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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages cmake)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system emacs)
  #:use-module (gnu packages)
  #:use-module (gnu packages backup)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages crypto)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages file)
  #:use-module (gnu packages libevent)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages xml))

(define-public cmake
  (package
    (name "cmake")
    (version "3.13.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://www.cmake.org/files/v"
                                  (version-major+minor version)
                                  "/cmake-" version ".tar.gz"))
              (sha256
               (base32
                "04123d7fgnn1fs5p0nwyq397ss89r0y4wkg9a09qiwkjsvk1rzmy"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Drop bundled software.
                  (with-directory-excursion "Utilities"
                    (for-each delete-file-recursively
                              '("cmbzip2"
                                ;; "cmcompress"
                                "cmcurl"
                                "cmexpat"
                                ;; "cmjsoncpp"
                                ;; "cmlibarchive"
                                "cmliblzma"
                                ;; "cmlibuv"
                                "cmzlib"))
                    #t)))))
    (build-system gnu-build-system)
    (arguments
     `(#:test-target "test"
       #:make-flags
       (let ((skipped-tests
              (list "BundleUtilities" ; This test fails on Guix.
                    "CTestTestSubdir" ; This test fails to build 2 of the 3 tests.
                    ;; These tests requires network access.
                    "CTestCoverageCollectGCOV"
                    "CTestTestUpload")))
         (list
          (string-append
           ;; These arguments apply for the tests only.
           "ARGS=-j " (number->string (parallel-job-count))
           " --output-on-failure"
           " --exclude-regex ^\\(" (string-join skipped-tests "\\|") "\\)$")))
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'split-package
           ;; Remove files that have been packaged in other package recipes.
           (lambda _
             (delete-file "Auxiliary/cmake-mode.el")
             (substitute* "Auxiliary/CMakeLists.txt"
               ((".*cmake-mode.el.*") ""))
             #t))
         (add-before 'configure 'patch-bin-sh
           (lambda _
             ;; Replace "/bin/sh" by the right path in... a lot of
             ;; files.
             (substitute*
                 '("Modules/CompilerId/Xcode-3.pbxproj.in"
                   "Modules/CPack.RuntimeScript.in"
                   "Source/cmakexbuild.cxx"
                   "Source/cmGlobalXCodeGenerator.cxx"
                   "Source/cmLocalUnixMakefileGenerator3.cxx"
                   "Source/cmExecProgramCommand.cxx"
                   "Utilities/Release/release_cmake.cmake"
                   "Utilities/cmlibarchive/libarchive/archive_write_set_format_shar.c"
                   "Tests/CMakeLists.txt"
                   "Tests/RunCMake/File_Generate/RunCMakeTest.cmake")
               (("/bin/sh") (which "sh")))
             #t))
         (add-before 'configure 'set-paths
           (lambda _
             ;; Help cmake's bootstrap process to find system libraries
             (begin
               (setenv "CMAKE_LIBRARY_PATH" (getenv "LIBRARY_PATH"))
               (setenv "CMAKE_INCLUDE_PATH" (getenv "C_INCLUDE_PATH"))
               #t)))
         (replace 'configure
           (lambda* (#:key outputs #:allow-other-keys)
             (let ((out (assoc-ref outputs "out")))
               (invoke
                "./configure" "--verbose"
                (string-append "--parallel=" (number->string (parallel-job-count)))
                (string-append "--prefix=" out)
                "--system-libs"
                "--no-system-jsoncpp" ; FIXME: Circular dependency.
                ;; By default, the man pages and other docs land
                ;; in PREFIX/man and PREFIX/doc, but we want them
                ;; in share/{man,doc}.  Note that unlike
                ;; autoconf-generated configure scripts, cmake's
                ;; configure prepends "PREFIX/" to what we pass
                ;; to --mandir and --docdir.
                "--mandir=share/man"
                ,(string-append
                  "--docdir=share/doc/cmake-"
                  (version-major+minor version)))))))))
    (inputs
     `(("bzip2" ,bzip2)
       ("curl" ,curl)
       ("expat" ,expat)
       ("file" ,file)
       ("libarchive" ,libarchive)
       ("libuv" ,libuv)
       ("ncurses" ,ncurses) ; required for ccmake
       ("rhash" ,rhash)
       ("zlib" ,zlib)))
    (native-search-paths
     (list (search-path-specification
            (variable "CMAKE_PREFIX_PATH")
            (files '("")))))
    (home-page "https://cmake.org/")
    (synopsis "Cross-platform build system")
    (description
     "CMake is a family of tools designed to build, test and package software.
CMake is used to control the software compilation process using simple platform
and compiler independent configuration files.  CMake generates native makefiles
and workspaces that can be used in the compiler environment of your choice.")
    (license (list license:bsd-3             ; cmake
                   license:bsd-4             ; cmcompress
                   license:bsd-2             ; cmlibarchive
                   license:expat             ; cmjsoncpp is dual MIT/public domain
                   license:public-domain)))) ; cmlibarchive/archive_getdate.c

(define-public cmake/fixed
  ;; This is a variant of CMake that fixes X.509 certificate lookup:
  ;; <https://issues.guix.gnu.org/issue/37371>.
  (package
    (inherit cmake)
    (version (string-append (package-version cmake) "-1"))
    (source (origin
              (inherit (package-source cmake))
              (patches
               (append (search-patches "cmake-curl-certificates.patch")
                       (origin-patches (package-source cmake))))))))

(define-public emacs-cmake-mode
  (package
    (inherit cmake)
    (name "emacs-cmake-mode")
    (build-system emacs-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'chdir-elisp
           ;; Elisp directory is not in root of the source.
           (lambda _
             (chdir "Auxiliary"))))))
    (synopsis "Emacs major mode for editing Cmake expressions")
    (description "@code{cmakeos-mode} provides an Emacs major mode for editing
Cmake files.  It supports syntax highlighting, indenting and refilling of
comments.")))
s 2020-11-17Merge remote-tracking branch 'origin/version-1.2.0' into master...Conflicts: gnu/packages/bioinformatics.scm The python-pysam package fixed in master was kept instead of the update done in the version-1.2.0 branch. Maxim Cournoyer 2020-11-16.dir-locals.el: Add upstream report link....Follow up from 1d6e7732b163c9e945c9e5b32c726fe3b5f09c3a. * .dir-locals.el: Modify comment to point at the report to bug-gnu-emacs. Miguel Ángel Arruga Vivas 2020-11-16.dir-locals.el: Use setq-local on guix-directory....* .dir-locals.el: Use setq-local on guix-directory. While a problem with using setq hasn't been identified, this seems like good hygiene. Christopher Lemmer Webber 2020-11-16.dir-locals.el: Prevent errors if .dir-locals.el isn't found....While this repo should presumably always have a .dir-locals.el by the nature of this file itself, it seems that this behavior "leaks". See added comment for more details on the fix to this strange bug, which is likely an upstream emacs or vc-mode issue. Thanks to Miguel Ángel Arruga Vivas and Maxim Cournoyer for helping investigate this problem. * .dir-locals.el: Don't error out if .dir-locals.el isn't found. Christopher Lemmer Webber 2020-11-12maint: update-guix-package: Optionally add sources to store....Following discussions in <https://issues.guix.gnu.org/43893>, keeping a copy of the updated package source is desirable when generating a release. * build-aux/update-guix-package.scm (version-controlled?): Remove variable. (call-with-temporary-git-worktree): Renamed from 'with-temporary-git-worktree'. Update doc. Do not change directory implicitly. Define as a procedure, not a syntax. (keep-source-in-store): New procedure. (main): Adjust to use with call-with-temporary-git-worktree. Add the sources to the store when GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT is set. Exit gracefully when FIND-ORIGIN-REMOTE returns #f. (%savannah-guix-git-repo-push-url-regexp): Adjust match for a potential colon separator. * Makefile.am (GUIX_ALLOW_ME_TO_USE_PRIVATE_COMMIT): Adjust. * .dir-locals.el (scheme-mode): Remove entry for with-temporary-git-worktree. * doc/contributing.texi (Updating the Guix Package): Update doc. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Maxim Cournoyer 2020-11-01.dir-locals.el: Require cl-lib at runtime....* .dir-locals.el (nil)<Geiser>: Load cl-lib when needed. Miguel Ángel Arruga Vivas 2020-10-31.dir-locals.el: Automatically set the GEISER-GUILE-LOAD-PATH variable....Thanks to Miguel Ángel Arruga Vivas and Pierre Neidhardt for their suggestions and improvements. * .dir-locals.el: Set the GUIX-DIRECTORY and GEISER-GUILE-LOAD-PATH Emacs variables based on the location of the .dir-locals file. Maxim Cournoyer 2020-10-19maint: update-guix-package: Prevent accidentally breaking guix pull....Fixes <https://issues.guix.gnu.org/43893>. This changes the 'update-guix-package' tool so that it: 1. Always uses a clean checkout to compute the hash of the updated 'guix' package. 2. Ensures the commit used in the updated 'guix' package definition has already been pushed upstream. * build-aux/update-guix-package.scm (%savannah-guix-git-repo-push-url): New variable. (with-input-pipe-to-string, with-temporary-git-worktree): New syntaxes. (find-origin-remote, git-add-worktree): New procedures. (commit-already-pushed?): New predicate. (main): Check the commit used has already been pushed upstream and compute the hash from a clean checkout. * doc/contributing.texi (Updating the Guix Package): Document it. * .dir-locals.el (scheme-mode): Fix indentation of with-temporary-git-worktree. Maxim Cournoyer 2020-09-14deduplication: pass store directory to replace-with-link....This causes with-writable-file to take into consideration the actual store being used, as passed to 'deduplicate', rather than whatever (%store-directory) may return. * guix/store/deduplication.scm (replace-with-link): new keyword argument 'store'. Pass to with-writable-file. (with-writable-file, call-with-writable-file): new store argument. (deduplicate): pass store to replace-with-link. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Caleb Ristvedt 2020-09-14.dir-locals.el: fix call-with-{retrying-}transaction indenting....* .dir-locals.el (call-with-transaction, call-with-retrying-transaction): change scheme-indent-function property from 2 to 1. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Caleb Ristvedt 2020-08-26.dir-locals.el: Add indentation rule for 'package/inherit'....* .dir-locals.el (scheme-mode): Add 'package/inherit'. Ludovic Courtès 2020-06-25deduplication: Use 'dynamic-wind' when changing permissions of the parent....Suggested by Caleb Ristvedt <caleb.ristvedt@cune.org>. * guix/store/deduplication.scm (call-with-writable-file): New procedure. (with-writable-file): New macro. (replace-with-link): Use it. Ludovic Courtès 2020-06-16channels: 'latest-channel-instance' authenticates Git checkouts....Fixes <https://bugs.gnu.org/22883>. * guix/channels.scm (<channel>)[introduction]: New field. (<channel-introduction>): New record type. (%guix-channel-introduction): New variable. (%default-channels): Use it. (<channel-metadata>)[keyring-reference]: New field. (%default-keyring-reference): New variable. (read-channel-metadata, read-channel-metadata-from-source): Initialize the 'keyring-reference' field. (commit-short-id, verify-introductory-commit) (authenticate-channel): New procedures. (latest-channel-instance): Call 'authenticate-channel' when CHANNEL has an introduction. * tests/channels.scm (gpg+git-available?, commit-id-string): New procedures. ("authenticate-channel, wrong first commit signer"): ("authenticate-channel, .guix-authorizations"): New tests. * doc/guix.texi (Invoking guix pull): Mention authentication. Ludovic Courtès 2020-06-10database: separate transaction-handling and retry-handling....Previously call-with-transaction would both retry when SQLITE_BUSY errors were thrown and do what its name suggested (start and rollback/commit a transaction). This changes it to do only what its name implies, which simplifies its implementation. Retrying is provided by the new call-with-SQLITE_BUSY-retrying procedure. * guix/store/database.scm (call-with-transaction): no longer restarts, new #:restartable? argument controls whether "begin" or "begin immediate" is used. (call-with-SQLITE_BUSY-retrying, call-with-retrying-transaction, call-with-retrying-savepoint): new procedures. (register-items): use call-with-retrying-transaction to preserve old behavior. * .dir-locals.el (call-with-retrying-transaction, call-with-retrying-savepoint): add indentation information. Caleb Ristvedt 2020-06-10database: ensure update-or-insert is run within a transaction...update-or-insert can break if an insert occurs between when it decides whether to update or insert and when it actually performs that operation. Putting the check and the update/insert operation in the same transaction ensures that the update/insert will only succeed if no other write has occurred in the middle. * guix/store/database.scm (call-with-savepoint): new procedure. (update-or-insert): use call-with-savepoint to ensure the read and the insert/update occur within the same transaction. Caleb Ristvedt 2020-06-10database: rewrite query procedures in terms of with-statement....Most of our queries would fail to finalize their statements properly if sqlite returned an error during their execution. This resolves that, and also makes them somewhat more concise as a side-effect. This also makes some small changes to improve certain queries where behavior was strange or overly verbose. * guix/store/database.scm (call-with-statement): new procedure. (with-statement): new macro. (last-insert-row-id, path-id, update-or-insert, add-references): rewrite to use with-statement. (update-or-insert): factor last-insert-row-id out of the end of both branches. (add-references): remove pointless last-insert-row-id call. * .dir-locals.el (with-statement): add indenting information. Caleb Ristvedt 2020-06-06ui: 'display-search-results' automatically invokes the pager....* guix/ui.scm (call-with-paginated-output-port): New procedure. (with-paginated-output-port): New macro. (display-search-results): Use it instead of displaying a hint. Ludovic Courtès 2020-06-05git-authenticate: Add tests....* guix/tests/git.scm (call-with-environment-variables) (with-environment-variables): Remove. * guix/tests/git.scm (populate-git-repository): Add clauses for signed commits and signed merges. * guix/tests/gnupg.scm: New file. * tests/git-authenticate.scm: New file. * tests/ed25519bis.key, tests/ed25519bis.sec: New files. * Makefile.am (dist_noinst_DATA): Add 'guix/tests/gnupg.scm'. (SCM_TESTS): Add 'tests/git-authenticate.scm'. (EXTRA_DIST): Add tests/ed25519bis.{key,sec}. Ludovic Courtès 2020-05-16gexp: Add 'let-system'....* guix/gexp.scm (<system-binding>): New record type. (let-system): New macro. (system-binding-compiler): New procedure. (default-expander): Add 'self-quoting?' case. (self-quoting?): New procedure. (lower-inputs): Add 'filterm'. Pass the result of 'mapm/accumulate-builds' through FILTERM. (gexp->sexp)[self-quoting?]: Remove. * tests/gexp.scm ("let-system", "let-system, target") ("let-system, ungexp-native, target") ("let-system, nested"): New tests. * doc/guix.texi (G-Expressions): Document it. Ludovic Courtès 2020-03-22store: Add 'with-build-handler'....* guix/store.scm (current-build-prompt): New variable. (call-with-build-handler, invoke-build-handler): New procedures. (with-build-handler): New macro. * tests/store.scm ("with-build-handler"): New test. Ludovic Courtès 2020-03-12gexp: Add 'with-parameters'....* guix/gexp.scm (<parameterized>): New record type. (with-parameters): New macro. (compile-parameterized): New gexp compiler. * tests/gexp.scm ("with-parameters for %current-system") ("with-parameters for %current-target-system") ("with-parameters + file-append"): New tests. * doc/guix.texi (G-Expressions): Document it. Ludovic Courtès