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 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 "2.13")
 109     (source (origin
 110               (method url-fetch)
 111               (uri (string-append "mirror://sourceforge/ssdeep/"
 112                                   name "-" version "/"
 113                                   name "-" version ".tar.gz"))
 114               (sha256
 115                (base32
 116                 "1igqy0j7jrklb8fdlrm6ald4cyl1fda5ipfl8crzyl6bax2ajk3f"))))
 117     (build-system gnu-build-system)
 118     (home-page "http://ssdeep.sourceforge.net")
 119     (synopsis "Context-triggered piecewise hashing algorithm")
 120     (description "ssdeep computes and matches context triggered piecewise
 121 hashes (CTPH), also called fuzzy checksums.  It can identify similar files
 122 that have sequences of identical bytes in the same order, even though bytes
 123 in between these sequences may be different in both content and length.")
 124     (license license:gpl2+)))
 125
 126 (define-public liburcu
 127   (package
 128     (name "liburcu")
 129     (version "0.11.1")
 130     (source (origin
 131               (method url-fetch)
 132               (uri (string-append "https://www.lttng.org/files/urcu/"
 133                                   "userspace-rcu-" version ".tar.bz2"))
 134               (sha256
 135                (base32
 136                 "0l1kxgzch4m8fxiz2hc8fwg56hrvzzspp7n0svnl7i7iycdrgfcj"))))
 137     (build-system gnu-build-system)
 138     (native-inputs
 139      `(("perl" ,perl)))                 ; for tests
 140     (home-page "https://liburcu.org/")
 141     (synopsis "User-space RCU data synchronisation library")
 142     (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data
 143 synchronisation library.  It provides read-side access that scales linearly
 144 with the number of cores.  liburcu-cds provides efficient data structures
 145 based on RCU and lock-free algorithms.  These structures include hash tables,
 146 queues, stacks, and doubly-linked lists.")
 147     (license license:lgpl2.1+)))
 148
 149 (define-public uthash
 150   (package
 151     (name "uthash")
 152     (version "2.0.2")
 153     (source
 154      (origin
 155        (method git-fetch)
 156        (uri (git-reference
 157              (url "https://github.com/troydhanson/uthash.git")
 158              (commit (string-append "v" version))))
 159        (file-name (git-file-name name version))
 160        (sha256
 161         (base32
 162          "0kslz8k6lssh7fl7ayzwlj62p0asxs3dq03357ls5ywjad238gqg"))))
 163     (build-system gnu-build-system)
 164     (native-inputs
 165      `(("perl" ,perl)))
 166     (arguments
 167      `(#:make-flags
 168        (list "CC=gcc")
 169        #:phases
 170        (modify-phases %standard-phases
 171          (delete 'configure)            ; nothing to configure
 172          (delete 'build)                ; nothing to build
 173          (replace 'check
 174            (lambda* (#:key make-flags #:allow-other-keys)
 175              (with-directory-excursion "tests"
 176                (apply invoke "make" make-flags))))
 177          (replace 'install
 178            ;; There is no top-level Makefile to do this for us.
 179            (lambda* (#:key outputs #:allow-other-keys)
 180              (let* ((out (assoc-ref outputs "out"))
 181                     (doc (string-append out "/share/doc/" ,name))
 182                     (include (string-append out "/include")))
 183                ;; Don't install HTML files: they're just the below .txt files
 184                ;; dolled up, can be stale, and regeneration requires asciidoc.
 185                (for-each (λ (file) (install-file file doc))
 186                          (find-files "doc" "\\.txt$"))
 187                (for-each (λ (file) (install-file file include))
 188                          (find-files "src" "\\.h$"))
 189                #t))))))
 190     (home-page "https://troydhanson.github.io/uthash/")
 191     (synopsis
 192      "Hash tables, lists, and other data structures implemented as C macros")
 193     (description
 194      "uthash implements a hash table and a few other basic data structures
 195 as C preprocessor macros.  It aims to be minimalistic and efficient: it's
 196 around 1,000 lines of code which, being macros, inline automatically.
 197
 198 Unlike function calls with fixed prototypes, macros operate on untyped
 199 arguments.  Thus, they are able to work with any type of structure and key.
 200 Any C structure can be stored in a hash table by adding @code{UT_hash_handle}
 201 to the structure and choosing one or more fields to act as the key.")
 202     (license license:bsd-2)))
 203
 204 (define-public sdsl-lite
 205   (package
 206     (name "sdsl-lite")
 207     (version "2.1.1")
 208     (source (origin
 209               (method url-fetch)
 210               (uri (string-append "https://github.com/simongog/sdsl-lite/"
 211                                   "releases/download/v" version "/"
 212                                   "sdsl-lite-" version
 213                                   ".tar.gz.offline.install.gz"))
 214               (sha256
 215                (base32
 216                 "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))
 217               (modules '((guix build utils)))
 218               (snippet
 219                '(begin
 220                   (delete-file-recursively "external") #t))
 221               (patches
 222                 (list (origin
 223                         (method url-fetch)
 224                         (uri "https://salsa.debian.org/science-team/libsdsl/raw/debian/2.1.1+dfsg-2/debian/patches/0001-Patch-cmake-files.patch")
 225                         (file-name "sdsl-lite-dont-use-bundled-libraries.patch")
 226                         (sha256
 227                          (base32
 228                           "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
 229     (build-system cmake-build-system)
 230     (arguments
 231      '(#:phases
 232        (modify-phases %standard-phases
 233          (add-after 'install 'install-static-library
 234            (lambda* (#:key outputs #:allow-other-keys)
 235              (let ((out (assoc-ref outputs "out")))
 236                (copy-file "lib/libsdsl_static.a"
 237                           (string-append out "/lib/libsdsl.a")))
 238              #t)))))
 239     (native-inputs
 240      `(("libdivsufsort" ,libdivsufsort)))
 241     (home-page "https://github.com/simongog/sdsl-lite")
 242     (synopsis "Succinct data structure library")
 243     (description "The Succinct Data Structure Library (SDSL) is a powerful and
 244 flexible C++11 library implementing succinct data structures.  In total, the
 245 library contains the highlights of 40 research publications.  Succinct data
 246 structures can represent an object (such as a bitvector or a tree) in space
 247 close to the information-theoretic lower bound of the object while supporting
 248 operations of the original object efficiently.  The theoretical time
 249 complexity of an operation performed on the classical data structure and the
 250 equivalent succinct data structure are (most of the time) identical.")
 251     (license license:gpl3+)))
 252
 253 (define-public libdivsufsort
 254   (package
 255     (name "libdivsufsort")
 256     (version "2.0.1")
 257     (source (origin
 258               (method git-fetch)
 259               (uri (git-reference
 260                     (url "https://github.com/y-256/libdivsufsort.git")
 261                     (commit version)))
 262               (file-name (git-file-name name version))
 263               (sha256
 264                (base32
 265                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
 266     (build-system cmake-build-system)
 267     (arguments
 268      '(#:tests? #f                      ; there are no tests
 269        #:configure-flags
 270        ;; Needed for rapmap and sailfish.
 271        '("-DBUILD_DIVSUFSORT64=ON")))
 272     (home-page "https://github.com/y-256/libdivsufsort")
 273     (synopsis "Lightweight suffix-sorting library")
 274     (description "libdivsufsort is a software library that implements a
 275 lightweight suffix array construction algorithm.  This library provides a
 276 simple and an efficient C API to construct a suffix array and a
 277 Burrows-Wheeler transformed string from a given string over a constant-size
 278 alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
 279 bytes of memory space, where n is the length of the string.")
 280     (license license:expat)))