home: Add home-environment.

* gnu/home.scm
(home-environment, home-environment?, this-home-environment)
(home-environment-derivation, home-environment-user-services)
(home-environment-essential-services, home-environment-services)
(home-environment-location, home-environment-with-provenance): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add xdg.

* gnu/home-services/xdg.scm
(home-xdg-base-directories-service-type)
(home-xdg-base-directories-configuration)
(home-xdg-base-directories-configuration?)
(home-xdg-user-directories-service-type)
(home-xdg-user-directories-configuration)
(home-xdg-user-directories-configuration?)
(xdg-desktop-action, xdg-desktop-entry)
(home-xdg-mime-applications-service-type)
(home-xdg-mime-applications-configuration): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/xdg.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add shells.

* gnu/home-services/shells.scm
(home-shell-profile-service-type, home-shell-profile-configuration)
(home-bash-service-type, home-bash-configuration, home-bash-extension)
(home-zsh-service-type, home-zsh-configuration, home-zsh-extension)
(home-fish-service-type, home-fish-configuration, home-fish-extension): New
variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/shells.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add helper functions for service configurations.

* gnu/home-services/configuration.scm (helper functions): New variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/configuration.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add fontutils.

* gnu/home-services/fontutils.scm (home-fontconfig-service-type): New
variable.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/fontutils.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add symlink-manager.

* gnu/home-services/symlink-manager.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services/symlink-manager.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add fold-home-service-types function.

* gnu/home-services.scm (parent-directory, %guix-home-root-directory,
%service-type-path, all-home-service-modules, fold-home-service-types): New
variables.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add home-provenance-service-type.

* gnu/home-services.scm (home-provenance-service-type, sexp->home-provenance,
home-provenance): New variables.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add home-run-on-change-service-type.

* gnu/home-services.scm (home-run-on-change-service-type): New variable.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

home-services: Add most essential home services.

* gnu/home-services.scm (home-service-type, home-profile-service-type)
(home-environment-variables-service-type, home-files-service-type)
(home-run-on-first-login-service-type, home-activation-service-type): New
variables.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add home-services.scm.

Signed-off-by: Oleg Pykhalov <go.wigust@gmail.com>

gnu: ghc-pandoc-types: Update home page.

* gnu/packages/haskell-xyz.scm (ghc-pandoc-types)[home-page]: Update.

Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>

gnu: python-pikepdf: Update to 3.0.0.

* gnu/packages/python-xyz.scm (python-pikepdf): Update to 3.0.0.

gnu: linux-libre 5.10: Update to 5.10.63.

* gnu/packages/linux.scm (linux-libre-5.10-version): Update to 5.10.63.
(linux-libre-5.10-pristine-source): Update hash.

gnu: linux-libre: Update to 5.13.15.

* gnu/packages/linux.scm (linux-libre-5.13-version): Update to 5.13.15.
(linux-libre-5.13-pristine-source): Update hash.

gnu: linux-libre 5.14: Update to 5.14.2.

* gnu/packages/linux.scm (linux-libre-5.14-version): Update to 5.14.2.
(linux-libre-5.14-pristine-source): Update hash.

gnu: qemu-minimal: Don't build static binaries.

* gnu/packages/virtualization.scm (qemu-minimal)[arguments]: Remove
inherited phases for static binaries.
[native-inputs]: Remove glib:static, pcre:static and zlib:static.
[outputs]: Remove static output.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>

gnu: Add vim-slime.

* gnu/packages/vim.scm (vim-slime): New variable.

gnu: Add vim-gemini-vim.

* gnu/packages/vim.scm (vim-gemini-vim): New variable.

swh: Adjust <vault-reply> to latest API changes.

Fixes uses of 'swh-download' as reported at
<https://lists.gnu.org/archive/html/guix-devel/2021-09/msg00115.html>.
Reported by zimoun.

* guix/swh.scm (<vault-reply>)[object-id, object-type]: Remove.  These
two fields are no longer provided in JSON replies.
[swhid]: New field.

gnu: autoconf: Unpatch shebangs on files that "autoconf -i" installs.

Fixes <https://issues.guix.gnu.org/50288>.
Reported by Maxim Cournoyer.

* gnu/packages/autotools.scm (autoconf-2.71)[arguments]: Add
'unpatch-shebangs' phase.

doc: add clarifications to Linode cookbook recipe

* doc/guix-cookbook.texi: clarify Linode recipe

Reword paragraph about adding the Guix device disk to Debian config.
Improve example commands for sftp-ing files to the server.
Minor wording fixes

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

transformations: Git tags and 'git describe' style IDs are used as version.

* guix/transformations.scm (commit->version-string): New procedure.  Use git
tags and 'git describe' style identifiers directly.
(transform-package-source-commit): Adjust accordingly.
* tests/transformations.scm
("options->transformation, with-commit, version transformation"): New test.
* doc/guix.texi (Package Transformation Options): Mention the 'git describe'
style.

git: 'resolve-reference' handles 'git describe'-style commit IDs.

* guix/git.scm (resolve-reference): Rewrite tag-or-commit case to recognize
'git describe' style identifiers and resolve them as commits.
* doc/guix.texi (origin Reference): Mention it.

gnu: emacs-org-reveal: Update to 20210902-1.fe9148b.

* gnu/packages/emacs-xyz.scm (emacs-org-reveal): Update to
20210902-1.fe9148b.

guix: dune-build-system: Put dune into a reproducible release mode.

* guix/build/dune-build-system.scm (build,check): Replace the profile parameter
with the appropriate release flags.
* guix/build-system/dune.scm: Remove the profile parameter.
* doc/guix.texi: Remove paragraph on profile parameter.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>

gnu: josm: Update to 18193.

* gnu/packages/geo.scm (josm): Update to 18193.

gnu: icecat: Update to 78.14.0-guix0-preview1 [fixes CVE-2021-38493].

* gnu/packages/gnuzilla.scm (%icecat-version, %icecat-build-id): Update.
(icecat-source): Update upstream source hash.

gnu: Add sniffglue.

* gnu/packages/rust-apps.scm (sniffglue): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-dhcp4r-0.2.

* gnu/packages/crates-io.scm (rust-dhcp4r-0.2): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-enum-primitive-derive-0.2.

* gnu/packages/crates-io.scm (rust-enum-primitive-derive-0.2): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-pcap-sys-0.1.

* gnu/packages/crates-io.scm (rust-pcap-sys-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-pktparse-0.5.

* gnu/packages/crates-io.scm (rust-pktparse-0.5): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-reduce-0.1.

* gnu/packages/crates-io.scm (rust-reduce-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-syscallz-0.15.

* gnu/packages/crates-io.scm (rust-syscallz-0.15): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-seccomp-sys-0.1.

* gnu/packages/crates-io.scm (rust-seccomp-sys-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-strum-0.19.

* gnu/packages/crates-io.scm (rust-strum-0.19): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-strum-macros-0.19.

* gnu/packages/crates-io.scm (rust-strum-macros-0.19): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-tls-parser-0.10.

* gnu/packages/crates-io.scm (rust-tls-parser-0.10): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-hex-literal-0.3.

* gnu/packages/crates-io.scm (rust-hex-literal-0.3): New variable.
(rust-hex-literal-0.2): Inherit from above.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-cookie-factory-0.3.

* gnu/packages/crates-io.scm (rust-cookie-factory-0.3): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-nom-derive-0.7.

* gnu/packages/crates-io.scm (rust-nom-derive-0.7): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-pretty-assertions-0.7.

* gnu/packages/crates-io.scm (rust-pretty-assertions-0.7): New variable.
(rust-pretty-assertions-0.6): Inherit from above.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-rusticata-macros-3.

* gnu/packages/crates-io.scm (rust-rusticata-macros-3): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-boxxy-0.11.

* gnu/packages/crates-io.scm (rust-boxxy-0.11): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-elf-0.0.10.

* gnu/packages/crates-io.scm (rust-elf-0.0.10): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-bufstream-0.1.

* gnu/packages/crates-io.scm (rust-bufstream-0.1): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-pledge-0.3.

* gnu/packages/crates-io.scm (rust-pledge-0.3): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-rustyline-5.

* gnu/packages/crates-io.scm (rust-rustyline-5): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add rust-rustyline-derive-0.2.

* gnu/packages/crates-io.scm (rust-rustyline-derive-0.2): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: mandoc: Add $MANPATH to native-search-paths.

* gnu/packages/man.scm (mandoc)[native-search-paths]: New field.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

emacs-org-roam: Add new phase after unpack.

* gnu/packages/emacs-xyz.scm (emacs-org-roam)[arguments]<phases>:
After the unpack phase add a move-source-files phase to include
the org-roam extensions to the package.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

import: go: Fix import when import path redirects.

* guix/import/go.scm (fetch-module-meta-data): If no meta entries
have a matching import prefix, return the first entry instead of #f.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

import: elpa: Support NonGNU ELPA.

* guix/import/elpa.scm (elpa-url): Add NonGNU ELPA URL.
* doc/guix.texi (Invoking guix import): Document it.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

system: Add hint for action typo.

* guix/scripts/system.scm (actions): New variable.
(define-command): Add hint for action typo.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

import: Add hint for importer typo.

* guix/scripts/import.scm (define-command): Add hint.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>

gnu: racket-minimal: Remove top-level reference to 'chez-scheme'.

This could cause build errors; for instance, doing:

  make && touch gnu/packages/chez.scm && make

would trigger a "chez-scheme: unbound variable" error.

* gnu/packages/racket.scm (racket-minimal)[source]: Add 'modules'
field.  In 'snippet', remove top-level reference to CHEZ-SCHEME, which
could cause build errors.  Simplify snippet.

gnu: Add r-biscuiteer.

* gnu/packages/bioconductor.scm (r-biscuiteer): New variable.

gnu: Add r-dmrseq.

* gnu/packages/bioconductor.scm (r-dmrseq): New variable.

gnu: Add r-bsseq.

* gnu/packages/bioconductor.scm (r-bsseq): New variable.

gnu: Add r-biotmle.

* gnu/packages/bioconductor.scm (r-biotmle): New variable.

gnu: Add r-biotip.

* gnu/packages/bioconductor.scm (r-biotip): New variable.

gnu: Add r-bioqc.

* gnu/packages/bioconductor.scm (r-bioqc): New variable.

gnu: Add r-bionetstat.

* gnu/packages/bioconductor.scm (r-bionetstat): New variable.

gnu: Add r-bionet.

* gnu/packages/bioconductor.scm (r-bionet): New variable.

gnu: Add r-bionero.

* gnu/packages/bioconductor.scm (r-bionero): New variable.

gnu: Add r-biomvrcns.

* gnu/packages/bioconductor.scm (r-biomvrcns): New variable.

gnu: Add r-biomvcclass.

* gnu/packages/bioconductor.scm (r-biomvcclass): New variable.

gnu: Add r-mvcclass.

* gnu/packages/bioconductor.scm (r-mvcclass): New variable.

gnu: Add r-biscuiteerdata.

* gnu/packages/bioconductor.scm (r-biscuiteerdata): New variable.

gnu: Add r-mus-musculus.

* gnu/packages/bioconductor.scm (r-mus-musculus): New variable.

gnu: Add slurm-monitor.

* gnu/packages/networking.scm (slurm-monitor): New variable.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-shell-command: Update source.

* gnu/packages/emacs-xyz.scm (emacs-shell-command+)[source]: Update URL.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: emacs-autocrypt: Update source and homepage.

* emacs-xyz.scm (emacs-autocrypt)[source, homepage]: Update URL.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

gnu: Add r-qualv.

* gnu/packages/cran.scm (r-qualv): New variable.

gnu: Add r-superheat.

* gnu/packages/cran.scm (r-superheat): New variable.

gnu: Add r-dofuture.

* gnu/packages/cran.scm (r-dofuture): New variable.

gnu: Add r-drtmle.

* gnu/packages/cran.scm (r-drtmle): New variable.

gnu: Add r-superlearner.

* gnu/packages/cran.scm (r-superlearner): New variable.

gnu: Add r-gam.

* gnu/packages/cran.scm (r-gam): New variable.

gnu: Add r-cvauc.

* gnu/packages/cran.scm (r-cvauc): New variable.

gnu: Add r-ggnetwork.

* gnu/packages/cran.scm (r-ggnetwork): New variable.

gnu: Add r-intergraph.

* gnu/packages/cran.scm (r-intergraph): New variable.

gnu: Add r-netrep.

* gnu/packages/cran.scm (r-netrep): New variable.

gnu: Add r-precrec.

* gnu/packages/cran.scm (r-precrec): New variable.

gnu: Add r-cmplot.

* gnu/packages/cran.scm (r-cmplot): New variable.

gnu: Add r-nsprcomp.

* gnu/packages/cran.scm (r-nsprcomp): New variable.

gnu: Add r-biomformat.

* gnu/packages/bioconductor.scm (r-biomformat): New variable.

gnu: Add r-biodb.

* gnu/packages/bioconductor.scm (r-biodb): New variable.

gnu: Add r-biocdockermanager.

* gnu/packages/bioconductor.scm (r-biocdockermanager): New variable.

gnu: Add r-biocthis.

* gnu/packages/bioconductor.scm (r-biocthis): New variable.

gnu: Add r-basilisk.

* gnu/packages/bioconductor.scm (r-basilisk): New variable.

gnu: Add r-basilisk-utils.

* gnu/packages/bioconductor.scm (r-basilisk-utils): New variable.

gnu: Add r-dir-expiry.

* gnu/packages/bioconductor.scm (r-dir-expiry): New variable.

gnu: Add r-genetclassifier.

* gnu/packages/bioconductor.scm (r-genetclassifier): New variable.

gnu: Add r-minet.

* gnu/packages/bioconductor.scm (r-minet): New variable.

gnu: Add r-biobtreer.

* gnu/packages/bioconductor.scm (r-biobtreer): New variable.

gnu: Add r-bgeedb.

* gnu/packages/bioconductor.scm (r-bgeedb): New variable.

gnu: Add r-org-bt-eg-db.

* gnu/packages/bioconductor.scm (r-org-bt-eg-db): New variable.

gnu: Add r-chk.

* gnu/packages/cran.scm (r-chk): New variable.

gnu: Add r-bgeecall.

* gnu/packages/bioconductor.scm (r-bgeecall): New variable.