5ymqjfj5zan9d2hipa3ahjmifgpjahqy1smlg5sb837x")))))
+    (build-system gnu-build-system)
-    (package
+    (arguments
-      (name "sassc")
+     `(#:make-flags
-      (version version)
+       (list "CC=gcc"
-      (source (origin
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
-                (method url-fetch)
+       ;; I don't believe sassc contains any tests
-                (uri (string-append "https://github.com/sass/sassc/archive/"
+       #:tests? #f
-                                    version ".tar.gz"))
+       #:phases
-                (file-name (string-append "sassc-" version ".tar.gz"))
+       (modify-phases %standard-phases
-                (sha256
+         (add-after 'unpack 'patch-Makefile
-                 (base32
+           (lambda _
-                  "1xk4kmmvziz9sal3swpqa10q0s289xjpcz8aggmly8mvxvmngsi9"))))
+             (substitute* "Makefile"
-      (build-system gnu-build-system)
+               (("build-shared: \\$\\(RESOURCES\\) \\$\\(OBJECTS\\) \\$\\(LIB_SHARED\\)")
-      (arguments
+                "build-shared: $(RESOURCES) $(OBJECTS)")
-       `(#:make-flags
+               (("\\$\\(SASSC_EXE\\): libsass build")
-         (list "CC=gcc"
+                "$(SASSC_EXE): build")
-               (string-append "PREFIX=" (assoc-ref %outputs "out")))
+               (("install: libsass-install-\\$\\(BUILD\\) \\\\")
-         #:test-target "test"
+                "install: \\"))
-         ;; FIXME: "make test" rebuilds the application and gets lost in a
+             #t))
-         ;; non-existing directory.
+         ;; This phase fails for some reason
-         #:tests? #f
+         (delete 'bootstrap)
-         #:phases
+         ;; There is no configure script
-         (modify-phases %standard-phases
+         (delete 'configure)
-           (delete 'bootstrap)
+         (add-before 'build 'setup-environment
-           (delete 'configure)
+           (lambda _
-           (add-after 'unpack 'unpack-libsass-and-set-path
+             (setenv "BUILD" "shared")
-             (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "SASSC_VERSION" ,version)
-               (invoke "tar" "xvf" (assoc-ref inputs "libsass"))
+             #t)))))
-               (setenv "SASS_LIBSASS_PATH"
+    (inputs
-                       (string-append (getcwd) "/libsass-" ,version))
+     `(("libsass" ,libsass)))
-               #t)))))
+    (synopsis "CSS pre-processor")
-      (inputs
+    (description "SassC is a compiler written in C for the CSS pre-processor
-       `(("libsass" ,libsass)))
-      (synopsis "CSS pre-processor")
-      (description "SassC is a compiler written in C for the CSS pre-processor
 language known as SASS.")
-      (home-page "http://sass-lang.com/libsass")
+    (home-page "http://sass-lang.com/libsass")
-      (license l:expat))))
+    (license l:expat)))
 
 
 (define-public perl-apache-logformat-compiler
@@ -5432,14 +5464,14 @@ encoder/decoder based on the draft-12 specification for UBJSON.")
 (define-public java-tomcat
   (package
     (name "java-tomcat")
-    (version "8.5.32")
+    (version "8.5.38")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://apache/tomcat/tomcat-8/v"
                                   version "/src/apache-tomcat-" version "-src.tar.gz"))
               (sha256
                (base32
-                "1qjsr6zmkdciakya4jqz0ssnsk02qlmmd898c05rasfwcrpj0xi6"))
+                "13pbsyk39g1qph82nngp54mqycmg60rxlxwy4yszsssahrqnggb2"))
               (modules '((guix build utils)))
               ;; Delete bundled jars.
               (snippet
@@ -5515,7 +5547,8 @@ technologies.")
        (modify-phases %standard-phases
          (add-before 'configure 'chdir
            (lambda _
-             (chdir "jetty-test-helper")))
+             (chdir "jetty-test-helper")
+             #t))
          (add-before 'build 'fix-paths
            (lambda _
              ;; TODO:
@@ -5779,7 +5812,8 @@ or embedded instantiation.  This package provides the JMX management.")))
        (modify-phases %standard-phases
          (add-before 'configure 'chdir
            (lambda _
-             (chdir "jetty-http"))))))
+             (chdir "jetty-http")
+             #t)))))
     (inputs
      `(("slf4j" ,java-slf4j-api)
        ("servlet" ,java-tomcat)

gnu/packages/webkit.scm

@@ -59,14 +59,14 @@
 (define-public webkitgtk
   (package
     (name "webkitgtk")
-    (version "2.22.6")
+    (version "2.22.7")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.webkitgtk.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0ny8azipr2dmdk79qrf4hvb2p4k5b3af38szjhmhg8mh1nfdp46z"))))
+                "1zrhmz90sn30zgyflj4i86fsscws10xsi2kfs87nj2nd0pbggrjb"))))
     (build-system cmake-build-system)
     (outputs '("out" "doc"))
     (arguments

gnu/packages/wine.scm

@@ -310,7 +310,7 @@ integrate Windows applications into your desktop.")
 (define-public wine-staging-patchset-data
   (package
     (name "wine-staging-patchset-data")
-    (version "4.2")
+    (version "4.3")
     (source
      (origin
        (method git-fetch)
@@ -320,7 +320,7 @@ integrate Windows applications into your desktop.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1dhv6y60g64bj3kgfknbfzxfzmy686dh7svxlvi4lfis2faikxmk"))))
+         "14plsw52s4w0wpm0rici8b7amb51krdrby03652isvzxqr4ndip6"))))
     (build-system trivial-build-system)
     (native-inputs
      `(("bash" ,bash)
@@ -366,8 +366,9 @@ integrate Windows applications into your desktop.")
               (file-name (string-append name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1ysvq2jyvh7r27iwpsrlrwzj672jnrihry91bx3m3fysz3sl3ld1"))))
+                "1d0gbwc8ll4mfxilw9j4vdzqlnracr6y8iss27nfg1qh0q7vbf9x"))))
     (inputs `(("autoconf" ,autoconf) ; for autoreconf
+              ("faudio" ,faudio)
               ("ffmpeg" ,ffmpeg)
               ("gtk+" ,gtk+)
               ("libva" ,libva)
@@ -406,7 +407,10 @@ integrate Windows applications into your desktop.")
                     (script (string-append (assoc-ref %build-inputs
                             "wine-staging-patchset-data")
                             "/share/wine-staging/patches/patchinstall.sh")))
-               (invoke script (string-append "DESTDIR=" ".") "--all")
+               ;; Exclude specific patches that conflict with FAudio.
+               (invoke script (string-append "DESTDIR=" ".") "--all" "-W"
+                       "xaudio2-revert" "-W" "xaudio2_CommitChanges" "-W"
+                       "xaudio2_7-WMA_support" "-W" "xaudio2_7-CreateFX-FXEcho")
                #t)))
          (add-after 'configure 'patch-dlopen-paths
            ;; Hardcode dlopened sonames to absolute paths.
@@ -482,7 +486,10 @@ integrated into the main branch.")
                     (script (string-append (assoc-ref %build-inputs
                             "wine-staging-patchset-data")
                             "/share/wine-staging/patches/patchinstall.sh")))
-               (invoke script (string-append "DESTDIR=" ".") "--all")
+               ;; Exclude specific patches that conflict with FAudio.
+               (invoke script (string-append "DESTDIR=" ".") "--all" "-W"
+                       "xaudio2-revert" "-W" "xaudio2_CommitChanges" "-W"
+                       "xaudio2_7-WMA_support" "-W" "xaudio2_7-CreateFX-FXEcho")
                #t)))
          (add-after 'install 'copy-wine32-binaries
            (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/xorg.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -5099,16 +5099,16 @@ over Xlib, including:
 (define-public xorg-server
   (package
     (name "xorg-server")
-    (version "1.20.3")
+    (version "1.20.4")
     (source
       (origin
         (method url-fetch)
         (uri (string-append
               "mirror://xorg/individual/xserver/"
-              name "-" version ".tar.bz2"))
+              "xorg-server-" version ".tar.bz2"))
         (sha256
          (base32
-          "1ph1j8gy5cazsq05krq9kppjx5v1sl75pbdka8ibxb1cq5kf8g0v"))
+          "1vk6j7hmigfill9x8m7a6vvgb3s50ji2yf6yprbgqfz9xf9x83zy"))
         (patches
          (list
           ;; See:

gnu/services/cuirass.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2016 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2017 Jan Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
@@ -136,7 +136,7 @@
            (system? #t)
            (comment "Cuirass privilege separation user")
            (home-directory (string-append "/var/lib/" cuirass-user))
-           (shell #~(string-append #$shadow "/sbin/nologin"))))))
+           (shell (file-append shadow "/sbin/nologin"))))))
 
 (define (cuirass-activation config)
   "Return the activation code for CONFIG."

gnu/services/monitoring.scm

@@ -258,7 +258,7 @@ configuration file."))
            (group zabbix-group)
            (comment "zabbix privilege separation user")
            (home-directory (string-append "/var/run/" zabbix-user))
-           (shell #~(string-append #$shadow "/sbin/nologin"))))))
+           (shell (file-append shadow "/sbin/nologin"))))))
 
 (define (zabbix-server-config-file config)
   "Return the zabbix-server configuration file corresponding to CONFIG."
@@ -387,7 +387,7 @@ configuration file."))
            (group zabbix-group)
            (comment "zabbix privilege separation user")
            (home-directory (string-append "/var/run/" zabbix-user))
-           (shell #~(string-append #$shadow "/sbin/nologin"))))))
+           (shell (file-append shadow "/sbin/nologin"))))))
 
 (define (zabbix-agent-activation config)
   "Return the activation gexp for CONFIG."

gnu/services/rsync.scm

@@ -88,7 +88,7 @@
            (comment "rsyncd privilege separation user")
            (home-directory (string-append "/var/run/"
                                           rsync-user))
-           (shell #~(string-append #$shadow "/sbin/nologin"))))))
+           (shell (file-append shadow "/sbin/nologin"))))))
 
 (define (rsync-activation config)
   "Return the activation GEXP for CONFIG."

gnu/services/ssh.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 David Craven <david@craven.ch>
 ;;; Copyright © 2016 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
@@ -349,7 +349,7 @@ The other options should be self-descriptive."
           (system? #t)
           (comment "sshd privilege separation user")
           (home-directory "/var/run/sshd")
-          (shell #~(string-append #$shadow "/sbin/nologin")))))
+          (shell (file-append shadow "/sbin/nologin")))))
 
 (define (openssh-activation config)
   "Return the activation GEXP for CONFIG."

gnu/tests/base.scm

@@ -397,7 +397,7 @@ info --version")
                                 (use-modules (srfi srfi-34) (guix store))
 
                                 (let ((system (readlink "/run/current-system")))
-                                  (guard (c ((nix-protocol-error? c)
+                                  (guard (c ((store-protocol-error? c)
                                              (and (file-exists? system)
                                                   'success!)))
                                     (with-store store

guix/scripts/environment.scm

@@ -141,7 +141,7 @@ COMMAND or an interactive shell in that environment.\n"))
   (display (G_ "
       --pure             unset existing environment variables"))
   (display (G_ "
-      --inherit=REGEXP   inherit environment variables that match REGEXP"))
+  -E, --preserve=REGEXP  preserve environment variables that match REGEXP"))
   (display (G_ "
       --search-paths     display needed environment variable definitions"))
   (display (G_ "
@@ -215,14 +215,18 @@ COMMAND or an interactive shell in that environment.\n"))
          (option '("pure") #f #f
                  (lambda (opt name arg result)
                    (alist-cons 'pure #t result)))
-         (option '("inherit") #t #f
+         (option '(#\E "preserve") #t #f
                  (lambda (opt name arg result)
                    (alist-cons 'inherit-regexp
                                (make-regexp* arg)
                                result)))
-         (option '(#\E "exec") #t #f ; deprecated
+         (option '("inherit") #t #f               ;deprecated
                  (lambda (opt name arg result)
-                   (alist-cons 'exec (list %default-shell "-c" arg) result)))
+                   (warning (G_ "'--inherit' is deprecated, \
+use '--preserve' instead~%"))
+                   (alist-cons 'inherit-regexp
+                               (make-regexp* arg)
+                               result)))
          (option '("search-paths") #f #f
                  (lambda (opt name arg result)
                    (alist-cons 'search-paths #t result)))

tests/guix-environment.sh

@@ -49,13 +49,13 @@ test -x `sed -r 's/^export PATH="(.*)"/\1/' "$tmpdir/a"`/guile
 
 cmp "$tmpdir/a" "$tmpdir/b"
 
-# Check '--inherit'.
+# Check '--preserve'.
 GUIX_TEST_ABC=1
 GUIX_TEST_DEF=2
 GUIX_TEST_XYZ=3
 export GUIX_TEST_ABC GUIX_TEST_DEF GUIX_TEST_XYZ
 guix environment --bootstrap --ad-hoc guile-bootstrap --pure	\
-     --inherit='^GUIX_TEST_A' --inherit='^GUIX_TEST_D'		\
+     --preserve='^GUIX_TEST_A' --preserve='^GUIX_TEST_D'	\
      -- "$SHELL" -c set > "$tmpdir/a"
 grep '^PATH=' "$tmpdir/a"
 grep '^GUIX_TEST_ABC=' "$tmpdir/a"
@@ -117,16 +117,6 @@ case "`uname -m`" in
 	;;
 esac
 
-
-# Same as above, but with deprecated -E flag.
-if guix environment --bootstrap --ad-hoc guile-bootstrap --pure \
-        -E "guile -c '(exit 42)'"
-then
-    false
-else
-    test $? = 42
-fi
-
 # Make sure we can build the environment of 'guix'.  There may be collisions
 # in its profile (e.g., for 'gzip'), but we have to accept them.
 guix environment guix --bootstrap -n