diff options
Diffstat (limited to 'gnu')
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. ;;; |