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authorMarius Bakke <mbakke@fastmail.com>2018-08-28 01:22:24 +0200
committerMarius Bakke <mbakke@fastmail.com>2018-08-28 01:22:24 +0200
commit61fca0fd22b81bcc0201a336a02cac74b42c6a44 (patch)
tree67cca9c72282f24b9ceb0b1706c314537e8c37ea /gnu
parent57dac1ee935edfab91e9b182c1f7c9ddae794656 (diff)
parent526ce419303ac511be8d51b41471022bed472e6b (diff)
downloadguix-61fca0fd22b81bcc0201a336a02cac74b42c6a44.tar
guix-61fca0fd22b81bcc0201a336a02cac74b42c6a44.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu')
-rw-r--r--gnu/local.mk5
-rw-r--r--gnu/packages/bootloaders.scm3
-rw-r--r--gnu/packages/c.scm2
-rw-r--r--gnu/packages/chemistry.scm80
-rw-r--r--gnu/packages/ci.scm6
-rw-r--r--gnu/packages/code.scm2
-rw-r--r--gnu/packages/compression.scm2
-rw-r--r--gnu/packages/disk.scm2
-rw-r--r--gnu/packages/emacs.scm63
-rw-r--r--gnu/packages/engineering.scm70
-rw-r--r--gnu/packages/firmware.scm2
-rw-r--r--gnu/packages/freedesktop.scm6
-rw-r--r--gnu/packages/golang.scm2
-rw-r--r--gnu/packages/guile.scm24
-rw-r--r--gnu/packages/haskell.scm42
-rw-r--r--gnu/packages/image-viewers.scm4
-rw-r--r--gnu/packages/image.scm2
-rw-r--r--gnu/packages/linux.scm16
-rw-r--r--gnu/packages/music.scm2
-rw-r--r--gnu/packages/networking.scm2
-rw-r--r--gnu/packages/password-utils.scm2
-rw-r--r--gnu/packages/patches/avogadro-boost148.patch69
-rw-r--r--gnu/packages/patches/avogadro-eigen3-update.patch603
-rw-r--r--gnu/packages/patches/avogadro-python-eigen-lib.patch161
-rw-r--r--gnu/packages/patches/grub-check-error-efibootmgr.patch176
-rw-r--r--gnu/packages/patches/python-pygit2-disable-network-tests.patch43
-rw-r--r--gnu/packages/perl-check.scm2
-rw-r--r--gnu/packages/perl.scm2
-rw-r--r--gnu/packages/photo.scm2
-rw-r--r--gnu/packages/python.scm6
-rw-r--r--gnu/packages/slang.scm4
-rw-r--r--gnu/packages/textutils.scm2
-rw-r--r--gnu/packages/video.scm2
-rw-r--r--gnu/packages/xdisorg.scm2
34 files changed, 1291 insertions, 122 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index c62e6ea50e..c19d992874 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -584,6 +584,9 @@ dist_patch_DATA = \
%D%/packages/patches/audacity-build-with-system-portaudio.patch \
%D%/packages/patches/automake-skip-amhello-tests.patch \
%D%/packages/patches/avahi-localstatedir.patch \
+ %D%/packages/patches/avogadro-boost148.patch \
+ %D%/packages/patches/avogadro-eigen3-update.patch \
+ %D%/packages/patches/avogadro-python-eigen-lib.patch \
%D%/packages/patches/avidemux-install-to-lib.patch \
%D%/packages/patches/awesome-reproducible-png.patch \
%D%/packages/patches/azr3.patch \
@@ -768,6 +771,7 @@ dist_patch_DATA = \
%D%/packages/patches/grep-timing-sensitive-test.patch \
%D%/packages/patches/groff-source-date-epoch.patch \
%D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \
+ %D%/packages/patches/grub-check-error-efibootmgr.patch \
%D%/packages/patches/gsl-test-i686.patch \
%D%/packages/patches/gspell-dash-test.patch \
%D%/packages/patches/guile-1.8-cpp-4.5.patch \
@@ -1082,7 +1086,6 @@ dist_patch_DATA = \
%D%/packages/patches/python-mox3-python3.6-compat.patch \
%D%/packages/patches/python-paste-remove-website-test.patch \
%D%/packages/patches/python-paste-remove-timing-test.patch \
- %D%/packages/patches/python-pygit2-disable-network-tests.patch \
%D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \
%D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
%D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \
diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm
index 727789a96e..e9abf399ab 100644
--- a/gnu/packages/bootloaders.scm
+++ b/gnu/packages/bootloaders.scm
@@ -85,7 +85,8 @@
(uri (string-append "mirror://gnu/grub/grub-" version ".tar.xz"))
(sha256
(base32
- "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))))
+ "03vvdfhdmf16121v7xs8is2krwnv15wpkhkf16a4yf8nsfc3f2w1"))
+ (patches (search-patches "grub-check-error-efibootmgr.patch"))))
(build-system gnu-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm
index d82db532aa..e6df1d23c7 100644
--- a/gnu/packages/c.scm
+++ b/gnu/packages/c.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2016, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 2d7cb7aad1..03120aaeee 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -23,16 +23,96 @@
#:use-module (guix download)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages documentation)
+ #:use-module (gnu packages gl)
#:use-module (gnu packages gv)
#:use-module (gnu packages maths)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages qt)
#:use-module (gnu packages xml)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python))
+(define-public avogadro
+ (package
+ (name "avogadro")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/cryos/avogadro/archive/"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "02v4h6hi1m7ilv0apdf74a8l1cm6dxnxyqp0rdaidrp3i9pf6lv4"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (patches
+ (search-patches "avogadro-eigen3-update.patch"
+ "avogadro-python-eigen-lib.patch"
+ "avogadro-boost148.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:tests? #f
+ #:configure-flags
+ (list "-DENABLE_GLSL=ON"
+ (string-append "-DPYTHON_LIBRARIES="
+ (assoc-ref %build-inputs "python")
+ "/lib")
+ (string-append "-DPYTHON_INCLUDE_DIRS="
+ (assoc-ref %build-inputs "python")
+ "/include/python2.7"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-python-lib-path
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; This is necessary to install the Python module in the correct
+ ;; directory.
+ (substitute* "libavogadro/src/python/CMakeLists.txt"
+ (("^EXECUTE_PROCESS.*$") "")
+ (("^.*from sys import stdout.*$") "")
+ (("^.*OUTPUT_VARIABLE.*")
+ (string-append "set(PYTHON_LIB_PATH \""
+ (assoc-ref outputs "out")
+ "/lib/python2.7/site-packages\")")))
+ #t))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Make sure 'avogadro' runs with the correct PYTHONPATH.
+ (let* ((out (assoc-ref outputs "out")))
+ (setenv "PYTHONPATH"
+ (string-append
+ (assoc-ref outputs "out")
+ "/lib/python2.7/site-packages:"
+ (getenv "PYTHONPATH")))
+ (wrap-program (string-append out "/bin/avogadro")
+ `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))))
+ #t)))))
+ (native-inputs
+ `(("doxygen" ,doxygen)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("boost" ,boost)
+ ("eigen" ,eigen)
+ ("glew" ,glew)
+ ("openbabel" ,openbabel)
+ ("python" ,python-2)
+ ("python-numpy" ,python2-numpy)
+ ("python-pyqt" ,python2-pyqt-4)
+ ("python-sip" ,python2-sip)
+ ("qt" ,qt-4)
+ ("zlib" ,zlib)))
+ (home-page "https://avogadro.cc")
+ (synopsis "Advanced molecule editor")
+ (description
+ "Avogadro is an advanced molecule editor and visualizer designed for use
+in computational chemistry, molecular modeling, bioinformatics, materials
+science, and related areas. It offers flexible high quality rendering and a
+powerful plugin architecture.")
+ (license license:gpl2+)))
+
(define-public domainfinder
(package
(name "domainfinder")
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index 599fd8cbbc..e26983da3b 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -185,8 +185,8 @@ their dependencies.")
(license l:gpl3+))))
(define-public cuirass
- (let ((commit "4db99f647b3677086a2007763726d05a59b0cdcb")
- (revision "18"))
+ (let ((commit "8d40c49170971ad7bbf8b97336934dbb3d949fc1")
+ (revision "19"))
(package
(name "cuirass")
(version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -198,7 +198,7 @@ their dependencies.")
(file-name (string-append name "-" version))
(sha256
(base32
- "1lg3w0xjg6b806y8gfxj2dq1g0djm5pyk886j8g7n5n9ljlhjzxj"))))
+ "0xxcapf9ag3zx6131v128vhin5m2j3w2gjbjbpdwr0qkaysh0gvf"))))
(build-system gnu-build-system)
(arguments
'(#:modules ((guix build utils)
diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index ee7447b024..be178a5f99 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -7,7 +7,7 @@
;;; Copyright © 2017, 2018 Clément Lassieur <clement@lassieur.org>
;;; Copyright © 2017 Andy Wingo <wingo@igalia.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index ac8c1fdbc0..f2ed53f036 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -22,7 +22,7 @@
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 34709b73fc..a095d0cd4f 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -12,7 +12,7 @@
;;; Copyright © 2018 Vasile Dumitrascu <va511e@yahoo.com>
;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 2322581a30..8665356f5c 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -34,7 +34,7 @@
;;; Copyright © 2017, 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2018 Sohom Bhattacharjee <soham.bhattacharjee15@gmail.com>
;;; Copyright © 2018 Mathieu Lirzin <mthl@gnu.org>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
;;; Copyright © 2018 Jack Hill <jackhill@jackhill.us>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
@@ -1179,16 +1179,18 @@ rather than the contents of files.")
(define-public emacs-async
(package
(name "emacs-async")
+ (home-page "https://github.com/jwiegley/emacs-async")
(version "1.9.3")
(source (origin
- (method url-fetch)
- (uri (string-append "https://stable.melpa.org/packages/async-"
- version ".tar"))
+ (method git-fetch)
+ (uri (git-reference
+ (url home-page)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0xvi50y96y2qh81qkhj8p6ar1xnfasg58qvlsvgvvmdf4g8srlij"))))
+ "1zsnb6dy8p6y68xgidv3dfxaga4biramfw8fq7wac0sc50vc98vq"))))
(build-system emacs-build-system)
- (home-page "https://elpa.gnu.org/packages/async.html")
(synopsis "Asynchronous processing in Emacs")
(description
"This package provides the ability to call asynchronous functions and
@@ -10025,8 +10027,8 @@ perform regression test for packages that provide font-lock rules.")
(license license:gpl3+))))
(define-public emacs-racket-mode
- (let ((commit "1b78827d310b6d655782b7bba0f2360c9ef34ff6")
- (revision "2"))
+ (let ((commit "add0190d3c9bdad25fee57f8efd0460c9a45c2ec")
+ (revision "1"))
(package
(name "emacs-racket-mode")
(version (string-append "0.0.2" "-" revision "."
@@ -10040,7 +10042,7 @@ perform regression test for packages that provide font-lock rules.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "04mzxcg32av8p6v0pqb0si6qk5qxbrbllx6m3j16fp32bdz71sps"))))
+ "0bf6s4nqjfacij20x9vppdnq8fq1bf53cch6p4g8xqcqri3ms4jw"))))
(build-system emacs-build-system)
(arguments
`(#:include '("\\.el$" "\\.rkt$")))
@@ -11374,8 +11376,8 @@ wiki.")
(license license:expat)))
(define-public emacs-recent-addresses
- (let ((commit "d9da58db542089a1ceb5ef29e420dbfbc4a36373")
- (revision "0"))
+ (let ((commit "afbbfdc43b81e620acf827ca20d297e0c517b6eb")
+ (revision "1"))
(package
(name "emacs-recent-addresses")
(home-page "http://nschum.de/src/emacs/recent-addresses/")
@@ -11383,18 +11385,20 @@ wiki.")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/nschum/recent-addresses.el")
+ ;; Note: Use a branch that works with Helm. Submitted
+ ;; at <https://github.com/nschum/recent-addresses.el/pull/1>.
+ (url "https://github.com/civodul/recent-addresses.el")
(commit commit)))
(sha256
(base32
- "175rvcwmkb5z7ss7q2y5178mvdvp5bhn39irz80qinlvaz8fm4nk"))
+ "0ajrq0galjmdyjdjyxazykjyax3gh6hvfk4s7l657pi11g0q5zax"))
(file-name (git-file-name name version))))
(build-system emacs-build-system)
(synopsis "Record recently-used email addressed and auto-complete them")
(description
- "@code{recent-addresses} is an Emacs allows you to quickly look up
-previously used email addresses. It can be used alongside the Gnus email
-client.")
+ "@code{recent-addresses} is an Emacs package that allows you to quickly
+look up previously used email addresses. It can be used alongside the Gnus
+email client.")
(license license:gpl2+))))
(define-public emacs-fold-dwim
@@ -11643,3 +11647,30 @@ comments and Org files in the Magit status buffer. Activating an item jumps
to it in its file. By default, it uses keywords from @code{hl-todo}, minus a
few (like NOTE).")
(license license:gpl3))))
+
+(define-public emacs-git-annex
+ ;; Unreleased version has a fontification fix.
+ (let ((commit "ebdb44aef1883f1b2b8058e05d30fb9315b03707")
+ (revision "1"))
+ (package
+ (name "emacs-git-annex")
+ (version (string-append "1.1-" revision "." (string-take commit 8)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/jwiegley/git-annex-el")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1mzv40gj7k10h7h5s43my8msgzjpj680qprqa9pp8nbyhl49v3wh"))))
+ (build-system emacs-build-system)
+ (home-page "https://github.com/jwiegley/git-annex-el")
+ (synopsis "Emacs integration for git-annex")
+ (description "Enhances Dired and buffers visiting annex files with
+git-annex functionality. In Dired, the names of annex files are shortened by
+hiding the symbolic links and fontified based on whether content is present.
+Commands for performing some common operations (e.g., unlocking and adding
+files) are provided.")
+ (license license:gpl2+))))
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index f11ce71f5a..3b433a1bfe 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -59,6 +59,7 @@
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gperf)
+ #:use-module (gnu packages groff)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages image)
@@ -76,6 +77,7 @@
#:use-module (gnu packages readline)
#:use-module (gnu packages swig)
#:use-module (gnu packages tcl)
+ #:use-module (gnu packages texinfo)
#:use-module (gnu packages tls)
#:use-module (gnu packages tex)
#:use-module (gnu packages wxwidgets)
@@ -224,6 +226,74 @@ tool to forward annotation from your schematic to layout using PCB; some minor
utilities.")
(license license:gpl2+)))
+(define-public lepton-eda
+ ;; This is a fork of gEDA/gaf started in late 2016. One of its goal is to
+ ;; keep and to extend Guile support.
+ (package
+ (inherit geda-gaf)
+ (name "lepton-eda")
+ (version "1.9.5-20180820")
+ (home-page "https://github.com/lepton-eda/lepton-eda")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (sha256
+ (base32
+ "1ayaccvw18zh4g7a4x5jf6yxkphi5xafb0hpc732g59qkgwfcmlr"))
+ (file-name (git-file-name name version))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)
+ ("gettext" ,gnu-gettext)
+ ("texinfo" ,texinfo)
+ ("groff" ,groff)
+ ("which" ,which)
+ ,@(package-native-inputs geda-gaf)))
+ ;; For now it's Guile 2.0, not 2.2.
+ (arguments
+ (substitute-keyword-arguments (package-arguments geda-gaf)
+ ((#:configure-flags flags ''())
+ ;; When running "make", the POT files are built with the build time as
+ ;; their "POT-Creation-Date". Later on, "make" notices that .pot
+ ;; files were updated and goes on to run "msgmerge"; as a result, the
+ ;; non-deterministic POT-Creation-Date finds its way into .po files,
+ ;; and then in .gmo files. To avoid that, simply make sure 'msgmerge'
+ ;; never runs. See <https://bugs.debian.org/792687>.
+ `(cons "ac_cv_path_MSGMERGE=true" ,flags))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'bootstrap 'prepare
+ (lambda _
+ ;; Some of the scripts there are invoked by autogen.sh.
+ (for-each patch-shebang (find-files "build-tools"))
+
+ ;; Make sure 'msgmerge' can modify the PO files.
+ (for-each (lambda (po)
+ (chmod po #o666))
+ (find-files "." "\\.po$"))
+
+ ;; This would normally be created by invoking 'git', but it
+ ;; doesn't work here.
+ (call-with-output-file "version.h"
+ (lambda (port)
+ (format port "#define PACKAGE_DATE_VERSION \"~a\"~%"
+ ,(string-drop version
+ (+ 1 (string-index version #\-))))
+ (format port "#define PACKAGE_DOTTED_VERSION \"~a\"~%"
+ ,(string-take version
+ (string-index version #\-)))
+ (format port "#define PACKAGE_GIT_COMMIT \"cabbag3\"~%")))
+ #t))))))
+ (description
+ "Lepton EDA ia an @dfn{electronic design automation} (EDA) tool set
+forked from gEDA/gaf in late 2016. EDA tools are used for electrical circuit
+design, schematic capture, simulation, prototyping, and production. Lepton
+EDA includes tools for schematic capture, attribute management, bill of
+materials (BOM) generation, netlisting into over 20 netlist formats, analog
+and digital simulation, and printed circuit board (PCB) layout, and many other
+features.")))
+
(define-public pcb
(package
(name "pcb")
diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 176eef5137..0b5a82e9e5 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -188,7 +188,7 @@ by the b43-open driver of Linux-libre.")
(version "1.11.0")
(source (origin
(method url-fetch)
- (uri (string-append "https://code.coreboot.org/p/seabios/downloads/get/"
+ (uri (string-append "https://www.seabios.org/downloads/"
"seabios-" version ".tar.gz"))
(sha256
(base32
diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 5352ea221b..ce67b6858b 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -12,7 +12,7 @@
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2017 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -495,7 +495,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
(define-public weston
(package
(name "weston")
- (version "4.0.0")
+ (version "5.0.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -503,7 +503,7 @@ applications, X servers (rootless or fullscreen) or other display servers.")
"weston-" version ".tar.xz"))
(sha256
(base32
- "0n2big8xw6g6n46zm1jyf00dv9r4d84visdz5b8vxpw3xzkhmz50"))))
+ "1bsc9ry566mpk6fdwkqpvwq2j7m79d9cvh7d3lgf6igsphik98hm"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)
diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 20b203aa6f..b4a088a051 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -11,7 +11,7 @@
;;; Copyright © 2018 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2018 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index b44db6a6bf..5c9f4d499c 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -1984,6 +1984,30 @@ Vicare Scheme and IronScheme. Right now it contains:
@end itemize\n")
(license license:bsd-3)))
+(define-public guile-aa-tree
+ (package
+ (name "guile-aa-tree")
+ (version "3.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://savannah/guile-aa-tree/guile-aa-tree-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0044c105r3q9vpl17pv3phl1b79kjm1llhkakqgiasixyav01blh"))))
+ (build-system guile-build-system)
+ (native-inputs `(("guile" ,guile-2.2)))
+ ;; https://savannah.nongnu.org/projects/guile-aa-tree
+ (home-page "https://qlfiles.net/guile-aa-tree/")
+ (synopsis "AA tree data structure for Guile")
+ (description
+ "This package provides an implementation of @dfn{AA trees}, a
+self-balancing binary tree data structure, for Guile. It ensure @math{O(log
+n)} worst case performance for core operations. The module provides
+non-mutating insert, delete, and search operations, with support for
+convenient nested tree operations.")
+ (license license:gpl3+)))
+
(define-public guile-simple-zmq
(let ((commit "1f3b7c0b9b249c6fde8e8a632b252d8a1b794424")
(revision "1"))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 759ca6044e..7d7d85f951 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -3268,7 +3268,7 @@ This is a better maintained fork of the \"temporary\" package.")
(define-public ghc-smallcheck
(package
(name "ghc-smallcheck")
- (version "1.1.1")
+ (version "1.1.5")
(source
(origin
(method url-fetch)
@@ -3278,7 +3278,7 @@ This is a better maintained fork of the \"temporary\" package.")
".tar.gz"))
(sha256
(base32
- "1ygrabxh40bym3grnzqyfqn96lirnxspb8cmwkkr213239y605sd"))))
+ "195fj7w3v03d1y1nm2ylavzrwxjcdbq0lb6zsw1dwyx5jmwfc84h"))))
(build-system haskell-build-system)
(inputs
`(("ghc-logict" ,ghc-logict)
@@ -4256,7 +4256,7 @@ simple general-purpose data structure\".")
(define-public ghc-optparse-applicative
(package
(name "ghc-optparse-applicative")
- (version "0.13.0.0")
+ (version "0.14.2.0")
(source
(origin
(method url-fetch)
@@ -4265,15 +4265,8 @@ simple general-purpose data structure\".")
"/optparse-applicative-" version ".tar.gz"))
(sha256
(base32
- "1b0c5fdq8bd070g24vrjrwlq979r8dk8mys6aji9hy1l9pcv3inf"))))
+ "0c3z1mvynlyv1garjbdmdd3npm40dabgm75js4r07cf766c1wd71"))))
(build-system haskell-build-system)
- ;; These tests fail because the package doesn't come with all needed test
- ;; files:
- ;; - prop_drops_back_contexts
- ;; - prop_context_carry
- ;; - prop_help_on_empty
- ;; - prop_help_on_empty_sub
- (arguments `(#:tests? #f))
(inputs
`(("ghc-transformers-compat" ,ghc-transformers-compat)
("ghc-ansi-wl-pprint" ,ghc-ansi-wl-pprint)))
@@ -5061,7 +5054,7 @@ occurrences of a substring (the first in case of overlaps) with another.")
(define-public ghc-integer-logarithms
(package
(name "ghc-integer-logarithms")
- (version "1.0.2")
+ (version "1.0.2.1")
(source
(origin
(method url-fetch)
@@ -5070,16 +5063,16 @@ occurrences of a substring (the first in case of overlaps) with another.")
version ".tar.gz"))
(sha256
(base32
- "0w5mhak181zi6qr5h2zbcs9ymaqacisp9jwk99naz6s8zz5rq1ii"))))
+ "1wj8kgjg5bn2yrs4zh9qfjv85cx6w998j9pi39yrbv305944mb9j"))))
(build-system haskell-build-system)
- (inputs
- `(("ghc-tasty" ,ghc-tasty)
- ("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)
- ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+ (native-inputs
+ `(("ghc-quickcheck" ,ghc-quickcheck)
+ ("ghc-smallcheck" ,ghc-smallcheck)
+ ("ghc-tasty" ,ghc-tasty)
("ghc-tasty-hunit" ,ghc-tasty-hunit)
- ("ghc-quickcheck" ,ghc-quickcheck)
- ("ghc-smallcheck" ,ghc-smallcheck)))
- (home-page "https://github.com/phadej/integer-logarithms")
+ ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+ ("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)))
+ (home-page "https://github.com/Bodigrim/integer-logarithms")
(synopsis "Integer logarithms")
(description
"This package provides the following modules:
@@ -5093,7 +5086,7 @@ in migrated modules.")
(define-public ghc-scientific
(package
(name "ghc-scientific")
- (version "0.3.5.2")
+ (version "0.3.6.2")
(source
(origin
(method url-fetch)
@@ -5103,14 +5096,15 @@ in migrated modules.")
".tar.gz"))
(sha256
(base32
- "0msnjz7ml0zycw9bssslxbg0nigziw7vs5km4q3vjbs8jpzpkr2w"))))
+ "03ql2f0ac8bsl524idy9xxa3kxisb2sj3avflzw580j5hzy0m397"))))
(build-system haskell-build-system)
(inputs
`(("ghc-integer-logarithms" ,ghc-integer-logarithms)
("ghc-text" ,ghc-text)
("ghc-hashable" ,ghc-hashable)
- ("ghc-primitive" ,ghc-primitive)
- ("ghc-tasty" ,ghc-tasty)
+ ("ghc-primitive" ,ghc-primitive)))
+ (native-inputs
+ `(("ghc-tasty" ,ghc-tasty)
("ghc-tasty-ant-xml" ,ghc-tasty-ant-xml)
("ghc-tasty-hunit" ,ghc-tasty-hunit)
("ghc-tasty-smallcheck" ,ghc-tasty-smallcheck)
diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm
index 3410880a67..87546045a6 100644
--- a/gnu/packages/image-viewers.scm
+++ b/gnu/packages/image-viewers.scm
@@ -74,12 +74,14 @@
'(#:phases (modify-phases %standard-phases (delete 'configure))
#:test-target "test"
#:make-flags
- (list "CC=gcc" (string-append "PREFIX=" (assoc-ref %outputs "out")))))
+ (list "CC=gcc" (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ "exif=1")))
(native-inputs
`(("perl" ,perl)
("perl-test-command" ,perl-test-command)))
(inputs `(("imlib2" ,imlib2)
("curl" ,curl)
+ ("libexif" ,libexif)
("libpng" ,libpng)
("libxt" ,libxt)
("libx11" ,libx11)
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index d70811bccf..c6010f1f56 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -18,7 +18,7 @@
;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 8bb0162a47..696544c368 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -398,8 +398,8 @@ It has been modified to remove all non-free binary blobs.")
;; supports qemu "virt" machine and possibly a large number of ARM boards.
;; See : https://wiki.debian.org/DebianKernel/ARMMP.
-(define %linux-libre-version "4.18.4")
-(define %linux-libre-hash "1q3bndhwxwcrlyi0qcgxjsp5fl92wkfgk4y41qwrrywfv9xj3sl7")
+(define %linux-libre-version "4.18.5")
+(define %linux-libre-hash "1y52ns34vh9p4pfj08xsycv8p0xywm6dbpdi0wwpkll1xgpqikvf")
(define %linux-libre-4.18-patches
(list %boot-logo-patch
@@ -429,8 +429,8 @@ It has been modified to remove all non-free binary blobs.")
#:patches %linux-libre-4.18-patches
#:configuration-file kernel-config))
-(define %linux-libre-4.14-version "4.14.66")
-(define %linux-libre-4.14-hash "1sf18m6xjyg535yviz3yjbislf57s180y67z7mzbcl5pq9352bg9")
+(define %linux-libre-4.14-version "4.14.67")
+(define %linux-libre-4.14-hash "050zvdxjy6sc64q75pr1gxsmh49chwav2pwxz8xlif39bvahnrpg")
(define-public linux-libre-4.14
(make-linux-libre %linux-libre-4.14-version
@@ -439,14 +439,14 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
- (make-linux-libre "4.9.123"
- "1rljdp3vzhmdc6qha6b9dq0d1a3xz06rn51pb4ad3a2y61mph9sv"
+ (make-linux-libre "4.9.124"
+ "0p78gx5jiqvaf2cadf5jp40lzgarrg0m0ybf9w2499v28vjsp30q"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
- (make-linux-libre "4.4.151"
- "0irzdq4p8a6dxyx5basgrc7af7w48hmyjwbk5hff8wn8jy71p9zm"
+ (make-linux-libre "4.4.152"
+ "082aajyr363ca95pxlg9iascf5d7k2gbw9ggsbsa1hj6nhspsxw6"
%intel-compatible-systems
#:configuration-file kernel-config))
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index af2dcf8eaf..edffcfce96 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -16,7 +16,7 @@
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 nee <nee.git@hidamari.blue>
;;; Copyright © 2018 Stefan Reichör <stefan@xsteve.at>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 95cdd5c513..943bcecb86 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -25,7 +25,7 @@
;;; Copyright © 2018 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm
index a63fd9bb36..e09bbea5cc 100644
--- a/gnu/packages/password-utils.scm
+++ b/gnu/packages/password-utils.scm
@@ -19,7 +19,7 @@
;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
;;; Copyright © 2018 Thomas Sigurdsen <tonton@riseup.net>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Amirouche Boubekki <amirouche@hypermove.net>
;;;
;;; This file is part of GNU Guix.
diff --git a/gnu/packages/patches/avogadro-boost148.patch b/gnu/packages/patches/avogadro-boost148.patch
new file mode 100644
index 0000000000..f244f14674
--- /dev/null
+++ b/gnu/packages/patches/avogadro-boost148.patch
@@ -0,0 +1,69 @@
+Index: avogadro-1.2.0/libavogadro/src/pythonengine_p.h
+===================================================================
+--- avogadro-1.2.0.orig/libavogadro/src/pythonengine_p.h
++++ avogadro-1.2.0/libavogadro/src/pythonengine_p.h
+@@ -31,7 +31,9 @@
+
+ #include <avogadro/global.h>
+ #include <avogadro/engine.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+
+ namespace Avogadro {
+
+Index: avogadro-1.2.0/libavogadro/src/pythonextension_p.h
+===================================================================
+--- avogadro-1.2.0.orig/libavogadro/src/pythonextension_p.h
++++ avogadro-1.2.0/libavogadro/src/pythonextension_p.h
+@@ -33,7 +33,9 @@
+ #include <avogadro/extension.h>
+ #include <avogadro/primitive.h>
+ #include <avogadro/glwidget.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+
+ #include <QWidget>
+ #include <QList>
+Index: avogadro-1.2.0/libavogadro/src/pythontool_p.h
+===================================================================
+--- avogadro-1.2.0.orig/libavogadro/src/pythontool_p.h
++++ avogadro-1.2.0/libavogadro/src/pythontool_p.h
+@@ -31,7 +31,9 @@
+
+ #include <avogadro/global.h>
+ #include <avogadro/tool.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+
+ #include <QObject>
+ #include <QAction>
+Index: avogadro-1.2.0/libavogadro/src/pythoninterpreter.h
+===================================================================
+--- avogadro-1.2.0.orig/libavogadro/src/pythoninterpreter.h
++++ avogadro-1.2.0/libavogadro/src/pythoninterpreter.h
+@@ -26,7 +26,9 @@
+ #define PYTHONINTERPRETER_H
+
+ #include <avogadro/global.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+ #include <avogadro/primitive.h>
+ #include <QString>
+
+Index: avogadro-1.2.0/libavogadro/src/pythonscript.h
+===================================================================
+--- avogadro-1.2.0.orig/libavogadro/src/pythonscript.h
++++ avogadro-1.2.0/libavogadro/src/pythonscript.h
+@@ -27,6 +27,8 @@
+ #define PYTHONSCRIPT_H
+
+ #include <avogadro/global.h>
++#ifndef Q_MOC_RUN
+ #include <boost/python.hpp>
++#endif
+
+ #include "pythonerror.h"
diff --git a/gnu/packages/patches/avogadro-eigen3-update.patch b/gnu/packages/patches/avogadro-eigen3-update.patch
new file mode 100644
index 0000000000..a5f669292f
--- /dev/null
+++ b/gnu/packages/patches/avogadro-eigen3-update.patch
@@ -0,0 +1,603 @@
+From 43af3c117b0b3220b15c2fe2895b94bbd83d3a60 Mon Sep 17 00:00:00 2001
+From: Claudio Fernandes <claudiosf.claudio@gmail.com>
+Date: Sun, 15 Jan 2017 21:23:39 -0200
+Subject: [PATCH] Adapt Avogadro to Eigen 3.3
+
+---
+ CMakeLists.txt | 9 +------
+ avogadro/src/mainwindow.cpp | 5 ++--
+ libavogadro/src/camera.cpp | 10 ++++----
+ libavogadro/src/camera.h | 14 +++++------
+ libavogadro/src/engines/wireengine.cpp | 4 ++--
+ .../crystallography/crystallographyextension.cpp | 2 +-
+ .../crystallography/ui/ceviewoptionswidget.cpp | 2 +-
+ .../src/extensions/orca/orcaanalysedialog.cpp | 1 -
+ .../src/extensions/orca/orcainputdialog.cpp | 1 -
+ .../src/extensions/qtaim/qtaimmathutilities.cpp | 1 +
+ .../qtaim/qtaimwavefunctionevaluator.cpp | 28 +++++++++++-----------
+ .../extensions/surfaces/openqube/gamessukout.cpp | 1 +
+ .../src/extensions/surfaces/openqube/slaterset.cpp | 6 +++--
+ libavogadro/src/glpainter_p.cpp | 14 +++++------
+ libavogadro/src/glwidget.cpp | 4 ++--
+ libavogadro/src/molecule.cpp | 26 ++++++++++++++++++--
+ libavogadro/src/navigate.cpp | 2 +-
+ libavogadro/src/tools/bondcentrictool.cpp | 28 +++++++++++-----------
+ libavogadro/src/tools/manipulatetool.cpp | 17 +++++++------
+ libavogadro/src/tools/navigatetool.cpp | 3 ++-
+ libavogadro/src/tools/skeletontree.cpp | 7 +++---
+ libavogadro/src/tools/skeletontree.h | 2 +-
+ 22 files changed, 102 insertions(+), 85 deletions(-)
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -231,14 +231,7 @@ if(NOT Linguist_FOUND)
+ message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
+ endif()
+
+-find_package(Eigen3) # find and setup Eigen3 if available
+-if(NOT EIGEN3_FOUND)
+- message(STATUS "Cannot find Eigen3, trying Eigen2")
+- find_package(Eigen2 REQUIRED) # Some version is required
+-else()
+-# Use Stage10 Eigen3 support
+- set (EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API TRUE)
+-endif()
++find_package(Eigen3 REQUIRED) # find and setup Eigen3 if available
+
+ find_package(ZLIB REQUIRED)
+ find_package(OpenBabel2 REQUIRED) # find and setup OpenBabel
+--- a/avogadro/src/mainwindow.cpp
++++ b/avogadro/src/mainwindow.cpp
+@@ -115,7 +115,6 @@
+ #include <QDebug>
+
+ #include <Eigen/Geometry>
+-#include <Eigen/Array>
+ #define USEQUAT
+ // This is a "hidden" exported Qt function on the Mac for Qt-4.x.
+ #ifdef Q_WS_MAC
+@@ -2775,7 +2774,7 @@ protected:
+ linearGoal.row(1) = linearGoal.row(2).cross(linearGoal.row(0));
+
+ // calculate the translation matrix
+- Transform3d goal(linearGoal);
++ Projective3d goal(linearGoal);
+
+ goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
+
+@@ -2840,7 +2839,7 @@ protected:
+ Matrix3d linearGoal = Matrix3d::Identity();
+
+ // calculate the translation matrix
+- Transform3d goal(linearGoal);
++ Projective3d goal(linearGoal);
+
+ goal.pretranslate(- 3.0 * (d->glWidget->radius() + CAMERA_NEAR_DISTANCE) * Vector3d::UnitZ());
+
+--- a/libavogadro/src/camera.cpp
++++ b/libavogadro/src/camera.cpp
+@@ -47,7 +47,7 @@ namespace Avogadro
+
+ CameraPrivate() {};
+
+- Eigen::Transform3d modelview, projection;
++ Eigen::Projective3d modelview, projection;
+ const GLWidget *parent;
+ double angleOfViewY;
+ double orthoScale;
+@@ -169,20 +169,20 @@ namespace Avogadro
+
+ double Camera::distance(const Eigen::Vector3d & point) const
+ {
+- return ( d->modelview * point ).norm();
++ return ( d->modelview * point.homogeneous() ).head<3>().norm();
+ }
+
+- void Camera::setModelview(const Eigen::Transform3d &matrix)
++ void Camera::setModelview(const Eigen::Projective3d &matrix)
+ {
+ d->modelview = matrix;
+ }
+
+- const Eigen::Transform3d & Camera::modelview() const
++ const Eigen::Projective3d & Camera::modelview() const
+ {
+ return d->modelview;
+ }
+
+- Eigen::Transform3d & Camera::modelview()
++ Eigen::Projective3d & Camera::modelview()
+ {
+ return d->modelview;
+ }
+--- a/libavogadro/src/camera.h
++++ b/libavogadro/src/camera.h
+@@ -101,16 +101,16 @@ namespace Avogadro {
+ double angleOfViewY() const;
+ /** Sets 4x4 "modelview" matrix representing the camera orientation and position.
+ * @param matrix the matrix to copy from
+- * @sa Eigen::Transform3d & modelview(), applyModelview() */
+- void setModelview(const Eigen::Transform3d &matrix);
++ * @sa Eigen::Projective3d & modelview(), applyModelview() */
++ void setModelview(const Eigen::Projective3d &matrix);
+ /** @return a constant reference to the 4x4 "modelview" matrix representing
+ * the camera orientation and position
+- * @sa setModelview(), Eigen::Transform3d & modelview() */
+- const Eigen::Transform3d & modelview() const;
++ * @sa setModelview(), Eigen::Projective3d & modelview() */
++ const Eigen::Projective3d & modelview() const;
+ /** @return a non-constant reference to the 4x4 "modelview" matrix representing
+ * the camera orientation and position
+- * @sa setModelview(), const Eigen::Transform3d & modelview() const */
+- Eigen::Transform3d & modelview();
++ * @sa setModelview(), const Eigen::Projective3d & modelview() const */
++ Eigen::Projective3d & modelview();
+ /** Calls gluPerspective() or glOrtho() with parameters automatically chosen
+ * for rendering the GLWidget's molecule with this camera. Should be called
+ * only in GL_PROJECTION matrix mode. Example code is given
+@@ -342,7 +342,7 @@ namespace Avogadro {
+ * @return {x/w, y/w, z/w} vector
+ */
+ Eigen::Vector3d V4toV3DivW(const Eigen::Vector4d & v4) {
+- return v4.start<3>()/v4.w();
++ return v4.head<3>()/v4.w();
+ }
+ };
+
+--- a/libavogadro/src/engines/wireengine.cpp
++++ b/libavogadro/src/engines/wireengine.cpp
+@@ -109,7 +109,7 @@ namespace Avogadro {
+ const Camera *camera = pd->camera();
+
+ // perform a rough form of frustum culling
+- Eigen::Vector3d transformedPos = pd->camera()->modelview() * v;
++ Eigen::Vector3d transformedPos = (pd->camera()->modelview() * v.homogeneous()).head<3>();
+ double dot = transformedPos.z() / transformedPos.norm();
+ if(dot > -0.8)
+ return true;
+@@ -167,7 +167,7 @@ namespace Avogadro {
+ map = pd->colorMap(); // fall back to global color map
+
+ // perform a rough form of frustum culling
+- Eigen::Vector3d transformedEnd1 = pd->camera()->modelview() * v1;
++ Eigen::Vector3d transformedEnd1 = (pd->camera()->modelview() * v1.homogeneous()).head<3>();
+ double dot = transformedEnd1.z() / transformedEnd1.norm();
+ if(dot > -0.8)
+ return true; // i.e., don't bother rendering
+--- a/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
++++ b/libavogadro/src/extensions/crystallography/crystallographyextension.cpp
+@@ -1989,7 +1989,7 @@ namespace Avogadro
+ // fix coordinates
+ // Apply COB matrix:
+ Eigen::Matrix3d invCob;
+- cob.computeInverse(&invCob);
++ invCob = cob.inverse();
+ for (QList<Eigen::Vector3d>::iterator
+ it = fcoords.begin(),
+ it_end = fcoords.end();
+--- a/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
++++ b/libavogadro/src/extensions/crystallography/ui/ceviewoptionswidget.cpp
+@@ -139,7 +139,7 @@ namespace Avogadro
+ {
+ // View into a Miller plane
+ Camera *camera = m_glWidget->camera();
+- Eigen::Transform3d modelView;
++ Eigen::Projective3d modelView;
+ modelView.setIdentity();
+
+ // OK, so we want to rotate to look along the normal at the plane
+--- a/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
++++ b/libavogadro/src/extensions/orca/orcaanalysedialog.cpp
+@@ -41,7 +41,6 @@
+ #include <openbabel/mol.h>
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
+
+ #include <vector>
+
+--- a/libavogadro/src/extensions/orca/orcainputdialog.cpp
++++ b/libavogadro/src/extensions/orca/orcainputdialog.cpp
+@@ -33,7 +33,6 @@
+ #include <openbabel/mol.h>
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
+
+ #include <vector>
+
+--- a/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
++++ b/libavogadro/src/extensions/qtaim/qtaimmathutilities.cpp
+@@ -28,6 +28,7 @@
+
+ #include <cmath>
+ #include <Eigen/QR>
++#include <Eigen/Eigenvalues>
+
+ namespace Avogadro {
+ namespace QTAIMMathUtilities {
+--- a/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
++++ b/libavogadro/src/extensions/qtaim/qtaimwavefunctionevaluator.cpp
+@@ -35,21 +35,21 @@ namespace Avogadro
+ m_nprim=wfn.numberOfGaussianPrimitives();
+ m_nnuc=wfn.numberOfNuclei();
+
+- m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.xNuclearCoordinates(),m_nnuc);
+- m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(wfn.yNuclearCoordinates(),m_nnuc);
+- m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(wfn.zNuclearCoordinates(),m_nnuc);
+- m_nucz=Map<Matrix<qint64,Dynamic,1> >(wfn.nuclearCharges(),m_nnuc);
+- m_X0=Map<Matrix<qreal,Dynamic,1> >(wfn.xGaussianPrimitiveCenterCoordinates(),m_nprim,1);
+- m_Y0=Map<Matrix<qreal,Dynamic,1> >(wfn.yGaussianPrimitiveCenterCoordinates(),m_nprim,1);
+- m_Z0=Map<Matrix<qreal,Dynamic,1> >(wfn.zGaussianPrimitiveCenterCoordinates(),m_nprim,1);
+- m_xamom=Map<Matrix<qint64,Dynamic,1> >(wfn.xGaussianPrimitiveAngularMomenta(),m_nprim,1);
+- m_yamom=Map<Matrix<qint64,Dynamic,1> >(wfn.yGaussianPrimitiveAngularMomenta(),m_nprim,1);
+- m_zamom=Map<Matrix<qint64,Dynamic,1> >(wfn.zGaussianPrimitiveAngularMomenta(),m_nprim,1);
+- m_alpha=Map<Matrix<qreal,Dynamic,1> >(wfn.gaussianPrimitiveExponentCoefficients(),m_nprim,1);
++ m_nucxcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xNuclearCoordinates()),m_nnuc);
++ m_nucycoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yNuclearCoordinates()),m_nnuc);
++ m_nuczcoord=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zNuclearCoordinates()),m_nnuc);
++ m_nucz=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.nuclearCharges()),m_nnuc);
++ m_X0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.xGaussianPrimitiveCenterCoordinates()),m_nprim,1);
++ m_Y0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.yGaussianPrimitiveCenterCoordinates()),m_nprim,1);
++ m_Z0=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.zGaussianPrimitiveCenterCoordinates()),m_nprim,1);
++ m_xamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.xGaussianPrimitiveAngularMomenta()),m_nprim,1);
++ m_yamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.yGaussianPrimitiveAngularMomenta()),m_nprim,1);
++ m_zamom=Map<Matrix<qint64,Dynamic,1> >(const_cast<qint64*>(wfn.zGaussianPrimitiveAngularMomenta()),m_nprim,1);
++ m_alpha=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.gaussianPrimitiveExponentCoefficients()),m_nprim,1);
+ // TODO Implement screening for unoccupied molecular orbitals.
+- m_occno=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalOccupationNumbers(),m_nmo,1);
+- m_orbe=Map<Matrix<qreal,Dynamic,1> >(wfn.molecularOrbitalEigenvalues(),m_nmo,1);
+- m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(wfn.molecularOrbitalCoefficients(),m_nmo,m_nprim);
++ m_occno=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalOccupationNumbers()),m_nmo,1);
++ m_orbe=Map<Matrix<qreal,Dynamic,1> >(const_cast<qreal*>(wfn.molecularOrbitalEigenvalues()),m_nmo,1);
++ m_coef=Map<Matrix<qreal,Dynamic,Dynamic,RowMajor> >(const_cast<qreal*>(wfn.molecularOrbitalCoefficients()),m_nmo,m_nprim);
+ m_totalEnergy=wfn.totalEnergy();
+ m_virialRatio=wfn.virialRatio();
+
+--- a/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
++++ b/libavogadro/src/extensions/surfaces/openqube/gamessukout.cpp
+@@ -19,6 +19,7 @@
+ using Eigen::Vector3d;
+ using std::vector;
+
++#include <iostream>
+ #include <fstream>
+
+ namespace OpenQube
+--- a/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
++++ b/libavogadro/src/extensions/surfaces/openqube/slaterset.cpp
+@@ -25,9 +25,9 @@
+
+ #include "cube.h"
+
+-#include <Eigen/Array>
+ #include <Eigen/LU>
+ #include <Eigen/QR>
++#include <Eigen/Eigenvalues>
+
+ #include <cmath>
+
+@@ -250,7 +250,9 @@ bool SlaterSet::initialize()
+
+ SelfAdjointEigenSolver<MatrixXd> s(m_overlap);
+ MatrixXd p = s.eigenvectors();
+- MatrixXd m = p * s.eigenvalues().cwise().inverse().cwise().sqrt().asDiagonal() * p.inverse();
++ // TODO check if this is correct
++ MatrixXd m1 = (s.eigenvalues().array().inverse().sqrt());
++ MatrixXd m = p.array()*(m1.diagonal().array())*p.inverse().array();
+ m_normalized = m * m_eigenVectors;
+
+ if (!(m_overlap*m*m).isIdentity())
+--- a/libavogadro/src/glpainter_p.cpp
++++ b/libavogadro/src/glpainter_p.cpp
+@@ -789,13 +789,13 @@ namespace Avogadro
+ } else {
+ points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
+ }
+- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
++ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
+ }
+
+ // Get vectors representing the points' positions in terms of the model view.
+- Eigen::Vector3d _origin = d->widget->camera()->modelview() * origin;
+- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin+u);
+- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin+v);
++ Eigen::Vector3d _origin = (d->widget->camera()->modelview() * origin.homogeneous()).head<3>();
++ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin+u).homogeneous()).head<3>();
++ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin+v).homogeneous()).head<3>();
+
+ glPushAttrib(GL_ALL_ATTRIB_BITS);
+ glPushMatrix();
+@@ -880,12 +880,12 @@ namespace Avogadro
+ } else {
+ points[theta-1] = Eigen::AngleAxisd(theta * (M_PI / 180.0) / 2, n) * u;
+ }
+- points[theta-1] = d->widget->camera()->modelview() * (origin + points[theta-1]);
++ points[theta-1] = (d->widget->camera()->modelview() * (origin + points[theta-1]).homogeneous()).head<3>();
+ }
+
+ // Get vectors representing the points' positions in terms of the model view.
+- Eigen::Vector3d _direction1 = d->widget->camera()->modelview() * (origin + u);
+- Eigen::Vector3d _direction2 = d->widget->camera()->modelview() * (origin + v);
++ Eigen::Vector3d _direction1 = (d->widget->camera()->modelview() * (origin + u).homogeneous()).head<3>();
++ Eigen::Vector3d _direction2 = (d->widget->camera()->modelview() * (origin + v).homogeneous()).head<3>();
+
+ glPushAttrib(GL_ALL_ATTRIB_BITS);
+ glPushMatrix();
+--- a/libavogadro/src/glwidget.cpp
++++ b/libavogadro/src/glwidget.cpp
+@@ -765,7 +765,7 @@ namespace Avogadro {
+ GLfloat fogColor[4]= {static_cast<GLfloat>(d->background.redF()), static_cast<GLfloat>(d->background.greenF()),
+ static_cast<GLfloat>(d->background.blueF()), static_cast<GLfloat>(d->background.alphaF())};
+ glFogfv(GL_FOG_COLOR, fogColor);
+- Vector3d distance = camera()->modelview() * d->center;
++ Vector3d distance = (camera()->modelview() * d->center.homogeneous()).head<3>();
+ double distanceToCenter = distance.norm();
+ glFogf(GL_FOG_DENSITY, 1.0);
+ glHint(GL_FOG_HINT, GL_NICEST);
+@@ -1711,7 +1711,7 @@ namespace Avogadro {
+
+ if (d->renderModelViewDebug) {
+ // Model view matrix:
+- const Eigen::Transform3d &modelview = d->camera->modelview();
++ const Eigen::Projective3d &modelview = d->camera->modelview();
+ y += d->pd->painter()->drawText
+ (x, y, tr("ModelView row 1: %L1 %L2 %L3 %L4")
+ .arg(modelview(0, 0), 6, 'f', 2, ' ')
+--- a/libavogadro/src/molecule.cpp
++++ b/libavogadro/src/molecule.cpp
+@@ -38,7 +38,7 @@
+ #include "zmatrix.h"
+
+ #include <Eigen/Geometry>
+-#include <Eigen/LeastSquares>
++#include <Eigen/Eigenvalues>
+
+ #include <vector>
+
+@@ -1907,7 +1907,29 @@ namespace Avogadro{
+ }
+ d->center /= static_cast<double>(nAtoms);
+ Eigen::Hyperplane<double, 3> planeCoeffs;
+- Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
++ //Eigen::fitHyperplane(numAtoms(), atomPositions, &planeCoeffs);
++
++ // TODO check if this is OK
++ /************************/
++ typedef Eigen::Matrix<double,3,3> CovMatrixType;
++ typedef Eigen::Vector3d VectorType;
++
++ VectorType mean = d->center;
++ int size=3;
++ int numPoints=numAtoms();
++ VectorType ** points=atomPositions;
++ CovMatrixType covMat = CovMatrixType::Zero(size, size);
++ VectorType remean = VectorType::Zero(size);
++ for(int i = 0; i < numPoints; ++i)
++ {
++ VectorType diff = (*(points[i]) - mean).conjugate();
++ covMat += diff * diff.adjoint();
++ }
++ Eigen::SelfAdjointEigenSolver<CovMatrixType> eig(covMat);
++ planeCoeffs.normal() = eig.eigenvectors().col(0);
++ /************************/
++
++
+ delete[] atomPositions;
+ d->normalVector = planeCoeffs.normal();
+ }
+--- a/libavogadro/src/navigate.cpp
++++ b/libavogadro/src/navigate.cpp
+@@ -40,7 +40,7 @@ namespace Avogadro {
+ void Navigate::zoom(GLWidget *widget, const Eigen::Vector3d &goal,
+ double delta)
+ {
+- Vector3d transformedGoal = widget->camera()->modelview() * goal;
++ Vector3d transformedGoal = (widget->camera()->modelview() * goal.homogeneous()).head<3>();
+ double distanceToGoal = transformedGoal.norm();
+
+ double t = ZOOM_SPEED * delta;
+--- a/libavogadro/src/tools/bondcentrictool.cpp
++++ b/libavogadro/src/tools/bondcentrictool.cpp
+@@ -578,8 +578,8 @@ namespace Avogadro {
+
+ Vector3d clicked = *m_clickedAtom->pos();
+
+- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
+- (widget->camera()->modelview() * center).z() ? -1 : 1));
++ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
++ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
+
+ Vector3d centerProj = widget->camera()->project(center);
+ centerProj -= Vector3d(0,0,centerProj.z());
+@@ -673,8 +673,8 @@ namespace Avogadro {
+
+ Vector3d clicked = *m_clickedAtom->pos();
+
+- Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other).z() >=
+- (widget->camera()->modelview() * center).z() ? -1 : 1));
++ Vector3d axis = Vector3d(0, 0, ((widget->camera()->modelview() * other.homogeneous()).z() >=
++ (widget->camera()->modelview() * center.homogeneous()).z() ? -1 : 1));
+
+ Vector3d centerProj = widget->camera()->project(center);
+ centerProj -= Vector3d(0,0,centerProj.z());
+@@ -1362,10 +1362,10 @@ namespace Avogadro {
+
+ planeVec = length * (planeVec / planeVec.norm());
+
+- Vector3d topLeft = widget->camera()->modelview() * (left + planeVec);
+- Vector3d topRight = widget->camera()->modelview() * (right + planeVec);
+- Vector3d botRight = widget->camera()->modelview() * (right - planeVec);
+- Vector3d botLeft = widget->camera()->modelview() * (left - planeVec);
++ Vector3d topLeft = (widget->camera()->modelview() * (left + planeVec).homogeneous()).head<3>();
++ Vector3d topRight = (widget->camera()->modelview() * (right + planeVec).homogeneous()).head<3>();
++ Vector3d botRight = (widget->camera()->modelview() * (right - planeVec).homogeneous()).head<3>();
++ Vector3d botLeft = (widget->camera()->modelview() * (left - planeVec).homogeneous()).head<3>();
+
+ float alpha = 0.4;
+ double lineWidth = 1.5;
+@@ -1444,10 +1444,10 @@ namespace Avogadro {
+ C = D + ((C-D).normalized() * minWidth);
+ }
+
+- Vector3d topLeft = widget->camera()->modelview() * D;
+- Vector3d topRight = widget->camera()->modelview() * C;
+- Vector3d botRight = widget->camera()->modelview() * B;
+- Vector3d botLeft = widget->camera()->modelview() * A;
++ Vector3d topLeft = (widget->camera()->modelview() * D.homogeneous()).head<3>();
++ Vector3d topRight = (widget->camera()->modelview() * C.homogeneous()).head<3>();
++ Vector3d botRight = (widget->camera()->modelview() * B.homogeneous()).head<3>();
++ Vector3d botLeft = (widget->camera()->modelview() * A.homogeneous()).head<3>();
+
+ float alpha = 0.4;
+ double lineWidth = 1.5;
+@@ -1506,12 +1506,12 @@ namespace Avogadro {
+ Vector3d positionVector)
+ {
+ //Rotate skeleton around a particular axis and center point
+- Eigen::Transform3d rotation;
++ Eigen::Projective3d rotation;
+ rotation = Eigen::AngleAxisd(angle, rotationVector);
+ rotation.pretranslate(centerVector);
+ rotation.translate(-centerVector);
+
+- return rotation*positionVector;
++ return (rotation*positionVector.homogeneous()).head<3>();
+ }
+
+ // ########## showAnglesChanged ##########
+--- a/libavogadro/src/tools/manipulatetool.cpp
++++ b/libavogadro/src/tools/manipulatetool.cpp
+@@ -40,7 +40,6 @@
+ #include <QAbstractButton>
+
+ using Eigen::Vector3d;
+-using Eigen::Transform3d;
+ using Eigen::AngleAxisd;
+
+ namespace Avogadro {
+@@ -138,7 +137,7 @@ namespace Avogadro {
+ double yRotate = m_settingsWidget->yRotateSpinBox->value() * DEG_TO_RAD;
+ double zRotate = m_settingsWidget->zRotateSpinBox->value() * DEG_TO_RAD;
+
+- Eigen::Transform3d rotation;
++ Eigen::Projective3d rotation;
+ rotation.matrix().setIdentity();
+ rotation.translation() = center;
+ rotation.rotate(AngleAxisd(xRotate, Vector3d::UnitX())
+@@ -152,12 +151,12 @@ namespace Avogadro {
+ if (p->type() == Primitive::AtomType) {
+ Atom *atom = static_cast<Atom*>(p);
+ tempPos = translate + *(atom->pos());
+- atom->setPos(rotation * tempPos);
++ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
+ }
+ } else {
+ foreach(Atom *atom, widget->molecule()->atoms()) {
+ tempPos = translate + *(atom->pos());
+- atom->setPos(rotation * tempPos);
++ atom->setPos((rotation * tempPos.homogeneous()).head<3>());
+ }
+ }
+
+@@ -199,7 +198,7 @@ namespace Avogadro {
+ widget->setCursor(Qt::SizeVerCursor);
+
+ // Move the selected atom(s) in to or out of the screen
+- Vector3d transformedGoal = widget->camera()->modelview() * *goal;
++ Vector3d transformedGoal = (widget->camera()->modelview() * goal->homogeneous()).head<3>();
+ double distanceToGoal = transformedGoal.norm();
+
+ double t = ZOOM_SPEED * delta;
+@@ -255,7 +254,7 @@ namespace Avogadro {
+
+ // Rotate the selected atoms about the center
+ // rotate only selected primitives
+- Transform3d fragmentRotation;
++ Eigen::Projective3d fragmentRotation;
+ fragmentRotation.matrix().setIdentity();
+ fragmentRotation.translation() = *center;
+ fragmentRotation.rotate(
+@@ -266,7 +265,7 @@ namespace Avogadro {
+
+ foreach(Primitive *p, widget->selectedPrimitives())
+ if (p->type() == Primitive::AtomType)
+- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
++ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
+ widget->molecule()->update();
+ }
+
+@@ -274,7 +273,7 @@ namespace Avogadro {
+ double delta) const
+ {
+ // Tilt the selected atoms about the center
+- Transform3d fragmentRotation;
++ Eigen::Projective3d fragmentRotation;
+ fragmentRotation.matrix().setIdentity();
+ fragmentRotation.translation() = *center;
+ fragmentRotation.rotate(AngleAxisd(delta * ROTATION_SPEED, widget->camera()->backTransformedZAxis()));
+@@ -282,7 +281,7 @@ namespace Avogadro {
+
+ foreach(Primitive *p, widget->selectedPrimitives())
+ if (p->type() == Primitive::AtomType)
+- static_cast<Atom *>(p)->setPos(fragmentRotation * *static_cast<Atom *>(p)->pos());
++ static_cast<Atom *>(p)->setPos((fragmentRotation * static_cast<Atom *>(p)->pos()->homogeneous()).head<3>());
+ widget->molecule()->update();
+ }
+
+--- a/libavogadro/src/tools/navigatetool.cpp
++++ b/libavogadro/src/tools/navigatetool.cpp
+@@ -92,7 +92,8 @@ namespace Avogadro {
+ double sumOfWeights = 0.;
+ QList<Atom*> atoms = widget->molecule()->atoms();
+ foreach (Atom *atom, atoms) {
+- Vector3d transformedAtomPos = widget->camera()->modelview() * *atom->pos();
++ Vector3d transformedAtomPos = (widget->camera()->modelview() *
++ atom->pos()->homogeneous()).head<3>();
+ double atomDistance = transformedAtomPos.norm();
+ double dot = transformedAtomPos.z() / atomDistance;
+ double weight = exp(-30. * (1. + dot));
+--- a/libavogadro/src/tools/skeletontree.cpp
++++ b/libavogadro/src/tools/skeletontree.cpp
+@@ -29,6 +29,7 @@
+ #include <avogadro/atom.h>
+ #include <avogadro/bond.h>
+ #include <avogadro/molecule.h>
++#include <iostream>
+
+ using namespace Eigen;
+ using namespace std;
+@@ -221,7 +222,7 @@ namespace Avogadro {
+ {
+ if (m_rootNode) {
+ //Rotate skeleton around a particular axis and center point
+- Eigen::Transform3d rotation;
++ Eigen::Projective3d rotation;
+ rotation = Eigen::AngleAxisd(angle, rotationAxis);
+ rotation.pretranslate(centerVector);
+ rotation.translate(-centerVector);
+@@ -248,11 +249,11 @@ namespace Avogadro {
+ // ########## recursiveRotate ##########
+
+ void SkeletonTree::recursiveRotate(Node* n,
+- const Eigen::Transform3d &rotationMatrix)
++ const Eigen::Projective3d &rotationMatrix)
+ {
+ // Update the root node with the new position
+ Atom* a = n->atom();
+- a->setPos(rotationMatrix * (*a->pos()));
++ a->setPos((rotationMatrix * (*a->pos()).homogeneous()).head<3>());
+ a->update();
+
+ // Now update the children
+--- a/libavogadro/src/tools/skeletontree.h
++++ b/libavogadro/src/tools/skeletontree.h
+@@ -230,6 +230,6 @@ namespace Avogadro {
+ * @param centerVector Center location to rotate around.
+ */
+ void recursiveRotate(Node* n,
+- const Eigen::Transform3d &rotationMatrix);
++ const Eigen::Projective3d &rotationMatrix);
+
+ };
+ } // End namespace Avogadro \ No newline at end of file
diff --git a/gnu/packages/patches/avogadro-python-eigen-lib.patch b/gnu/packages/patches/avogadro-python-eigen-lib.patch
new file mode 100644
index 0000000000..ac9f2e30af
--- /dev/null
+++ b/gnu/packages/patches/avogadro-python-eigen-lib.patch
@@ -0,0 +1,161 @@
+From 2d4be7ede177a8df7340fe3b209698d591ee8a04 Mon Sep 17 00:00:00 2001
+From: Claudio Fernandes <claudiosf.claudio@gmail.com>
+Date: Mon, 16 Jan 2017 19:48:23 -0200
+Subject: [PATCH] Adapt libavogadro/python to Eigen 3.3
+
+---
+ libavogadro/src/python/camera.cpp | 2 +-
+ libavogadro/src/python/eigen.cpp | 60 +++++++++++++++++++--------------------
+ 2 files changed, 31 insertions(+), 31 deletions(-)
+
+diff --git a/libavogadro/src/python/camera.cpp b/libavogadro/src/python/camera.cpp
+index 69ca87bf8..30b32af7d 100644
+--- a/libavogadro/src/python/camera.cpp
++++ b/libavogadro/src/python/camera.cpp
+@@ -10,7 +10,7 @@ using namespace Avogadro;
+ void export_Camera()
+ {
+
+- const Eigen::Transform3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
++ const Eigen::Projective3d& (Camera::*modelview_ptr)() const = &Camera::modelview;
+ Eigen::Vector3d (Camera::*unProject_ptr1)(const Eigen::Vector3d&) const = &Camera::unProject;
+ Eigen::Vector3d (Camera::*unProject_ptr2)(const QPoint&, const Eigen::Vector3d&) const = &Camera::unProject;
+ Eigen::Vector3d (Camera::*unProject_ptr3)(const QPoint&) const = &Camera::unProject;
+diff --git a/libavogadro/src/python/eigen.cpp b/libavogadro/src/python/eigen.cpp
+index c1faedbcc..20b4e719d 100644
+--- a/libavogadro/src/python/eigen.cpp
++++ b/libavogadro/src/python/eigen.cpp
+@@ -305,9 +305,9 @@ template <> struct ScalarTraits<double>
+ struct innerclass
+ {
+ //
+- // Eigen::Transform3d --> python array (4x4)
++ // Eigen::Projective3d --> python array (4x4)
+ //
+- static PyObject* convert(Eigen::Transform3d const &trans)
++ static PyObject* convert(Eigen::Projective3d const &trans)
+ {
+ npy_intp dims[2] = { 4, 4 };
+ PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
+@@ -321,9 +321,9 @@ template <> struct ScalarTraits<double>
+ return incref(result);
+ }
+ //
+- // Eigen::Transform3d* --> python array (4x4)
++ // Eigen::Projective3d* --> python array (4x4)
+ //
+- static PyObject* convert(Eigen::Transform3d *trans)
++ static PyObject* convert(Eigen::Projective3d *trans)
+ {
+ npy_intp dims[2] = { 4, 4 };
+ PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
+@@ -337,9 +337,9 @@ template <> struct ScalarTraits<double>
+ return incref(result);
+ }
+ //
+- // const Eigen::Transform3d* --> python array (4x4)
++ // const Eigen::Projective3d* --> python array (4x4)
+ //
+- static PyObject* convert(const Eigen::Transform3d *trans)
++ static PyObject* convert(const Eigen::Projective3d *trans)
+ {
+ npy_intp dims[2] = { 4, 4 };
+ PyObject *result = PyArray_SimpleNew(2, dims, PyArray_DOUBLE);
+@@ -358,10 +358,10 @@ template <> struct ScalarTraits<double>
+ Transform3d_to_python_array()
+ {
+ #ifndef WIN32
+- to_python_converter<Eigen::Transform3d, innerclass>();
++ to_python_converter<Eigen::Projective3d, innerclass>();
+ #endif
+- to_python_converter<Eigen::Transform3d*, innerclass>();
+- to_python_converter<const Eigen::Transform3d*, innerclass>();
++ to_python_converter<Eigen::Projective3d*, innerclass>();
++ to_python_converter<const Eigen::Projective3d*, innerclass>();
+ }
+
+ };
+@@ -373,17 +373,17 @@ template <> struct ScalarTraits<double>
+ // Insert an rvalue from_python converter at the tail of the
+ // chain. Used for implicit conversions
+ //
+- // python array --> Eigen::Transform3d
++ // python array --> Eigen::Projective3d
+ //
+ // used for:
+ //
+- // void function(Eigen::Transform3d vec)
+- // void function(Eigen::Transform3d & vec)
+- // void function(const Eigen::Transform3d & vec)
++ // void function(Eigen::Projective3d vec)
++ // void function(Eigen::Projective3d & vec)
++ // void function(const Eigen::Projective3d & vec)
+ //
+- converter::registry::push_back( &convertible, &construct, type_id<Eigen::Transform3d>() );
++ converter::registry::push_back( &convertible, &construct, type_id<Eigen::Projective3d>() );
+
+- converter::registry::insert( &convert, type_id<Eigen::Transform3d>() );
++ converter::registry::insert( &convert, type_id<Eigen::Projective3d>() );
+ }
+
+ static void* convert(PyObject *obj_ptr)
+@@ -401,7 +401,7 @@ template <> struct ScalarTraits<double>
+ throw_error_already_set(); // the 1D array does not have exactly 3 elements
+
+ double *values = reinterpret_cast<double*>(array->data);
+- Eigen::Transform3d *c_obj = new Eigen::Transform3d();
++ Eigen::Projective3d *c_obj = new Eigen::Projective3d();
+ double *dataPtr = c_obj->data();
+
+ for (int i = 0; i < 16; ++i)
+@@ -432,7 +432,7 @@ template <> struct ScalarTraits<double>
+ // I think this is a better way to get at the double array, where is this
+ // deleted though? Does Boost::Python do it?
+ double *values = reinterpret_cast<double*>(array->data);
+- Eigen::Transform3d *storage = new Eigen::Transform3d();
++ Eigen::Projective3d *storage = new Eigen::Projective3d();
+ double *dataPtr = storage->data();
+
+ for (int i = 0; i < 16; ++i)
+@@ -467,21 +467,21 @@ class EigenUnitTestHelper
+ void set_vector3d_ptr(Eigen::Vector3d* vec) { m_vector3d = *vec; }
+ void set_const_vector3d_ptr(const Eigen::Vector3d* const vec) { m_vector3d = *vec; }
+
+- //Eigen::Transform3d transform3d() { return m_transform3d; }
+- //Eigen::Transform3d& transform3d_ref() { return m_transform3d; }
+- const Eigen::Transform3d& const_transform3d_ref() { return m_transform3d; }
+- Eigen::Transform3d* transform3d_ptr() { return &m_transform3d; }
+- const Eigen::Transform3d* const_transform3d_ptr() { return &m_transform3d; }
+-
+- //void set_transform3d(Eigen::Transform3d vec) { m_transform3d = vec; }
+- //void set_transform3d_ref(Eigen::Transform3d& vec) { m_transform3d = vec; }
+- void set_const_transform3d_ref(const Eigen::Transform3d& vec) { m_transform3d = vec; }
+- void set_transform3d_ptr(Eigen::Transform3d* vec) { m_transform3d = *vec; }
+- void set_const_transform3d_ptr(const Eigen::Transform3d* const vec) { m_transform3d = *vec; }
++ //Eigen::Projective3d transform3d() { return m_transform3d; }
++ //Eigen::Projective3d& transform3d_ref() { return m_transform3d; }
++ const Eigen::Projective3d& const_transform3d_ref() { return m_transform3d; }
++ Eigen::Projective3d* transform3d_ptr() { return &m_transform3d; }
++ const Eigen::Projective3d* const_transform3d_ptr() { return &m_transform3d; }
++
++ //void set_transform3d(Eigen::Projective3d vec) { m_transform3d = vec; }
++ //void set_transform3d_ref(Eigen::Projective3d& vec) { m_transform3d = vec; }
++ void set_const_transform3d_ref(const Eigen::Projective3d& vec) { m_transform3d = vec; }
++ void set_transform3d_ptr(Eigen::Projective3d* vec) { m_transform3d = *vec; }
++ void set_const_transform3d_ptr(const Eigen::Projective3d* const vec) { m_transform3d = *vec; }
+
+ private:
+ Eigen::Vector3d m_vector3d;
+- Eigen::Transform3d m_transform3d;
++ Eigen::Projective3d m_transform3d;
+
+ };
+ #endif
+@@ -529,6 +529,6 @@ void export_Eigen()
+ Vector3x_to_python_array<Eigen::Vector3i>();
+ Vector3x_from_python_array<Eigen::Vector3i>();
+
+- // Eigen::Transform3d
++ // Eigen::Projective3d
+ Transform3d_to_python_array();
+ Transform3d_from_python_array();
diff --git a/gnu/packages/patches/grub-check-error-efibootmgr.patch b/gnu/packages/patches/grub-check-error-efibootmgr.patch
new file mode 100644
index 0000000000..b2fd160c9a
--- /dev/null
+++ b/gnu/packages/patches/grub-check-error-efibootmgr.patch
@@ -0,0 +1,176 @@
+Without this patch, GRUB may proceed to wipe all firmware boot entries
+and report a successful installation, even if efibootmgr hit an error.
+
+Origin URL:
+https://git.sv.gnu.org/cgit/grub.git/commit/?id=6400613ad0b463abc93362086a491cd2a5e99b0d
+
+From 6400613ad0b463abc93362086a491cd2a5e99b0d Mon Sep 17 00:00:00 2001
+From: Steve McIntyre <steve@einval.com>
+Date: Wed, 31 Jan 2018 21:49:36 +0000
+Subject: Make grub-install check for errors from efibootmgr
+
+Code is currently ignoring errors from efibootmgr, giving users
+clearly bogus output like:
+
+ Setting up grub-efi-amd64 (2.02~beta3-4) ...
+ Installing for x86_64-efi platform.
+ Could not delete variable: No space left on device
+ Could not prepare Boot variable: No space left on device
+ Installation finished. No error reported.
+
+and then potentially unbootable systems. If efibootmgr fails, grub-install
+should know that and report it!
+
+We've been using similar patch in Debian now for some time, with no ill effects.
+
+diff --git a/grub-core/osdep/unix/platform.c b/grub-core/osdep/unix/platform.c
+index a3fcfca..ca448bc 100644
+--- a/grub-core/osdep/unix/platform.c
++++ b/grub-core/osdep/unix/platform.c
+@@ -78,19 +78,20 @@ get_ofpathname (const char *dev)
+ dev);
+ }
+
+-static void
++static int
+ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+ {
+ int fd;
+ pid_t pid = grub_util_exec_pipe ((const char * []){ "efibootmgr", NULL }, &fd);
+ char *line = NULL;
+ size_t len = 0;
++ int rc;
+
+ if (!pid)
+ {
+ grub_util_warn (_("Unable to open stream from %s: %s"),
+ "efibootmgr", strerror (errno));
+- return;
++ return errno;
+ }
+
+ FILE *fp = fdopen (fd, "r");
+@@ -98,7 +99,7 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+ {
+ grub_util_warn (_("Unable to open stream from %s: %s"),
+ "efibootmgr", strerror (errno));
+- return;
++ return errno;
+ }
+
+ line = xmalloc (80);
+@@ -119,23 +120,25 @@ grub_install_remove_efi_entries_by_distributor (const char *efi_distributor)
+ bootnum = line + sizeof ("Boot") - 1;
+ bootnum[4] = '\0';
+ if (!verbosity)
+- grub_util_exec ((const char * []){ "efibootmgr", "-q",
++ rc = grub_util_exec ((const char * []){ "efibootmgr", "-q",
+ "-b", bootnum, "-B", NULL });
+ else
+- grub_util_exec ((const char * []){ "efibootmgr",
++ rc = grub_util_exec ((const char * []){ "efibootmgr",
+ "-b", bootnum, "-B", NULL });
+ }
+
+ free (line);
++ return rc;
+ }
+
+-void
++int
+ grub_install_register_efi (grub_device_t efidir_grub_dev,
+ const char *efifile_path,
+ const char *efi_distributor)
+ {
+ const char * efidir_disk;
+ int efidir_part;
++ int ret;
+ efidir_disk = grub_util_biosdisk_get_osdev (efidir_grub_dev->disk);
+ efidir_part = efidir_grub_dev->disk->partition ? efidir_grub_dev->disk->partition->number + 1 : 1;
+
+@@ -151,23 +154,26 @@ grub_install_register_efi (grub_device_t efidir_grub_dev,
+ grub_util_exec ((const char * []){ "modprobe", "-q", "efivars", NULL });
+ #endif
+ /* Delete old entries from the same distributor. */
+- grub_install_remove_efi_entries_by_distributor (efi_distributor);
++ ret = grub_install_remove_efi_entries_by_distributor (efi_distributor);
++ if (ret)
++ return ret;
+
+ char *efidir_part_str = xasprintf ("%d", efidir_part);
+
+ if (!verbosity)
+- grub_util_exec ((const char * []){ "efibootmgr", "-q",
++ ret = grub_util_exec ((const char * []){ "efibootmgr", "-q",
+ "-c", "-d", efidir_disk,
+ "-p", efidir_part_str, "-w",
+ "-L", efi_distributor, "-l",
+ efifile_path, NULL });
+ else
+- grub_util_exec ((const char * []){ "efibootmgr",
++ ret = grub_util_exec ((const char * []){ "efibootmgr",
+ "-c", "-d", efidir_disk,
+ "-p", efidir_part_str, "-w",
+ "-L", efi_distributor, "-l",
+ efifile_path, NULL });
+ free (efidir_part_str);
++ return ret;
+ }
+
+ void
+diff --git a/include/grub/util/install.h b/include/grub/util/install.h
+index 5910b0c..0dba8b6 100644
+--- a/include/grub/util/install.h
++++ b/include/grub/util/install.h
+@@ -210,7 +210,7 @@ grub_install_create_envblk_file (const char *name);
+ const char *
+ grub_install_get_default_x86_platform (void);
+
+-void
++int
+ grub_install_register_efi (grub_device_t efidir_grub_dev,
+ const char *efifile_path,
+ const char *efi_distributor);
+diff --git a/util/grub-install.c b/util/grub-install.c
+index 5e4cdfd..690f180 100644
+--- a/util/grub-install.c
++++ b/util/grub-install.c
+@@ -1848,9 +1848,13 @@ main (int argc, char *argv[])
+ if (!removable && update_nvram)
+ {
+ /* Try to make this image bootable using the EFI Boot Manager, if available. */
+- grub_install_register_efi (efidir_grub_dev,
+- "\\System\\Library\\CoreServices",
+- efi_distributor);
++ int ret;
++ ret = grub_install_register_efi (efidir_grub_dev,
++ "\\System\\Library\\CoreServices",
++ efi_distributor);
++ if (ret)
++ grub_util_error (_("efibootmgr failed to register the boot entry: %s"),
++ strerror (ret));
+ }
+
+ grub_device_close (ins_dev);
+@@ -1871,6 +1875,7 @@ main (int argc, char *argv[])
+ {
+ char * efifile_path;
+ char * part;
++ int ret;
+
+ /* Try to make this image bootable using the EFI Boot Manager, if available. */
+ if (!efi_distributor || efi_distributor[0] == '\0')
+@@ -1887,8 +1892,11 @@ main (int argc, char *argv[])
+ efidir_grub_dev->disk->name,
+ (part ? ",": ""), (part ? : ""));
+ grub_free (part);
+- grub_install_register_efi (efidir_grub_dev,
+- efifile_path, efi_distributor);
++ ret = grub_install_register_efi (efidir_grub_dev,
++ efifile_path, efi_distributor);
++ if (ret)
++ grub_util_error (_("efibootmgr failed to register the boot entry: %s"),
++ strerror (ret));
+ }
+ break;
+
diff --git a/gnu/packages/patches/python-pygit2-disable-network-tests.patch b/gnu/packages/patches/python-pygit2-disable-network-tests.patch
deleted file mode 100644
index 5578e4c375..0000000000
--- a/gnu/packages/patches/python-pygit2-disable-network-tests.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Disable tests trying to look up remote servers.
-
-diff --git a/test/test_credentials.py b/test/test_credentials.py
---- a/test/test_credentials.py
-+++ b/test/test_credentials.py
-@@ -68,6 +68,7 @@ class CredentialCreateTest(utils.NoRepoTestCase):
- self.assertEqual((username, None, None, None), cred.credential_tuple)
-
-
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class CredentialCallback(utils.RepoTestCase):
- def test_callback(self):
- class MyCallbacks(pygit2.RemoteCallbacks):
-@@ -92,6 +93,7 @@ class CredentialCallback(utils.RepoTestCase):
- remote = self.repo.create_remote("github", url)
- self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks()))
-
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class CallableCredentialTest(utils.RepoTestCase):
-
- def test_user_pass(self):
-diff --git a/test/test_repository.py b/test/test_repository.py
---- a/test/test_repository.py
-+++ b/test/test_repository.py
-@@ -573,6 +573,7 @@ class CloneRepositoryTest(utils.NoRepoTestCase):
- self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references())
- self.assertIsNotNone(repo.remotes["custom_remote"])
-
-+ @unittest.skipIf(True, "network tests are not supported in Guix")
- def test_clone_with_credentials(self):
- repo = clone_repository(
- "https://bitbucket.org/libgit2/testgitrepository.git",
-diff --git a/test/test_submodule.py b/test/test_submodule.py
---- a/test/test_submodule.py
-+++ b/test/test_submodule.py
-@@ -42,6 +42,7 @@ SUBM_PATH = 'submodule'
- SUBM_URL = 'https://github.com/libgit2/pygit2'
- SUBM_HEAD_SHA = '819cbff552e46ac4b8d10925cc422a30aa04e78e'
-
-+@unittest.skipIf(True, "network tests are not supported in Guix")
- class SubmoduleTest(utils.SubmoduleRepoTestCase):
-
- def test_lookup_submodule(self):
diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm
index a2900c34c0..16010b441f 100644
--- a/gnu/packages/perl-check.scm
+++ b/gnu/packages/perl-check.scm
@@ -12,7 +12,7 @@
;;; Copyright © 2017 Petter <petter@mykolab.ch>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;;
;;; This file is part of GNU Guix.
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 8bdd221a53..47d5d8bbb2 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -19,7 +19,7 @@
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
;;;
;;; This file is part of GNU Guix.
diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm
index 5b5ec89fc2..3fd3d0854b 100644
--- a/gnu/packages/photo.scm
+++ b/gnu/packages/photo.scm
@@ -109,7 +109,7 @@ cameras (CRW/CR2, NEF, RAF, DNG, and others).")
(base32
"06nlsibr3ylfwp28w8f5466l6drgrnydgxrm4jmxzrmk5svaxk8n"))))
(build-system gnu-build-system)
- (home-page "http://libexif.sourceforge.net/")
+ (home-page "https://libexif.github.io/")
(synopsis "Read and manipulate EXIF data in digital photographs")
(description
"The libexif C library allows applications to read, edit, and save EXIF
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 15f6d33121..dd33ba8e0c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3172,16 +3172,14 @@ association studies (GWAS) on extremely large data sets.")
(define-public python-pygit2
(package
(name "python-pygit2")
- (version "0.26.0")
+ (version "0.26.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pygit2" version))
(sha256
(base32
- "1cbc488ra3kg7r3qky17ms0szi3cda2d96qfkv1l9djsy9hnvw57"))
- (patches
- (search-patches "python-pygit2-disable-network-tests.patch"))))
+ "145k3fsd21274swia7mcc7n3kzlbd47xmg55mxsjdb5d9b7fr858"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)
diff --git a/gnu/packages/slang.scm b/gnu/packages/slang.scm
index f9956d0113..24eb5fa137 100644
--- a/gnu/packages/slang.scm
+++ b/gnu/packages/slang.scm
@@ -37,14 +37,14 @@
(define-public slang
(package
(name "slang")
- (version "2.3.1a")
+ (version "2.3.2")
(source (origin
(method url-fetch)
(uri (string-append "http://www.jedsoft.org/releases/slang/slang-"
version ".tar.bz2"))
(sha256
(base32
- "0dlcy0hn0j6cj9qj5x6hpb0axifnvzzmv5jqq0wq14fygw0c7w2l"))
+ "06p379fqn6w38rdpqi98irxi2bf4llb0rja3dlgkqz7nqh7kp7pw"))
(modules '((guix build utils)))
(snippet
'(begin
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 355683df8a..ce34423713 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -14,7 +14,7 @@
;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 01e41b1914..6825cd7d2d 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -24,7 +24,7 @@
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
;;; Copyright © 2018 Brendan Tildesley <brendan.tildesley@openmailbox.org>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
diff --git a/gnu/packages/xdisorg.scm b/gnu/packages/xdisorg.scm
index ffd9e252e8..2e64ce35ad 100644
--- a/gnu/packages/xdisorg.scm
+++ b/gnu/packages/xdisorg.scm
@@ -23,7 +23,7 @@
;;; Copyright © 2017 Mike Gerwitz <mtg@gnu.org>
;;; Copyright © 2018 Thomas Sigurdsen <tonton@riseup.net>
;;; Copyright © 2018 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Pierre Neidhardt <ambrevar@gmail.com>
+;;; Copyright © 2018 Pierre Neidhardt <mail@ambrevar.xyz>
;;;
;;; This file is part of GNU Guix.
;;;