gnu/packages/datastructures.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2016, 2017, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   4 ;;; Copyright © 2018 Meiyo Peng <meiyo.peng@gmail.com>
   5 ;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
   6 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages datastructures)
  23   #:use-module (gnu packages)
  24   #:use-module (gnu packages perl)
  25   #:use-module ((guix licenses) #:prefix license:)
  26   #:use-module (guix packages)
  27   #:use-module (guix download)
  28   #:use-module (guix git-download)
  29   #:use-module (guix build-system cmake)
  30   #:use-module (guix build-system gnu))
  31
  32 (define-public gdsl
  33   (package
  34     (name "gdsl")
  35     (version "1.8")
  36     (source (origin
  37               (method url-fetch)
  38               (uri (string-append "http://download.gna.org/gdsl/"
  39                                   "gdsl-" version ".tar.gz"))
  40               (sha256
  41                (base32
  42                 "1v64jvlnj8jfpphphgjgb36p0kv50kwfyqncf0y12f16v8ydyiaw"))))
  43     (build-system gnu-build-system)
  44     (home-page "http://home.gna.org/gdsl/")
  45     (synopsis "Generic data structures library")
  46     (description "The Generic Data Structures Library (GDSL) is a collection
  47 of routines for generic data structures manipulation.  It is a re-entrant
  48 library fully written from scratch in pure ANSI C.  It is designed to offer
  49 for C programmers common data structures with powerful algorithms, and hidden
  50 implementation.  Available structures are lists, queues, stacks, hash tables,
  51 binary trees, binary search trees, red-black trees, 2D arrays, permutations
  52 and heaps.")
  53     (license license:gpl2+)))
  54
  55 (define-public marisa
  56   (package
  57     (name "marisa")
  58     (version "0.2.5")
  59     (source
  60      (origin
  61        (method url-fetch)
  62        (uri (string-append "https://github.com/s-yata/marisa-trie"
  63                            "/releases/download/v" version "/" name "-"
  64                            version ".tar.gz"))
  65        (sha256
  66         (base32 "19ifrcmnbr9whaaf4ly3s9ndyiq9sjqhnfkrxbz9zsb44w2n36hf"))))
  67     (build-system gnu-build-system)
  68     (home-page "https://github.com/s-yata/marisa-trie")
  69     (synopsis "Trie data structure C++ library")
  70     (description "Matching Algorithm with Recursively Implemented
  71 StorAge (MARISA) is a static and space-efficient trie data structure C++
  72 library.")
  73
  74     ;; Dual-licensed, according to docs/readme.en.html (source files lack
  75     ;; copyright/license headers.)
  76     (license (list license:bsd-2 license:lgpl2.1+))))
  77
  78 (define-public sparsehash
  79   (package
  80     (name "sparsehash")
  81     (version "2.0.3")
  82     (source (origin
  83               (method git-fetch)
  84               (uri (git-reference
  85                      (url "https://github.com/sparsehash/sparsehash.git")
  86                      (commit (string-append name "-" version))))
  87               (file-name (git-file-name name version))
  88               (sha256
  89                (base32
  90                 "0m3f0cnpnpf6aak52wn8xbrrdw8p0yhq8csgc8nlvf9zp8c402na"))))
  91     (build-system gnu-build-system)
  92     (synopsis "Memory-efficient hashtable implementations")
  93     (description
  94      "This library contains several hash-map implementations, similar in API
  95 to SGI's @code{hash_map} class, but with different performance
  96 characteristics.  @code{sparse_hash_map} uses very little space overhead, 1-2
  97 bits per entry.  @code{dense_hash_map} is very fast, particularly on lookup.
  98 @code{sparse_hash_set} and @code{dense_hash_set} are the set versions of these
  99 routines.  All these implementation use a hashtable with internal quadratic
 100 probing.  This method is space-efficient -- there is no pointer overhead --
 101 and time-efficient for good hash functions.")
 102     (home-page "https://github.com/sparsehash/sparsehash")
 103     (license license:bsd-3)))
 104
 105 (define-public ssdeep
 106   (package
 107     (name "ssdeep")
 108     (version "2.14.1")
 109     (source
 110      (origin
 111        (method url-fetch)
 112        (uri (string-append "https://github.com/ssdeep-project/ssdeep/"
 113                            "releases/download/release-" version "/"
 114                            "ssdeep-" version ".tar.gz"))
 115        (sha256
 116         (base32 "04qkjc6kksxkv7xbnk32rwmf3a8czdv2vvrdzfs0kw06h73snbpz"))))
 117     (build-system gnu-build-system)
 118     (arguments
 119      `(#:configure-flags
 120        (list "--disable-static")))
 121     (home-page "https://ssdeep-project.github.io")
 122     (synopsis "Context-triggered piecewise hashing algorithm")
 123     (description "ssdeep computes and matches context triggered piecewise
 124 hashes (CTPH), also called fuzzy checksums.  It can identify similar files
 125 that have sequences of identical bytes in the same order, even though bytes
 126 in between these sequences may be different in both content and length.")
 127     (license license:gpl2+)))
 128
 129 (define-public liburcu
 130   (package
 131     (name "liburcu")
 132     (version "0.12.1")
 133     (source (origin
 134               (method url-fetch)
 135               (uri (string-append "https://www.lttng.org/files/urcu/"
 136                                   "userspace-rcu-" version ".tar.bz2"))
 137               (sha256
 138                (base32
 139                 "03nd1gy2c3fdb6xwdrd5lr1jcjxbzffqh3z91mzbjhjn6k8fmymv"))))
 140     (build-system gnu-build-system)
 141     (native-inputs
 142      `(("perl" ,perl)))                 ; for tests
 143     (home-page "https://liburcu.org/")
 144     (synopsis "User-space RCU data synchronisation library")
 145     (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data
 146 synchronisation library.  It provides read-side access that scales linearly
 147 with the number of cores.  liburcu-cds provides efficient data structures
 148 based on RCU and lock-free algorithms.  These structures include hash tables,
 149 queues, stacks, and doubly-linked lists.")
 150     (license license:lgpl2.1+)))
 151
 152 (define-public uthash
 153   (package
 154     (name "uthash")
 155     (version "2.1.0")
 156     (source
 157      (origin
 158        (method git-fetch)
 159        (uri (git-reference
 160              (url "https://github.com/troydhanson/uthash.git")
 161              (commit (string-append "v" version))))
 162        (file-name (git-file-name name version))
 163        (sha256
 164         (base32 "0k80bjbb6ss5wpmfmfji6xbyjm990hg9kcshwwnhdnh73vxkcd1m"))))
 165     (build-system gnu-build-system)
 166     (native-inputs
 167      `(("perl" ,perl)))
 168     (arguments
 169      `(#:make-flags
 170        (list "CC=gcc")
 171        #:phases
 172        (modify-phases %standard-phases
 173          (delete 'configure)            ; nothing to configure
 174          (delete 'build)                ; nothing to build
 175          (replace 'check
 176            (lambda* (#:key make-flags #:allow-other-keys)
 177              (with-directory-excursion "tests"
 178                (apply invoke "make" make-flags))))
 179          (replace 'install
 180            ;; There is no top-level Makefile to do this for us.
 181            (lambda* (#:key outputs #:allow-other-keys)
 182              (let* ((out (assoc-ref outputs "out"))
 183                     (doc (string-append out "/share/doc/" ,name "-" ,version))
 184                     (include (string-append out "/include")))
 185                ;; Don't install HTML files: they're just the below .txt files
 186                ;; dolled up, can be stale, and regeneration requires asciidoc.
 187                (for-each (λ (file) (install-file file doc))
 188                          (find-files "doc" "\\.txt$"))
 189                (for-each (λ (file) (install-file file include))
 190                          (find-files "src" "\\.h$"))
 191                #t))))))
 192     (home-page "https://troydhanson.github.io/uthash/")
 193     (synopsis
 194      "Hash tables, lists, and other data structures implemented as C macros")
 195     (description
 196      "uthash implements a hash table and a few other basic data structures
 197 as C preprocessor macros.  It aims to be minimalistic and efficient: it's
 198 around 1,000 lines of code which, being macros, inline automatically.
 199
 200 Unlike function calls with fixed prototypes, macros operate on untyped
 201 arguments.  Thus, they are able to work with any type of structure and key.
 202 Any C structure can be stored in a hash table by adding @code{UT_hash_handle}
 203 to the structure and choosing one or more fields to act as the key.")
 204     (license license:bsd-2)))
 205
 206 (define-public sdsl-lite
 207   (package
 208     (name "sdsl-lite")
 209     (version "2.1.1")
 210     (source (origin
 211               (method url-fetch)
 212               (uri (string-append "https://github.com/simongog/sdsl-lite/"
 213                                   "releases/download/v" version "/"
 214                                   "sdsl-lite-" version
 215                                   ".tar.gz.offline.install.gz"))
 216               (sha256
 217                (base32
 218                 "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))
 219               (modules '((guix build utils)))
 220               (snippet
 221                '(begin
 222                   (delete-file-recursively "external") #t))
 223               (patches
 224                 (list (origin
 225                         (method url-fetch)
 226                         (uri "https://salsa.debian.org/science-team/libsdsl/raw/debian/2.1.1+dfsg-2/debian/patches/0001-Patch-cmake-files.patch")
 227                         (file-name "sdsl-lite-dont-use-bundled-libraries.patch")
 228                         (sha256
 229                          (base32
 230                           "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
 231     (build-system cmake-build-system)
 232     (arguments
 233      '(#:phases
 234        (modify-phases %standard-phases
 235          (add-after 'install 'install-static-library
 236            (lambda* (#:key outputs #:allow-other-keys)
 237              (let ((out (assoc-ref outputs "out")))
 238                (copy-file "lib/libsdsl_static.a"
 239                           (string-append out "/lib/libsdsl.a")))
 240              #t)))))
 241     (native-inputs
 242      `(("libdivsufsort" ,libdivsufsort)))
 243     (home-page "https://github.com/simongog/sdsl-lite")
 244     (synopsis "Succinct data structure library")
 245     (description "The Succinct Data Structure Library (SDSL) is a powerful and
 246 flexible C++11 library implementing succinct data structures.  In total, the
 247 library contains the highlights of 40 research publications.  Succinct data
 248 structures can represent an object (such as a bitvector or a tree) in space
 249 close to the information-theoretic lower bound of the object while supporting
 250 operations of the original object efficiently.  The theoretical time
 251 complexity of an operation performed on the classical data structure and the
 252 equivalent succinct data structure are (most of the time) identical.")
 253     (license license:gpl3+)))
 254
 255 (define-public libdivsufsort
 256   (package
 257     (name "libdivsufsort")
 258     (version "2.0.1")
 259     (source (origin
 260               (method git-fetch)
 261               (uri (git-reference
 262                     (url "https://github.com/y-256/libdivsufsort.git")
 263                     (commit version)))
 264               (file-name (git-file-name name version))
 265               (sha256
 266                (base32
 267                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
 268     (build-system cmake-build-system)
 269     (arguments
 270      '(#:tests? #f                      ; there are no tests
 271        #:configure-flags
 272        ;; Needed for rapmap and sailfish.
 273        '("-DBUILD_DIVSUFSORT64=ON")))
 274     (home-page "https://github.com/y-256/libdivsufsort")
 275     (synopsis "Lightweight suffix-sorting library")
 276     (description "libdivsufsort is a software library that implements a
 277 lightweight suffix array construction algorithm.  This library provides a
 278 simple and an efficient C API to construct a suffix array and a
 279 Burrows-Wheeler transformed string from a given string over a constant-size
 280 alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
 281 bytes of memory space, where n is the length of the string.")
 282     (license license:expat)))