;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2026 Daniel Patrick Fahey <dpf@helmcontrol.ltd>
;;;
;;; 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 admin)
  #: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 networking)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages tls)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix gexp)
  #: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 "64dca9083dcfa485dcb70fd6fe7ba1f80e0f4082")
        (revision "2"))
    (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")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "01rr39sq9wakw1wnfzg7m4zl7g8qh3d35ww6q39irx19d6nq66h9"))))
      (build-system cmake-build-system)
      (arguments
       (list
        ;; Skip ldconfig, which requires root and is unnecessary in Guix.
        #:configure-flags
        #~(list "-DSKIP_LDCONF=ON")
        #:modules '((guix build cmake-build-system)
                    ((guix build gnu-build-system) #:prefix gnu:)
                    (guix build utils))
        #:phases
        #~(modify-phases %standard-phases
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys #:rest args)
                (when tests?
                  (apply (assoc-ref gnu:%standard-phases 'check)
                         #:tests? tests? #:test-target "tests" args)
                  (for-each
                   (lambda (file)
                     (invoke file))
                   (find-files "tests" "UTest$"))))))))
      (inputs
       (list 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.
  (let ((commit "c8d633bf272b838c2132c21b7c8ddf169a18dd22")
        (revision "2"))
    (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")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0fdqmskjh9d7363ldwmh3zhwal847shm15nhb2nan4g4aqdmckrz"))))
      (build-system cmake-build-system)
      (arguments
       (list
        #:configure-flags
        #~(list "-DSKIP_LDCONF=ON"
                (string-append "-DGUILE_INCLUDE_DIR=" #$guile-3.0.11
                               "/include/guile/3.0/")
                (string-append "-DGUILE_SITE_DIR=" #$output
                               "/share/guile/site/3.0/")
                (string-append "-DGUILE_CCACHE_DIR=" #$output
                               "/lib/guile/3.0/site-ccache")
                (string-append "-DPYTHON_INSTALL_PREFIX=" #$output
                               "/lib/python3.11/site-packages"))
        #:modules '((guix build cmake-build-system)
                    ((guix build gnu-build-system) #:prefix gnu:)
                    (guix build utils))
        #:phases
        #~(modify-phases %standard-phases
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys #:rest args)
                (when tests?
                  (apply (assoc-ref gnu:%standard-phases 'check)
                         #:tests? tests? #:test-target "tests" args)
                  ;; Failing tests.
                  (for-each delete-file
                            '("tests/scm/MultiAtomSpaceUTest"))
                  (setenv "GUILE_LOAD_PATH" ".:opencog/scm")
                  (for-each invoke
                            (find-files "tests" "UTest$"))))))))
      (inputs
       (list boost cogutil gmp guile-3.0-latest postgresql))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("python-cython" ,python-cython)
         ("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 atomspace-storage
  ;; Storage backends for AtomSpace.
  (let ((commit "ecd88d673258e51f65cc0605400003affdf4d694")
        (revision "0"))
    (package
      (name "atomspace-storage")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/atomspace-storage")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "12ssnc313cm5n8bc6zw53dkjm9crrry90lpsknzxafnm61mzcgx3"))))
      (build-system cmake-build-system)
      (arguments
       (list
        #:configure-flags
        #~(list "-DSKIP_LDCONF=ON"
                (string-append "-DGUILE_INCLUDE_DIR=" #$guile-3.0.11
                               "/include/guile/3.0/")
                (string-append "-DGUILE_SITE_DIR=" #$output
                               "/share/guile/site/3.0/")
                (string-append "-DGUILE_CCACHE_DIR=" #$output
                               "/lib/guile/3.0/site-ccache"))
        #:modules '((guix build cmake-build-system)
                    ((guix build gnu-build-system) #:prefix gnu:)
                    (guix build utils))
        #:phases
        #~(modify-phases %standard-phases
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys #:rest args)
                (when tests?
                  (apply (assoc-ref gnu:%standard-phases 'check)
                         #:tests? tests? #:test-target "tests" args)
                  (for-each invoke
                            (find-files "tests" "UTest$"))))))))
      (inputs
       (list atomspace boost cogutil gmp guile-3.0-latest))
      (native-inputs
       (list cxxtest pkg-config python-minimal))
      (home-page "https://github.com/opencog/atomspace-storage")
      (synopsis "Storage backends for AtomSpace")
      (description "AtomSpace-Storage provides various storage backends
for the AtomSpace hypergraph database.")
      (license license:agpl3))))

(define-public cogserver
  ;; There are no releases.
  (let ((commit "3c4da0bd786262bd69a8306f9da88b13f0add1f2")
        (revision "3"))
    (package
      (name "cogserver")
      (version (git-version "0" revision commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/opencog/cogserver")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "0hfz9z44wpzrabs9fgxhv02jzn0i40di2ncbiizn03g7gccawds5"))))
      (build-system cmake-build-system)
      (arguments
       (list
        #:tests? #f ;tests start network server and hang
        #:configure-flags
        #~(list "-DSKIP_LDCONF=ON"
                (string-append "-DGUILE_INCLUDE_DIR=" #$guile-3.0.11
                               "/include/guile/3.0/")
                (string-append "-DGUILE_SITE_DIR=" #$output
                               "/share/guile/site/3.0/")
                (string-append "-DGUILE_CCACHE_DIR=" #$output
                               "/lib/guile/3.0/site-ccache")
                (string-append "-DPYTHON_INSTALL_PREFIX=" #$output
                               "/lib/python3.11/site-packages"))
        #:modules '((guix build cmake-build-system)
                    ((guix build gnu-build-system) #:prefix gnu:)
                    (guix build utils))
        #:phases
        #~(modify-phases %standard-phases
            (replace 'check
              (lambda* (#:key tests? #:allow-other-keys #:rest args)
                (when tests?
                  (apply (assoc-ref gnu:%standard-phases 'check)
                         #:tests? tests? #:test-target "tests" args)
                  ;; Failing test.
                  (delete-file "tests/shell/ShellUTest")
                  (for-each invoke
                            (find-files "tests" "UTest$"))))))))
      (inputs
       (list asio atomspace atomspace-storage boost cogutil
             gmp guile-3.0-latest jsoncpp openssl))
      (native-inputs
       `(("cxxtest" ,cxxtest)
         ("netcat" ,netcat-openbsd)
         ("python" ,python)
         ("python-cython" ,python-cython)
         ("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 agi-bio
  ;; There are no releases.
  (let ((commit "2f723ad79afc38df9dce73d340ee24c38efb2199")
        (revision "2"))
    (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")
                      (commit commit)))
                (file-name (git-file-name name version))
                (sha256
                 (base32
                  "1gqmwjbqdjr0qz4wpsxh0k8wam59fvd3pnjxhfswdpvapcl9syk0"))))
      (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/3.0/")
          (string-append "-DGUILE_SITE_DIR="
                         (assoc-ref %outputs "out")
                         "/share/guile/site/3.0/"))
         #: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/3.0/opencog")))))))))
      (inputs
       (list atomspace cogutil gmp guile-3.0-latest))
      (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))))