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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2023 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2023 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; 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 mold)
  #:use-module (guix gexp)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages base)
  #:use-module (gnu packages c)
  #:use-module (gnu packages digest)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages compression)
  #:use-module ((guix licenses) #:prefix license:))

(define-public mold
  (package
    (name "mold")
    (version "2.33.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/rui314/mold")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0wsb0aiqia3jfc9k3h2d446y0mzmaq6rz9xkjf9125npdygm7kpb"))
       (modules '((guix build utils)))
       (snippet
        #~(begin
            (for-each
             (lambda (x)
               (delete-file-recursively (string-append "third-party/" x)))
             '("mimalloc" "tbb" "xxhash" "zlib" "zstd"))))))
    (build-system cmake-build-system)
    (arguments
     (list
      #:configure-flags #~(list "-DMOLD_USE_SYSTEM_MIMALLOC=ON"
                                "-DMOLD_USE_SYSTEM_TBB=ON"
                                "-DBUILD_TESTING=ON")
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'configure 'force-system-xxhash
            (lambda _
              (substitute* "common/common.h"
                (("#include \"../third-party/xxhash/xxhash.h\"")
                 "#include <xxhash.h>"))))
          (add-before 'configure 'fix-compiler-name-in-test
            (lambda _
              (substitute* "test/elf/common.inc"
                (("CC=\"\\$\\{TEST_CC:-cc\\}\"") "CC=gcc")
                (("CXX=\"\\$\\{TEST_CXX:-c\\+\\+\\}\"")
                 "CXX=g++"))))
          (add-before 'configure 'skip-tbb-lto-test
            (lambda _
              ;; This test needs tbb 2021.9.0 or newer
              (delete-file "test/elf/lto-version-script.sh")))
          (add-before 'configure 'disable-rpath-test
            (lambda _
              ;; This test fails because mold expect the RUNPATH as-is,
              ;; but compiler in Guix will insert the path of gcc-lib and
              ;; glibc into the output binary.
              (delete-file "test/elf/rpath.sh"))))))
    (inputs (list mimalloc tbb xxhash zlib `(,zstd "lib")))
    (home-page "https://github.com/rui314/mold")
    (synopsis "Fast linker")
    (description
     "Mold is a faster drop-in replacement for existing linkers.
It is designed to increase developer productivity by reducing build time,
especially in rapid debug-edit-rebuild cycles.")
    (license license:agpl3)))

(define* (make-mold-wrapper mold #:key mold-as-ld?)
  "Return a MOLD wrapper.  When MOLD-AS-LD? is true, create a 'ld' symlink that
points to 'mold'."
  (package
    (inherit mold)
    (name (if mold-as-ld? "mold-as-ld-wrapper" "mold-wrapper"))
    (source #f)
    (native-inputs '())
    (inputs (list (make-ld-wrapper "ld.mold-wrapper" #:binutils mold
                                   #:linker "ld.mold")
                  (make-ld-wrapper "mold-wrapper" #:binutils mold #:linker
                                   "mold")))
    (propagated-inputs '())
    (build-system trivial-build-system)
    (arguments
     (list #:builder
           #~(let ((ld.mold (string-append #$(this-package-input
                                              "ld.mold-wrapper")
                                           "/bin/ld.mold"))
                   (mold (string-append #$(this-package-input "mold-wrapper")
                                        "/bin/mold")))
               (mkdir #$output)
               (mkdir (string-append #$output "/bin"))
               (symlink ld.mold (string-append #$output "/bin/ld.mold"))
               (symlink mold (string-append #$output "/bin/mold"))
               (when #$mold-as-ld?
                 (symlink ld.mold (string-append #$output "/bin/ld"))))))
    (synopsis "Mold linker wrapper")
    (description "This is a linker wrapper for Mold; like @code{ld-wrapper}, it
wraps the linker to add any missing @code{-rpath} flags, and to detect any
misuse of libraries outside of the store.")))

(define-public mold-wrapper
  (make-mold-wrapper mold))

(define-public mold-as-ld-wrapper
  (make-mold-wrapper mold #:mold-as-ld? #t))
href='#n299'>299 300 301 302 303 304
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2020 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; 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 opencog)
  #:use-module (gnu packages)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages guile)
  #:use-module (gnu packages language)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix utils))

(define-public cogutil
  ;; The last release was in 2016.  Other OpenCog packages require a later
  ;; version.
  (let ((commit "b07b41b2eaf01627c78b27f1f28bb09ef7086f8e")
        (revision "1"))
    (package
      (name "cogutil")
      (version (git-version "2.0.3" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/cogutil.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1ymmcrinp0prlxsmxmwdjjl4kgaj7wzq39d5b1q2apgg94yfdhqb"))))
      (build-system cmake-build-system)
      (arguments
       `(#:test-target "tests"))
      (inputs
       `(("boost" ,boost)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/cogutil/")
      (synopsis "Low-level C++ programming utilities used by OpenCog components")
      (description "The OpenCog utilities is a miscellaneous collection of C++
utilities use for typical programming tasks in multiple OpenCog projects.")
      ;; Either of these licenses.
      (license (list license:agpl3 license:asl2.0)))))

(define-public atomspace
  ;; The last release was in 2016 and doesn't build with our Boost package.
  (let ((commit "86c848dfc7135b3c47deb581f8da54a60f6711c9")
        (revision "1"))
    (package
      (name "atomspace")
      (version (git-version "5.0.3" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/atomspace.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0vxzhszb0z8081li38hid07a5axzxyflsmq1mcn4b1k4z1j8ggch"))))
      (build-system cmake-build-system)
      (arguments
       `(#:test-target "tests"
         #:configure-flags
         (list (string-append "-DGUILE_INCLUDE_DIR="
                              (assoc-ref %build-inputs "guile")
                              "/include/guile/2.2/")
               (string-append "-DGUILE_SITE_DIR="
                              (assoc-ref %outputs "out")
                              "/share/guile/site/2.2/"))))
      (inputs
       `(("boost" ,boost)
         ("cogutil" ,cogutil)
         ("gmp" ,gmp)
         ("guile" ,guile-2.2)
         ("postgresql" ,postgresql)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/atomspace/")
      (synopsis "OpenCog hypergraph database, query system and rule engine")
      (description "The OpenCog AtomSpace is an in-RAM @dfn{knowledge
representation} (KR) database, an associated query engine and graph-re-writing
system, and a rule-driven inferencing engine that can apply and manipulate
sequences of rules to perform reasoning.  It is a layer that sits on top of
ordinary distributed (graph) databases, providing a large variety of advanced
features not otherwise available.")
      (license license:agpl3))))

(define-public cogserver
  ;; There are no releases.
  (let ((commit "ec5f3b9590db0f6a085b5d0320f5d3710e0f1635")
        (revision "2"))
    (package
      (name "cogserver")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/cogserver.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1h0vcxb6n5dc654xqinqcxc7dxwcs6bsywgir8rhrqiykk760mzl"))))
      (build-system cmake-build-system)
      (arguments
       `(#:test-target "tests"
         #:configure-flags
         (list (string-append "-DGUILE_INCLUDE_DIR="
                              (assoc-ref %build-inputs "guile")
                              "/include/guile/2.2/")
               (string-append "-DGUILE_SITE_DIR="
                              (assoc-ref %outputs "out")
                              "/share/guile/site/2.2/"))))
      (inputs
       `(("atomspace" ,atomspace)
         ("boost" ,boost)
         ("cogutil" ,cogutil)
         ("gmp" ,gmp)
         ("guile" ,guile-2.2)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/cogserver/")
      (synopsis "OpenCog network server")
      (description "The OpenCog Cogserver is a network and job server for the
OpenCog framework.")
      (license license:agpl3))))

(define-public attention
  ;; There are no releases.
  (let ((commit "87d43679280ce486cd6757765d2e1df6d502991d")
        (revision "1"))
    (package
      (name "attention")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/attention.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0sndslphicv6w9qpag168rqkxq5sf71l5qbfx6zhsd5bzlf5fhwv"))))
      (build-system cmake-build-system)
      (arguments
       `(#:test-target "tests"
         #:configure-flags
         (list
          (string-append "-DGUILE_INCLUDE_DIR="
                         (assoc-ref %build-inputs "guile")
                         "/include/guile/2.2/")
          (string-append "-DGUILE_SITE_DIR="
                         (assoc-ref %outputs "out")
                         "/share/guile/site/2.2/"))))
      (inputs
       `(("atomspace" ,atomspace)
         ("boost" ,boost)
         ("cogserver" ,cogserver)
         ("cogutil" ,cogutil)
         ("gmp" ,gmp)
         ("guile" ,guile-2.2)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/attention/")
      (synopsis "OpenCog attention allocation subsystem")
      (description "Attention Allocation is an OpenCog subsystem meant to
control the application of processing and memory resources to specific
tasks.")
      (license license:agpl3))))

(define-public opencog
  ;; There are no recent releases.
  (let ((commit "ceac90507610cb2d0ee98f97a2086865292b1204")
        (revision "1"))
    (package
      (name "opencog")
      (version (git-version "0.1.4" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/opencog.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1j8wv910fvrmph370wv5pv2f4bc2s9vl6i7bw3pkmwbdhxkhjbhm"))))
      (build-system cmake-build-system)
      (arguments
       `(#:test-target "tests"
         #:configure-flags
         (list
          (string-append "-DGUILE_INCLUDE_DIR="
                         (assoc-ref %build-inputs "guile")
                         "/include/guile/2.2/")
          (string-append "-DGUILE_SITE_DIR="
                         (assoc-ref %outputs "out")
                         "/share/guile/site/2.2/"))))
      (inputs
       `(("attention" ,attention)
         ("atomspace" ,atomspace)
         ("boost" ,boost)
         ("cogserver" ,cogserver)
         ("cogutil" ,cogutil)
         ("gmp" ,gmp)
         ("guile" ,guile-2.2)
         ("libuuid" ,util-linux "lib")
         ("link-grammar" ,link-grammar)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/attention/")
      (synopsis "Framework for integrated artificial intelligence")
      (description "OpenCog is a framework for developing AI systems,
especially appropriate for integrative multi-algorithm systems, and artificial
general intelligence systems.  It currently contains a functional core
framework, and a number of cognitive agents at varying levels of completion,
some already displaying interesting and useful functionalities alone and in
combination.")
      (license license:agpl3))))

(define-public agi-bio
  ;; There are no releases.
  (let ((commit "b5c6f3d99e8cca3798bf0cdf2c32f4bdb8098efb")
        (revision "1"))
    (package
      (name "agi-bio")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/agi-bio.git")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0c3q0nhmd03nvqm1ih10y28n596cjvfhkcfvzw2fmz1sn3ywdah4"))))
      (build-system cmake-build-system)
      (arguments
       `(#:tests? #f ; there are none
         #:configure-flags
         (list
          (string-append "-DGUILE_INCLUDE_DIR="
                         (assoc-ref %build-inputs "guile")
                         "/include/guile/2.2/")
          (string-append "-DGUILE_SITE_DIR="
                         (assoc-ref %outputs "out")
                         "/share/guile/site/2.2/"))
         #:phases
         (modify-phases %standard-phases
           (add-after 'unpack 'fix-unqualified-load
             (lambda* (#:key outputs #:allow-other-keys)
               (substitute* "bioscience/bioscience.scm"
                 (("\\(load \"bioscience/types/bioscience_types.scm\"\\)")
                  (format #f "(load \"~a/bioscience/types/bioscience_types.scm\")"
                          (string-append (assoc-ref outputs "out")
                                         "/share/guile/site/2.2/opencog"))))
               #t)))))
      (inputs
       `(("atomspace" ,atomspace)
         ("cogutil" ,cogutil)
         ("gmp" ,gmp)
         ("guile" ,guile-2.2)))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python" ,python-minimal)
         ("pkg-config" ,pkg-config)))
      (home-page "https://github.com/opencog/agi-bio")
      (synopsis "Genomic and proteomic data exploration and pattern mining")
      (description "This is a package for genomic and proteomic research using
the OpenCog toolset with Guile.  This includes experiments in applying pattern
mining and other OpenCog components.")
      (license license:agpl3))))