gnu: r-fields: Update to 11.4.
[jackhill/guix/guix.git] / gnu / packages / package-management.scm
index e1e7d6a..bcd7c69 100644 (file)
@@ -1,17 +1,21 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2015, 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2017, 2020 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017 Muriithi Frederick Muriuki <fredmanglis@gmail.com>
 ;;; Copyright © 2017, 2018 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2018 Sou Bunnbu <iyzsong@member.fsf.org>
-;;; Copyright © 2018 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2019 Vagrant Cascadian <vagrant@reproducible-builds.org>
+;;; Copyright © 2018, 2019 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2019 Jonathan Brielmaier <jonathan.brielmaier@web.de>
+;;; Copyright © 2020 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2020 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
+;;; Copyright © 2020 Giacomo Leidi <goodoldpaul@autistici.org>
+;;; Copyright © 2020 Jesse Gibbons <jgibbons2357+guix@gmail.com>
+;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages bdw-gc)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages bootstrap)          ;for 'bootstrap-guile-origin'
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)
+  #:use-module (gnu packages hurd)
+  #:use-module (gnu packages libedit)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lisp)
   #:use-module (gnu packages man)
   #:use-module (gnu packages nettle)
+  #:use-module (gnu packages networking)
   #:use-module (gnu packages nss)
   #:use-module (gnu packages patchutils)
   #:use-module (gnu packages perl)
                         arch "-linux"
                         "/20131110/guile-2.0.9.tar.xz"))))
 
+;; NOTE: The commit IDs used here form a linked list threaded through the git
+;; history. In a phenomenon known as boot-stripping, not only the head of this
+;; list is used, but also a few older versions, when a guix from this package is
+;; used to build something also depending on guix.
+;;
+;; Therefore, if, by accident, you set this package to a non-existent commit ID,
+;; it is insufficient to simply correct it with the latest commit.
+;; Instead, please push one commit that rolls back Guix to before the mistake,
+;; and then another that points to the first one. That way, the faulty commit
+;; won't appear on the linked list.
 (define-public guix
   ;; Latest version of Guix, which may or may not correspond to a release.
   ;; Note: the 'update-guix-package.scm' script expects this definition to
   ;; start precisely like this.
-  (let ((version "1.0.1")
-        (commit "4a54ed774913480c0f8dad3caf0cd627e4fa8ebf")
-        (revision 3))
+  (let ((version "1.1.0")
+        (commit "44c6e6f590b706f1ecfea6a7e7406bbd7cb70736")
+        (revision 25))
     (package
       (name "guix")
 
                       (commit commit)))
                 (sha256
                  (base32
-                  "14m4a4bn0d5hav6mrks5d7r223knx9dpswgbsc875wgr2921na2h"))
+                  "17kmn9yrk9pxi88v4d48h9q3m5dpd2j0pf15fhxzh4k915jv8n6k"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (build-system gnu-build-system)
       (arguments
                             ;; To avoid problems with the length of shebangs,
                             ;; choose a fixed-width and short directory name
                             ;; for tests.
-                            "ac_cv_guix_test_root=/tmp/guix-tests")
+                            "ac_cv_guix_test_root=/tmp/guix-tests"
+                            ,@(if (hurd-target?) '("--with-courage") '()))
          #:parallel-tests? #f         ;work around <http://bugs.gnu.org/21097>
 
          #:modules ((guix build gnu-build-system)
                           (lambda (port)
                             (display ,version port)))
 
+                        ;; Install SysV init files to $(prefix)/etc rather
+                        ;; than to /etc.
+                        (substitute* "nix/local.mk"
+                          (("^sysvinitservicedir = .*$")
+                           (string-append "sysvinitservicedir = \
+$(prefix)/etc/init.d\n")))
+
                         (invoke "sh" "bootstrap")))
+                    (add-before 'build 'use-host-compressors
+                      (lambda* (#:key inputs target #:allow-other-keys)
+                        (when target
+                          ;; Use host compressors.
+                          (let ((bzip2 (assoc-ref inputs "bzip2"))
+                                (gzip (assoc-ref inputs "gzip"))
+                                (xz (assoc-ref inputs "xz")))
+                            (substitute* "guix/config.scm"
+                              (("\"[^\"]*/bin/bzip2")
+                               (string-append "\"" bzip2 "/bin/bzip2"))
+                              (("\"[^\"]*/bin/gzip") gzip
+                               (string-append "\"" gzip "/bin/gzip"))
+                              (("\"[^\"]*/bin//xz")
+                               (string-append "\"" xz "/bin/xz")))))
+                        #t))
                     (add-before 'check 'copy-bootstrap-guile
-                      (lambda* (#:key system inputs #:allow-other-keys)
-                        ;; Copy the bootstrap guile tarball in the store used
-                        ;; by the test suite.
-                        (define (intern tarball)
-                          (let ((base (strip-store-file-name tarball)))
-                            (copy-file tarball base)
-                            (invoke "./test-env" "guix" "download"
-                                    (string-append "file://" (getcwd)
-                                                   "/" base))
-                            (delete-file base)))
+                      (lambda* (#:key system target inputs #:allow-other-keys)
+                        ;; Copy the bootstrap guile tarball in the store
+                        ;; used by the test suite.
+                        (define (intern file recursive?)
+                          ;; Note: don't use 'guix download' here because we
+                          ;; need to set the 'recursive?' argument.
+                          (define base
+                            (strip-store-file-name file))
+
+                          (define code
+                            `(begin
+                               (use-modules (guix))
+                               (with-store store
+                                 (let* ((item (add-to-store store ,base
+                                                            ,recursive?
+                                                            "sha256" ,file))
+                                        (root (string-append "/tmp/gc-root-"
+                                                             (basename item))))
+                                   ;; Register a root so that the GC tests
+                                   ;; don't delete those.
+                                   (symlink item root)
+                                   (add-indirect-root store root)))))
 
+                          (invoke "./test-env" "guile" "-c"
+                                  (object->string code)))
 
-                        (intern (assoc-ref inputs "boot-guile"))
+                        (unless target
+                          (intern (assoc-ref inputs "boot-guile") #f)
 
-                        ;; On x86_64 some tests need the i686 Guile.
-                        ,@(if (and (not (%current-target-system))
-                                   (string=? (%current-system)
-                                             "x86_64-linux"))
-                              '((intern (assoc-ref inputs "boot-guile/i686")))
-                              '())
+                          ;; On x86_64 some tests need the i686 Guile.
+                          ,@(if (and (not (%current-target-system))
+                                     (string=? (%current-system)
+                                               "x86_64-linux"))
+                                '((intern (assoc-ref inputs "boot-guile/i686") #f))
+                                '())
+
+                          ;; Copy the bootstrap executables.
+                          (for-each (lambda (input)
+                                      (intern (assoc-ref inputs input) #t))
+                                    '("bootstrap/bash" "bootstrap/mkdir"
+                                      "bootstrap/tar" "bootstrap/xz")))
                         #t))
                     (add-after 'unpack 'disable-failing-tests
                       ;; XXX FIXME: These tests fail within the build container.
                         (setenv "SHELL" (which "sh"))
                         #t))
                     (add-after 'install 'wrap-program
-                      (lambda* (#:key inputs outputs #:allow-other-keys)
+                      (lambda* (#:key inputs native-inputs outputs target
+                                #:allow-other-keys)
                         ;; Make sure the 'guix' command finds GnuTLS,
                         ;; Guile-JSON, and Guile-Git automatically.
                         (let* ((out    (assoc-ref outputs "out"))
-                               (guile  (assoc-ref inputs "guile"))
+                               (guile  ,@(if (%current-target-system)
+                                             '((assoc-ref native-inputs "guile"))
+                                             '((assoc-ref inputs "guile"))))
                                (gcrypt (assoc-ref inputs "guile-gcrypt"))
                                (json   (assoc-ref inputs "guile-json"))
                                (sqlite (assoc-ref inputs "guile-sqlite3"))
+                               (zlib   (assoc-ref inputs "guile-zlib"))
+                               (lzlib  (assoc-ref inputs "guile-lzlib"))
                                (git    (assoc-ref inputs "guile-git"))
                                (bs     (assoc-ref inputs
                                                   "guile-bytestructures"))
                                (gnutls (assoc-ref inputs "gnutls"))
                                (locales (assoc-ref inputs "glibc-utf8-locales"))
                                (deps   (list gcrypt json sqlite gnutls
-                                             git bs ssh))
+                                             git bs ssh zlib lzlib))
                                (effective
                                 (read-line
                                  (open-pipe* OPEN_READ
                             `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,gopath))
                             `("GUIX_LOCPATH" ":" suffix (,locpath)))
 
+                          (when target
+                            ;; XXX Touching wrap-program rebuilds world
+                            (let ((bash (assoc-ref inputs "bash")))
+                              (substitute* (string-append out "/bin/guix")
+                                (("^#!.*/bash") (string-append "#! " bash "/bin/bash")))))
                           #t))))))
       (native-inputs `(("pkg-config" ,pkg-config)
 
+                       ;; Guile libraries are needed here for
+                       ;; cross-compilation.
+                       ("guile" ,guile-3.0-latest) ;for faster builds
+                       ("gnutls" ,gnutls)
+                       ("guile-gcrypt" ,guile-gcrypt)
+                       ("guile-json" ,guile-json-4)
+                       ("guile-sqlite3" ,guile-sqlite3)
+                       ("guile-zlib" ,guile-zlib)
+                       ("guile-lzlib" ,guile-lzlib)
+                       ("guile-ssh" ,guile-ssh)
+                       ("guile-git" ,guile-git)
+
                        ;; XXX: Keep the development inputs here even though
                        ;; they're unnecessary, just so that 'guix environment
                        ;; guix' always contains them.
       (inputs
        `(("bzip2" ,bzip2)
          ("gzip" ,gzip)
-         ("zlib" ,zlib)                           ;for 'guix publish'
-         ("lzlib" ,lzlib)            ;for 'guix publish' and 'guix substitute'
-
          ("sqlite" ,sqlite)
          ("libgcrypt" ,libgcrypt)
 
-         ("guile" ,guile-2.2)
+         ("guile" ,guile-3.0-latest)
+
+         ;; Some of the tests use "unshare" when it is available.
+         ("util-linux" ,util-linux)
 
          ;; Many tests rely on the 'guile-bootstrap' package, which is why we
          ;; have it here.
          ("boot-guile" ,(bootstrap-guile-origin (%current-system)))
-         ;; Some of the tests use "unshare" when it is available.
-         ("util-linux" ,util-linux)
          ,@(if (and (not (%current-target-system))
                     (string=? (%current-system) "x86_64-linux"))
                `(("boot-guile/i686" ,(bootstrap-guile-origin "i686-linux")))
                '())
+         ,@(if (%current-target-system)
+               `(("bash" ,bash-minimal)
+                 ("xz" ,xz))
+               '())
+
+         ;; Tests also rely on these bootstrap executables.
+         ("bootstrap/bash" ,(bootstrap-executable "bash" (%current-system)))
+         ("bootstrap/mkdir" ,(bootstrap-executable "mkdir" (%current-system)))
+         ("bootstrap/tar" ,(bootstrap-executable "tar" (%current-system)))
+         ("bootstrap/xz" ,(bootstrap-executable "xz" (%current-system)))
 
          ("glibc-utf8-locales" ,glibc-utf8-locales)))
       (propagated-inputs
-       `(("gnutls" ,gnutls)
+       `(("gnutls" ,(if (%current-target-system) gnutls-3.6.14 guile3.0-gnutls))
          ("guile-gcrypt" ,guile-gcrypt)
-         ("guile-json" ,guile-json)
+         ("guile-json" ,guile-json-4)
          ("guile-sqlite3" ,guile-sqlite3)
          ("guile-ssh" ,guile-ssh)
-         ("guile-git" ,guile-git)))
+         ("guile-git" ,guile-git)
+         ("guile-zlib" ,guile-zlib)
+         ("guile-lzlib" ,guile-lzlib)))
 
       (home-page "https://www.gnu.org/software/guix/")
       (synopsis "Functional package manager for installed software packages and versions")
@@ -323,9 +418,9 @@ the Nix package manager.")
      (fold alist-delete (package-native-inputs guix)
            '("po4a" "graphviz" "help2man")))
     (inputs
-     `(("gnutls" ,gnutls)
+     `(("gnutls" ,guile3.0-gnutls)
        ("guile-git" ,guile-git)
-       ("guile-json" ,guile-json)
+       ("guile-json" ,guile-json-3)
        ("guile-gcrypt" ,guile-gcrypt)
        ,@(fold alist-delete (package-inputs guix)
                '("boot-guile" "boot-guile/i686" "util-linux"))))
@@ -343,6 +438,19 @@ the Nix package manager.")
         #f)
        ((#:phases phases '%standard-phases)
         `(modify-phases ,phases
+           (add-after 'unpack 'change-default-guix
+             (lambda _
+               ;; We need to tell 'guix-daemon' which 'guix' command to use.
+               ;; Here we use a questionable hack where we hard-code root's
+               ;; current guix, which could be wrong (XXX).  Note that scripts
+               ;; like 'guix perform-download' do not run as root so we assume
+               ;; that they have access to /var/guix/profiles/per-user/root.
+               (substitute* "nix/libstore/globals.cc"
+                 (("guixProgram = (.*)nixBinDir + \"/guix\"" _ before)
+                  (string-append "guixProgram = " before
+                                 "/var/guix/profiles/per-user/root\
+/current-guix/bin/guix")))
+               #t))
            (replace 'build
              (lambda _
                (invoke "make" "nix/libstore/schema.sql.hh")
@@ -352,23 +460,38 @@ the Nix package manager.")
            (delete 'copy-bootstrap-guile)
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
-               (invoke "make" "install-binPROGRAMS"
-                       "install-nodist_pkglibexecSCRIPTS")
-
-               ;; We need to tell 'guix-daemon' which 'guix' command to use.
-               ;; Here we use a questionable hack where we hard-code root's
-               ;; current guix, which could be wrong (XXX).  Note that scripts
-               ;; like 'guix perform-download' do not run as root so we assume
-               ;; that they have access to /var/guix/profiles/per-user/root.
-               (let ((out (assoc-ref outputs "out")))
-                 (substitute* (find-files (string-append out "/libexec"))
-                   (("exec \".*/bin/guix\"")
-                    "exec \"${GUIX:-/var/guix/profiles/per-user/root/current-guix/bin/guix}\""))
-                 #t)))
+               (invoke "make" "install-binPROGRAMS")))
            (delete 'wrap-program)))))))
 
-(define-public guile2.0-guix
-  (deprecated-package "guile2.0-guix" guix))
+
+(define-public guile2.2-guix
+  (package
+    (inherit guix)
+    (name "guile2.2-guix")
+    (native-inputs
+     `(("guile" ,guile-2.2)
+       ("gnutls" ,guile2.2-gnutls)
+       ("guile-gcrypt" ,guile2.2-gcrypt)
+       ("guile-json" ,guile2.2-json)
+       ("guile-sqlite3" ,guile2.2-sqlite3)
+       ("guile-ssh" ,guile2.2-ssh)
+       ("guile-git" ,guile2.2-git)
+       ,@(fold alist-delete (package-native-inputs guix)
+               '("guile" "gnutls" "guile-gcrypt" "guile-json"
+                 "guile-sqlite3" "guile-ssh" "guile-git"))))
+    (inputs
+     `(("guile" ,guile-2.2)
+       ,@(alist-delete "guile" (package-inputs guix))))
+    (propagated-inputs
+     `(("gnutls" ,gnutls)
+       ("guile-gcrypt" ,guile2.2-gcrypt)
+       ("guile-json" ,guile2.2-json)
+       ("guile-sqlite3" ,guile2.2-sqlite3)
+       ("guile-ssh" ,guile2.2-ssh)
+       ("guile-git" ,guile2.2-git)))))
+
+(define-public guile3.0-guix
+  (deprecated-package "guile3.0-guix" guix))
 
 (define-public guix-minimal
   ;; A version of Guix which is built with the minimal set of dependencies, as
@@ -378,9 +501,10 @@ the Nix package manager.")
    (package
      (inherit guix)
      (name "guix-minimal")
-     (inputs
-      `(("guile" ,guile-2.2)
-        ,@(alist-delete "guile" (package-inputs guix))))
+     (native-inputs
+      (fold alist-delete
+            (package-native-inputs guix)
+            '("guile-ssh")))
      (propagated-inputs
       (fold alist-delete
             (package-propagated-inputs guix)
@@ -434,18 +558,35 @@ out) and returning a package that uses that as its 'source'."
 (define-public nix
   (package
     (name "nix")
-    (version "2.0.4")
+    (version "2.3.7")
     (source (origin
              (method url-fetch)
              (uri (string-append "http://nixos.org/releases/nix/nix-"
                                  version "/nix-" version ".tar.xz"))
              (sha256
               (base32
-               "0ss9svxlh1pvrdmnqjvjyqjmbqmrdbyfarvbb14i9d4bggzl0r8n"))))
+               "15p50jkss6szinisb7axhxybgfi29sm9grz7mxwair8ljj2553yx"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags '("--sysconfdir=/etc" "--enable-gc")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           ;; Don't try & fail to create subdirectories in /etc, but keep them
+           ;; in the output as examples.
+           (lambda* (#:key (make-flags '()) outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (etc (string-append out "/etc")))
+               (apply invoke "make" "install"
+                      (string-append "sysconfdir=" etc)
+                      (string-append "profiledir=" etc "/profile.d")
+                      make-flags)))))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (inputs `(("curl" ,curl)
+    (inputs `(("boost" ,boost)
+              ("brotli" ,brotli)
               ("bzip2" ,bzip2)
+              ("curl" ,curl)
+              ("editline" ,editline)
               ("libgc" ,libgc)
               ("libseccomp" ,libseccomp)
               ("libsodium" ,libsodium)
@@ -466,14 +607,14 @@ sub-directory.")
 (define-public stow
   (package
     (name "stow")
-    (version "2.2.2")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/stow/stow-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "1pvky9fayms4r6fhns8jd0vavszd7d979w62vfd5n88v614pdxz2"))))
+                "0jrxy12ywn7smdzdnvwzjw77l6knx6jkj2rckgykg1dpf6bdkm89"))))
     (build-system gnu-build-system)
     (inputs
      `(("perl" ,perl)))
@@ -490,7 +631,7 @@ of data and makes them appear to be merged into the same directory.  It is
 typically used for managing software packages installed from source, by
 letting you install them apart in distinct directories and then create
 symlinks to the files in a common directory such as /usr/local.")
-    (license license:gpl2+)))
+    (license license:gpl3+)))
 
 (define-public rpm
   (package
@@ -527,7 +668,6 @@ symlinks to the files in a common directory such as /usr/local.")
        ("nss" ,nss)
        ("nspr" ,nspr)
        ("libarchive" ,libarchive)
-       ("nettle" ,nettle)            ;XXX: actually a dependency of libarchive
        ("file" ,file)
        ("bzip2" ,bzip2)
        ("zlib" ,zlib)
@@ -545,139 +685,20 @@ transactions from C or Python.")
     ;; The whole is GPLv2+; librpm itself is dual-licensed LGPLv2+ | GPLv2+.
     (license license:gpl2+)))
 
-(define-public diffoscope
-  (package
-    (name "diffoscope")
-    (version (git-version "115" "1" "7f3416ffd12572b42c814e43ac15cee44ef48155"))
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://salsa.debian.org/reproducible-builds/diffoscope.git")
-                    (commit "7f3416ffd12572b42c814e43ac15cee44ef48155")))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1pn2rwlz5shdx7s63798wx2v7029bl5if6dlq3i2r6zsnpp0laki"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  ;; setup.py mistakenly requires python-magic from PyPi, even
-                  ;; though the Python bindings of `file` are sufficient.
-                  ;; https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=815844
-                  (add-after 'unpack 'dependency-on-python-magic
-                    (lambda _
-                      (substitute* "setup.py"
-                        (("'python-magic',") ""))))
-                  ;; This test is broken because our `file` package has a
-                  ;; bug in berkeley-db file type detection.
-                  (add-after 'unpack 'remove-berkeley-test
-                    (lambda _
-                      (delete-file "tests/comparators/test_berkeley_db.py")
-                      #t))
-                  (add-after 'unpack 'embed-tool-references
-                    (lambda* (#:key inputs #:allow-other-keys)
-                      (substitute* "diffoscope/comparators/utils/compare.py"
-                        (("\\['xxd',")
-                         (string-append "['" (which "xxd") "',")))
-                      (substitute* "diffoscope/comparators/elf.py"
-                        (("@tool_required\\('readelf'\\)") "")
-                        (("get_tool_name\\('readelf'\\)")
-                         (string-append "'" (which "readelf") "'")))
-                      (substitute* "diffoscope/comparators/directory.py"
-                        (("@tool_required\\('stat'\\)") "")
-                        (("@tool_required\\('getfacl'\\)") "")
-                        (("\\['stat',")
-                         (string-append "['" (which "stat") "',"))
-                        (("\\['getfacl',")
-                         (string-append "['" (which "getfacl") "',")))
-                      #t))
-                  (add-before 'check 'delete-failing-test
-                    (lambda _
-                      ;; this requires /sbin to be on the path
-                      (delete-file "tests/test_tools.py")
-                      #t)))))
-    (inputs `(("rpm" ,rpm)                        ;for rpm-python
-              ("python-file" ,python-file)
-              ("python-debian" ,python-debian)
-              ("python-libarchive-c" ,python-libarchive-c)
-              ("python-tlsh" ,python-tlsh)
-              ("acl" ,acl)                        ;for getfacl
-              ("colordiff" ,colordiff)
-              ("xxd" ,xxd)))
-    ;; Below are modules used for tests.
-    (native-inputs `(("python-pytest" ,python-pytest)
-                     ("python-chardet" ,python-chardet)))
-    (home-page "https://diffoscope.org/")
-    (synopsis "Compare files, archives, and directories in depth")
-    (description
-     "Diffoscope tries to get to the bottom of what makes files or directories
-different.  It recursively unpacks archives of many kinds and transforms
-various binary formats into more human readable forms to compare them.  It can
-compare two tarballs, ISO images, or PDFs just as easily.")
-    (license license:gpl3+)))
-
-(define-public trydiffoscope
- (package
-   (name "trydiffoscope")
-   (version "67.0.1")
-   (source
-    (origin
-      (method git-fetch)
-      (uri (git-reference
-            (url "https://salsa.debian.org/reproducible-builds/trydiffoscope.git")
-            (commit version)))
-      (file-name (git-file-name name version))
-      (sha256
-       (base32
-        "03b66cjii7l2yiwffj6ym6mycd5drx7prfp4j2550281pias6mjh"))))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'install 'install-doc
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((share (string-append (assoc-ref outputs "out") "/share/")))
-               (mkdir-p (string-append share "/man/man1/" ))
-               (invoke "rst2man.py"
-                       "trydiffoscope.1.rst"
-                       (string-append share "/man/man1/trydiffoscope.1"))
-               (mkdir-p (string-append share "/doc/" ,name "-" ,version))
-               (install-file "./README.rst"
-                          (string-append share "/doc/" ,name "-" ,version)))
-             #t)))))
-    (propagated-inputs
-     `(("python-requests" ,python-requests)))
-    (native-inputs
-     `(("gzip" ,gzip)
-       ("python-docutils" ,python-docutils)))
-    (build-system python-build-system)
-    (home-page "https://try.diffoscope.org")
-    (synopsis "Client for remote diffoscope service")
-    (description "This is a client for the @url{https://try.diffoscope.org,
-remote diffoscope service}.
-
-Diffoscope tries to get to the bottom of what makes files or directories
-different.  It recursively unpacks archives of many kinds and transforms
-various binary formats into more human readable forms to compare them.  It can
-compare two tarballs, ISO images, or PDFs just as easily.
-
-Results are displayed by default, stored as local text or html files, or made
-available via a URL on @url{https://try.diffoscope.org}.  Results stored on the
-server are purged after 30 days.")
-    (license license:gpl3+)))
-
 (define-public python-anaconda-client
   (package
     (name "python-anaconda-client")
     (version "1.6.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/Anaconda-Platform/"
-                           "anaconda-client/archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Anaconda-Platform/anaconda-client")
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1wv4wi6k5jz7rlwfgvgfdizv77x3cr1wa2aj0k1595g7fbhkjhz2"))))
+         "0w1bfxnydjl9qp53r2gcvr6vlpdqqilcrzqxrll9sgg6vwdyiyyp"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-pyyaml" ,python-pyyaml)
@@ -720,68 +741,185 @@ environments.")
 (define-public python2-anaconda-client
   (package-with-python2 python-anaconda-client))
 
-(define-public python-conda
+(define-public python-conda-package-handling
   (package
-    (name "python-conda")
-    (version "4.3.16")
+    (name "python-conda-package-handling")
+    (version "1.6.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/conda/conda/archive/"
-                           version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/conda/conda-package-handling/")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "1jq8hyrc5npb5sf4vw6s6by4602yj8f79vzpbwdfgpkn02nfk1dv"))))
+         "0bqbs6a8jbjmbn47n5n1p529cx7pf4vgfnhqca9mflgidfb5i0jf"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'use-unmodified-libarchive
+           (lambda _
+             (substitute* "setup.py"
+               (("archive_and_deps") "archive"))
+             #t))
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv" "tests"
+                     "-k"
+                     (string-append
+                      ;; TODO: these three fail because the mocker fixture
+                      ;; cannot be found
+                      "not test_rename_to_trash"
+                      " and not test_api_extract_tarball_with_libarchive_import_error"
+                      " and not test_delete_trash"
+                      ;; TODO: this one does not raise an exception when it
+                      ;; should.
+                      " and not test_secure_refusal_to_extract_abs_paths")))))))
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-tqdm" ,python-tqdm)))
+    (inputs
+     `(("libarchive" ,libarchive)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-mock" ,python-mock)))
+    (home-page "https://conda.io")
+    (synopsis "Create and extract conda packages of various formats")
+    (description
+     "This library is an abstraction of Conda package handling and a tool for
+extracting, creating, and converting between formats.")
+    (license license:bsd-3)))
+
+(define-public conda
+  (package
+    (name "conda")
+    (version "4.8.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/conda/conda")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0iv1qzk21jsk6vdp3106xvpvl68zgfdqb3kyzpya87jhkl204l7r"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-permissions
+           (lambda _
+             ;; This file is no longer writable after downloading with
+             ;; 'git-fetch'
+             (make-file-writable
+              "tests/conda_env/support/saved-env/environment.yml")
+             #t))
+         (add-after 'unpack 'correct-python-executable-name
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((python (assoc-ref inputs "python-wrapper")))
+               #;
+               (substitute* "conda/common/path.py"
+                 (("python_version or ''")
+                  "python_version or '3'"))
+               (substitute* "conda/core/initialize.py"
+                 (("python_exe = join")
+                  (format #f "python_exe = \"~a/bin/python\" #"
+                          python))))
+             #t))
+         (add-after 'unpack 'do-not-use-python-root-as-prefix
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (python (assoc-ref inputs "python-wrapper")))
+               (substitute* "tests/core/test_initialize.py"
+                 (("\"\"\"\\) % conda_prefix")
+                  (format #f "\"\"\") % \"~a\"" python))
+                 (("CONDA_PYTHON_EXE \"%s\"' % join\\(conda_prefix")
+                  (format #f "CONDA_PYTHON_EXE \"%s\"' % join(\"~a\""
+                          python))
+                 (("conda_prefix = abspath\\(sys.prefix\\)")
+                  (format #f "conda_prefix = abspath(\"~a\")" out)))
+               (substitute* "conda/base/context.py"
+                 (("os.chdir\\(sys.prefix\\)")
+                  (format #f "os.chdir(\"~a\")" out))
+                 (("sys.prefix, '.condarc'")
+                  (format #f "\"~a\", '.condarc'" out))
+                 (("return abspath\\(sys.prefix\\)")
+                  (format #f "return abspath(\"~a\")" out))
+                 (("os.path.join\\(sys.prefix, bin_dir, exe\\)")
+                  (format #f "\"~a/bin/conda\"" out))
+                 (("'CONDA_EXE', sys.executable")
+                  (format #f "'CONDA_EXE', \"~a/bin/conda\"" out))))
+             #t))
          (add-before 'build 'create-version-file
            (lambda _
              (with-output-to-file "conda/.version"
                (lambda () (display ,version)))
              #t))
-         (add-before 'check 'remove-failing-tests
-           (lambda _
-             ;; These tests require internet/network access
-             (let ((network-tests '("test_cli.py"
-                                    "test_create.py"
-                                    "test_export.py"
-                                    "test_fetch.py"
-                                    "test_history.py"
-                                    "test_info.py"
-                                    "test_install.py"
-                                    "test_priority.py"
-                                    "conda_env/test_cli.py"
-                                    "conda_env/test_create.py"
-                                    "conda_env/specs/test_notebook.py"
-                                    "conda_env/utils/test_notebooks.py"
-                                    "core/test_index.py"
-                                    "core/test_repodata.py")))
-               (with-directory-excursion "tests"
-                 (for-each delete-file network-tests)
-
-                 ;; FIXME: This test creates a file, then deletes it and tests
-                 ;; that the file was deleted.  For some reason it fails when
-                 ;; building with guix, but does not when you run it in the
-                 ;; directory left when you build with the --keep-failed
-                 ;; option
-                 (delete-file "gateways/disk/test_delete.py")
-                 #t))))
          (replace 'check
            (lambda _
              (setenv "HOME" "/tmp")
-             (invoke "py.test"))))))
-    (native-inputs
-     `(("python-cytoolz" ,python-cytoolz)
-       ("python-ruamel.yaml" ,python-ruamel.yaml)
-       ("python-requests" ,python-requests)
+             (invoke "py.test" "-vv"
+                     "-k"
+                     (string-append
+                      "not integration"
+                      ;; This one reports a newer version of conda than
+                      ;; expected.
+                      " and not test_auto_update_conda"
+                      ;; This fails because the output directory is not a
+                      ;; Conda environment.
+                      " and not test_list"
+                      ;; This fails because we patched the default root
+                      ;; prefix.
+                      " and not test_default_target_is_root_prefix"
+                      ;; TODO: I don't understand what this failure means
+                      " and not test_PrefixData_return_value_contract"
+                      ;; TODO: same here
+                      " and not test_install_1"
+                      ;; Not sure if this is really wrong.  This fails because
+                      ;; /gnu/store/...python-conda-4.8.3/bin/python
+                      ;; is not /gnu/store/...python-wrapper-3.8.2/bin/python
+                      " and not test_make_entry_point"))))
+         (add-after 'install 'init
+           ;; This writes a whole bunch of shell initialization files to the
+           ;; prefix directory.  Many features of conda can only be used after
+           ;; running "conda init".
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (setenv "HOME" "/tmp")
+
+             ;; "conda init" insists on using sudo, because it is hell-bent on
+             ;; modifying system files.
+             (mkdir-p "/tmp/fake-sudo")
+             (with-output-to-file "/tmp/fake-sudo/sudo"
+               (lambda () (format #t "#!~/bin/sh~%exec $@" (which "sh"))))
+             (chmod "/tmp/fake-sudo/sudo" #o700)
+             (setenv "PATH" (string-append "/tmp/fake-sudo:"
+                                           (getenv "PATH")))
+
+             (invoke (string-append (assoc-ref outputs "out")
+                                    "/bin/conda")
+                     "init"))))))
+    (inputs
+     `(("python-wrapper" ,python-wrapper)))
+    (propagated-inputs
+     `(("python-anaconda-client" ,python-anaconda-client)
+       ("python-conda-package-handling" ,python-conda-package-handling)
+       ("python-cytoolz" ,python-cytoolz)
        ("python-pycosat" ,python-pycosat)
        ("python-pytest" ,python-pytest)
-       ("python-responses" ,python-responses)
        ("python-pyyaml" ,python-pyyaml)
-       ("python-anaconda-client" ,python-anaconda-client)))
+       ("python-requests" ,python-requests)
+       ("python-responses" ,python-responses)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-tqdm" ,python-tqdm)
+       ;; XXX: This is dragged in by libarchive and is needed at runtime.
+       ("zstd" ,zstd)))
     (home-page "https://github.com/conda/conda")
     (synopsis "Cross-platform, OS-agnostic, system-level binary package manager")
     (description
@@ -789,120 +927,172 @@ environments.")
 is the package manager used by Anaconda installations, but it may be used for
 other systems as well.  Conda makes environments first-class citizens, making
 it easy to create independent environments even for C libraries.  Conda is
-written entirely in Python.
-
-This package provides Conda as a library.")
+written entirely in Python.")
     (license license:bsd-3)))
 
-(define-public python2-conda
-  (let ((base (package-with-python2
-               (strip-python2-variant python-conda))))
-    (package (inherit base)
-             (native-inputs
-              `(("python2-enum34" ,python2-enum34)
-                ,@(package-native-inputs base))))))
-
-(define-public conda
-  (package (inherit python-conda)
-    (name "conda")
-    (arguments
-     (substitute-keyword-arguments (package-arguments python-conda)
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (replace 'build
-             (lambda* (#:key outputs #:allow-other-keys)
-               ;; This test fails when run before installation.
-               (delete-file "tests/test_activate.py")
-
-               ;; Fix broken defaults
-               (substitute* "conda/base/context.py"
-                 (("return sys.prefix")
-                  (string-append "return \"" (assoc-ref outputs "out") "\""))
-                 (("return (prefix_is_writable\\(self.root_prefix\\))" _ match)
-                  (string-append "return False if self.root_prefix == self.conda_prefix else "
-                                 match)))
-
-               ;; The util/setup-testing.py is used to build conda in
-               ;; application form, rather than the default, library form.
-               ;; With this, we are able to run commands like `conda --help`
-               ;; directly on the command line
-               (invoke "python" "utils/setup-testing.py" "build_py")))
-           (replace 'install
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (let* ((out (assoc-ref outputs "out"))
-                      (target (string-append out "/lib/python"
-                                             ((@@ (guix build python-build-system)
-                                                  get-python-version)
-                                              (assoc-ref inputs "python"))
-                                             "/site-packages/")))
-                 ;; The installer aborts if the target directory is not on
-                 ;; PYTHONPATH.
-                 (setenv "PYTHONPATH"
-                         (string-append target ":" (getenv "PYTHONPATH")))
-
-                 ;; And it aborts if the directory doesn't exist.
-                 (mkdir-p target)
-                 (invoke "python" "utils/setup-testing.py" "install"
-                         (string-append "--prefix=" out)))))
-           ;; The "activate" and "deactivate" scripts don't need wrapping.
-           ;; They also break when they are renamed.
-           (add-after 'wrap 'undo-wrap
-             (lambda* (#:key outputs #:allow-other-keys)
-               (with-directory-excursion (string-append (assoc-ref outputs "out") "/bin/")
-                 (delete-file "deactivate")
-                 (rename-file ".deactivate-real" "deactivate")
-                 (delete-file "activate")
-                 (rename-file ".activate-real" "activate")
-                 #t)))))))
-    (description
-     "Conda is a cross-platform, Python-agnostic binary package manager.  It
-is the package manager used by Anaconda installations, but it may be used for
-other systems as well.  Conda makes environments first-class citizens, making
-it easy to create independent environments even for C libraries.  Conda is
-written entirely in Python.")))
+(define-public python-conda
+  (deprecated-package "python-conda" conda))
 
 (define-public gwl
   (package
     (name "gwl")
-    (version "0.1.1")
+    (version "0.2.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://www.guixwl.org/releases/gwl-"
-                                  version ".tar.gz"))
+              (uri (string-append "mirror://gnu/gwl/gwl-" version ".tar.gz"))
               (sha256
                (base32
-                "06pm967mq1wyggx7l0nfapw5s0k5qc5r9lawk2v3db868br779a7"))))
+                "1ji5jvzni8aml9fmimlr11g3k8isrnlvnbzhmwgdjh72hils0alc"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'fix-tests
+           (lambda _
+             ;; Avoid cross-device link.
+             (substitute* "tests/cache.scm"
+               (("/tmp/gwl-test-input-XXXXXX")
+                (string-append (getcwd) "/gwl-test-input-XXXXXX")))
+             #t)))))
     (native-inputs
      `(("autoconf" ,autoconf)
        ("automake" ,automake)
-       ("pkg-config" ,pkg-config)))
+       ("pkg-config" ,pkg-config)
+       ("texinfo" ,texinfo)
+       ("graphviz" ,graphviz)))
     (inputs
-     `(("guile" ,guile-2.2)))
+     `(("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))))
     (propagated-inputs
      `(("guix" ,guix)
-       ("guile-commonmark" ,guile-commonmark)))
-    (home-page "https://www.guixwl.org")
+       ("guile-commonmark" ,guile-commonmark)
+       ("guile-gcrypt" ,guile-gcrypt)
+       ("guile-pfds" ,guile-pfds)
+       ("guile-syntax-highlight" ,guile-syntax-highlight)
+       ("guile-wisp" ,guile-wisp)))
+    (home-page "https://workflows.guix.info")
     (synopsis "Workflow management extension for GNU Guix")
-    (description "This project provides two subcommands to GNU Guix and
-introduces two record types that provide a workflow management extension built
-on top of GNU Guix.")
+    (description "The @dfn{Guix Workflow Language} (GWL) provides an
+extension to GNU Guix's declarative language for package management to
+automate the execution of programs in scientific workflows.  The GWL
+can use process engines to integrate with various computing
+environments.")
     ;; The Scheme modules in guix/ and gnu/ are licensed GPL3+,
     ;; the web interface modules in gwl/ are licensed AGPL3+,
     ;; and the fonts included in this package are licensed OFL1.1.
     (license (list license:gpl3+ license:agpl3+ license:silofl1.1))))
 
+(define-public guix-jupyter
+  (package
+    (name "guix-jupyter")
+    (version "0.1.0")
+    (home-page "https://gitlab.inria.fr/guix-hpc/guix-kernel")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference (url home-page)
+                                  (commit (string-append "v" version))))
+              (sha256
+               (base32
+                "01z7jjkc7r7lj6637rcgpz40v8xqqyfp6871h94yvcnwm7zy9h1n"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Allow builds with Guile 3.0.
+                  (substitute* "configure.ac"
+                    (("^GUILE_PKG.*")
+                     "GUILE_PKG([3.0 2.2])\n"))
+
+                  ;; Avoid name clash and build failure now that
+                  ;; 'define-json-mapping' is also provided by Guile-JSON, as
+                  ;; of version 4.3.
+                  (substitute* (find-files "." "\\.scm$")
+                    (("define-json-mapping")
+                     "define-json-mapping*")
+                    (("<=>")
+                     "<->"))
+                  #t))
+              (file-name (string-append "guix-jupyter-" version "-checkout"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:modules ((srfi srfi-26)
+                  (ice-9 match)
+                  (ice-9 popen)
+                  (ice-9 rdelim)
+                  (guix build utils)
+                  (guix build gnu-build-system))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'install 'sed-kernel-json
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (guix  (assoc-ref inputs  "guix"))
+                    (guile (assoc-ref inputs  "guile"))
+                    (json  (assoc-ref inputs  "guile-json"))
+                    (git   (assoc-ref inputs  "guile-git"))
+                    (bs    (assoc-ref inputs  "guile-bytestructures"))
+                    (s-zmq (assoc-ref inputs  "guile-simple-zmq"))
+                    (gcrypt (assoc-ref inputs  "guile-gcrypt"))
+                    (deps  (list out s-zmq guix json git bs gcrypt))
+                    (effective
+                     (read-line
+                      (open-pipe* OPEN_READ
+                                  (string-append guile "/bin/guile")
+                                  "-c" "(display (effective-version))")))
+                    (path (map (cut string-append "-L\", \"" <>
+                                    "/share/guile/site/"
+                                    effective)
+                               deps))
+                    (gopath (map (cut string-append "-C\", \"" <>
+                                      "/lib/guile/" effective
+                                      "/site-ccache")
+                                 deps))
+                    (kernel-dir (string-append out "/share/jupyter/kernels/guix/")))
+               (substitute* (string-append kernel-dir "kernel.json")
+                 (("-s")
+                  (string-join
+                   (list (string-join path "\",\n\t\t\"")
+                         (string-join gopath "\",\n\t\t\"")
+                         "-s")
+                   "\",\n\t\t\""))
+                 (("guix-jupyter-kernel.scm")
+                  (string-append out "/share/guile/site/3.0/"
+                                 "guix-jupyter-kernel.scm")))
+               #t))))))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)
+
+       ;; For testing.
+       ("jupyter" ,jupyter)
+       ("python-ipython" ,python-ipython)
+       ("python-ipykernel" ,python-ipykernel)))
+    (inputs
+     `(("guix" ,guix)
+       ("guile" ,@(assoc-ref (package-native-inputs guix) "guile"))))
+    (propagated-inputs
+     `(("guile-json" ,guile-json-4)
+       ("guile-simple-zmq" ,guile-simple-zmq)
+       ("guile-gcrypt" ,guile-gcrypt)))
+    (synopsis "Guix kernel for Jupyter")
+    (description
+     "Guix-Jupyter is a Jupyter kernel.  It allows you to annotate notebooks
+with information about their software dependencies, such that code is executed
+in the right software environment.  Guix-Jupyter spawns the actual kernels
+such as @code{python-ipykernel} on behalf of the notebook user and runs them
+in an isolated environment, in separate namespaces.")
+    (license license:gpl3+)))
+
 (define-public gcab
   (package
     (name "gcab")
-    (version "1.2")
+    (version "1.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/gcab/"
                                   version "/gcab-" version ".tar.xz"))
               (sha256
                (base32
-                "038h5kk41si2hc9d9169rrlvp8xgsxq27kri7hv2vr39gvz9cbas"))))
+                "13q43iqld4l50yra45lhvkd376pn6qpk7rkx374zn8y9wsdzm9b7"))))
     (build-system meson-build-system)
     (native-inputs
      `(("glib:bin" ,glib "bin")         ; for glib-mkenums
@@ -929,14 +1119,14 @@ Microsoft cabinet (.@dfn{CAB}) files.")
 (define-public msitools
   (package
     (name "msitools")
-    (version "0.99")
+    (version "0.100")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/msitools/"
                                   version "/msitools-" version ".tar.xz"))
               (sha256
                (base32
-                "0d9nidn5zc81bc30w119933rn2g87mrsqyqkndg20srkbsd96xfl"))))
+                "1skq17qr2ic4qr3779j49byfm8rncwbsq9rj1a33ncn2m7isdwdv"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("bison" ,bison)
@@ -946,7 +1136,7 @@ Microsoft cabinet (.@dfn{CAB}) files.")
        ("glib" ,glib)
        ("libgsf" ,libgsf)
        ("libxml2" ,libxml2)
-       ("uuid" ,util-linux)))
+       ("uuid" ,util-linux "lib")))
     (home-page "https://wiki.gnome.org/msitools")
     (synopsis "Windows Installer file manipulation tool")
     (description
@@ -958,15 +1148,15 @@ for packaging and deployment of cross-compiled Windows applications.")
 (define-public libostree
   (package
     (name "libostree")
-    (version "2018.9.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/ostreedev/ostree/releases/download/v"
-                    (version-major+minor version) "/libostree-" version ".tar.xz"))
-              (sha256
-               (base32
-                "01mygpkbl9sk2vr3hjbpih6qlg8lwx0q5lklm09f7jfwfpnwyqzj"))))
+    (version "2020.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/ostreedev/ostree/releases/download/v"
+             (version-major+minor version) "/libostree-" version ".tar.xz"))
+       (sha256
+        (base32 "0wk9fgj9jl25ns2hcgcb6j24k5mvfn13b02ka0p8l4hdh8c4hpc6"))))
     (build-system gnu-build-system)
     (arguments
      '(#:phases
@@ -978,13 +1168,14 @@ for packaging and deployment of cross-compiled Windows applications.")
              (setenv "TEST_TMPDIR" (getenv "TMPDIR"))
              #t)))
        ;; XXX: fails with:
+       ;;     tap-driver.sh: missing test plan
        ;;     tap-driver.sh: internal error getting exit status
        ;;     tap-driver.sh: fatal: I/O or internal error
        #:tests? #f))
     (native-inputs
      `(("attr" ,attr)                   ; for tests
        ("bison" ,bison)
-       ("glib:bin" ,glib "bin")          ; for 'glib-mkenums'
+       ("glib:bin" ,glib "bin")         ; for 'glib-mkenums'
        ("gobject-introspection" ,gobject-introspection)
        ("pkg-config" ,pkg-config)
        ("xsltproc" ,libxslt)))
@@ -998,7 +1189,6 @@ for packaging and deployment of cross-compiled Windows applications.")
        ("gpgme" ,gpgme)
        ("libarchive" ,libarchive)
        ("libsoup" ,libsoup)
-       ("nettle" ,nettle)               ; required by 'libarchive.la'
        ("util-linux" ,util-linux)))
     (home-page "https://ostree.readthedocs.io/en/latest/")
     (synopsis "Operating system and container binary deployment and upgrades")
@@ -1012,56 +1202,141 @@ the boot loader configuration.")
 (define-public flatpak
   (package
    (name "flatpak")
-   (version "1.2.4")
+   (version "1.8.2")
    (source
     (origin
      (method url-fetch)
      (uri (string-append "https://github.com/flatpak/flatpak/releases/download/"
                          version "/flatpak-" version ".tar.xz"))
      (sha256
-      (base32
-       "1qf3ys84fzv11z6f6li59rxjdjbyrv7cyi9539k73r9i9pckjr8v"))))
+      (base32 "1c45a0k7wx685n5b3ihv7dk0mm2kmwbw7cx8w5g2la62yxfn49kr"))))
 
    ;; Wrap 'flatpak' so that GIO_EXTRA_MODULES is set, thereby allowing GIO to
    ;; find the TLS backend in glib-networking.
    (build-system glib-or-gtk-build-system)
 
    (arguments
-    '(#:tests? #f ;; Tests fail due to trying to create files where it can't.
-      #:configure-flags (list
-                         "--enable-documentation=no" ;; FIXME
-                         "--enable-system-helper=no"
-                         "--localstatedir=/var"
-                         (string-append "--with-system-bubblewrap="
-                                        (assoc-ref %build-inputs "bubblewrap")
-                                        "/bin/bwrap"))))
-   (native-inputs `(("bison" ,bison)
-                    ("gettext" ,gnu-gettext)
-                    ("glib:bin" ,glib "bin") ; for glib-mkenums + gdbus-codegen
-                    ("gobject-introspection" ,gobject-introspection)
-                    ("libcap" ,libcap)
-                    ("pkg-config" ,pkg-config)))
+    '(#:configure-flags
+      (list
+       "--enable-documentation=no" ;; FIXME
+       "--enable-system-helper=no"
+       "--localstatedir=/var"
+       (string-append "--with-system-bubblewrap="
+                      (assoc-ref %build-inputs "bubblewrap")
+                      "/bin/bwrap")
+       (string-append "--with-system-dbus-proxy="
+                      (assoc-ref %build-inputs "xdg-dbus-proxy")
+                      "/bin/xdg-dbus-proxy"))
+      #:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'fix-tests
+          (lambda* (#:key inputs #:allow-other-keys)
+            (copy-recursively
+             (string-append (assoc-ref inputs "glibc-utf8-locales")
+                            "/lib/locale/") "/tmp/locale")
+            (for-each make-file-writable (find-files "/tmp"))
+            (substitute* "tests/make-test-runtime.sh"
+              (("cp `which.*") "echo guix\n")
+              (("cp -r /usr/lib/locale/C\\.\\*")
+               (string-append "mkdir ${DIR}/usr/lib/locale/en_US; \
+cp -r /tmp/locale/*/en_US.*")))
+            (substitute* "tests/libtest.sh"
+              (("/bin/kill") (which "kill"))
+              (("/usr/bin/python3") (which "python3")))
+            #t))
+        ;; Many tests fail for unknown reasons, so we just run a few basic
+        ;; tests.
+        (replace 'check
+          (lambda _
+            (setenv "HOME" "/tmp")
+            (invoke "make" "check"
+                    "TESTS=tests/test-basic.sh tests/test-config.sh testcommon"))))))
+    (native-inputs
+    `(("bison" ,bison)
+      ("dbus" ,dbus) ; for dbus-daemon
+      ("gettext" ,gettext-minimal)
+      ("glib:bin" ,glib "bin")          ; for glib-mkenums + gdbus-codegen
+      ("glibc-utf8-locales" ,glibc-utf8-locales)
+      ("gobject-introspection" ,gobject-introspection)
+      ("libcap" ,libcap)
+      ("pkg-config" ,pkg-config)
+      ("python" ,python)
+      ("python-pyparsing" ,python-pyparsing)
+      ("socat" ,socat)
+      ("which" ,which)))
    (propagated-inputs `(("glib-networking" ,glib-networking)
                         ("gnupg" ,gnupg)
                         ("gsettings-desktop-schemas"
                          ,gsettings-desktop-schemas)))
-   (inputs `(("appstream-glib" ,appstream-glib)
-             ("bubblewrap" ,bubblewrap)
-             ("dconf" ,dconf)
-             ("gdk-pixbuf" ,gdk-pixbuf)
-             ("gpgme" ,gpgme)
-             ("json-glib" ,json-glib)
-             ("libarchive" ,libarchive)
-             ("libostree" ,libostree)
-             ("libseccomp" ,libseccomp)
-             ("libsoup" ,libsoup)
-             ("libxau" ,libxau)
-             ("libxml2" ,libxml2)
-             ("nettle" ,nettle)
-             ("util-linux" ,util-linux)))
+   (inputs
+    `(("appstream-glib" ,appstream-glib)
+      ("bubblewrap" ,bubblewrap)
+      ("dconf" ,dconf)
+      ("fuse" ,fuse)
+      ("gdk-pixbuf" ,gdk-pixbuf)
+      ("gpgme" ,gpgme)
+      ("json-glib" ,json-glib)
+      ("libarchive" ,libarchive)
+      ("libostree" ,libostree)
+      ("libseccomp" ,libseccomp)
+      ("libsoup" ,libsoup)
+      ("libxau" ,libxau)
+      ("libxml2" ,libxml2)
+      ("util-linux" ,util-linux)
+      ("xdg-dbus-proxy" ,xdg-dbus-proxy)))
    (home-page "https://flatpak.org")
    (synopsis "System for building, distributing, and running sandboxed desktop
 applications")
    (description "Flatpak is a system for building, distributing, and running
 sandboxed desktop applications on GNU/Linux.")
    (license license:lgpl2.1+)))
+
+(define-public akku
+  (package
+    (name "akku")
+    (version "1.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/akkuscm/akku.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256 (base32 "1dm32ws3nshnnscd7k75zswxxs1pp25y2q4k8j5ms241hz47by3c"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'bootstrap
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (for-each patch-shebang
+                                '("bootstrap"
+                                  ".akku/env"))
+                      (let* ((home "/tmp")
+                             (datadir (string-append home "/.local/share/akku/")))
+                        (mkdir-p datadir)
+                        (invoke "touch" (string-append datadir "index.db"))
+                        (setenv "HOME" home))
+                      (invoke "./bootstrap")
+                      #t))
+                  (add-after 'install 'wrap-executables
+                    (lambda* (#:key outputs inputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out"))
+                            (curl (assoc-ref inputs "curl")))
+                        (wrap-program (string-append out "/bin/akku")
+                          `("LD_LIBRARY_PATH" ":" prefix (,(string-append curl "/lib"))))
+                        #t))))))
+    (native-inputs
+     `(("which" ,which)
+       ("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("guile" ,guile-3.0)
+       ("curl" ,curl)))
+    (home-page "https://akkuscm.org/")
+    (synopsis "Language package manager for Scheme")
+    (description
+     "Akku.scm is a project-based language package manager for R6RS and R7RS Scheme.
+It is mainly meant for programmers who develop portable programs or libraries in Scheme,
+but could potentially work for end-users of those programs.  It also has a translator
+from R7RS, which allows most R7RS code to run on R6RS implementations.")
+    (license license:gpl3+)))