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, 2020 Efraim Flashner <efraim@flashner.co.il>
   6 ;;; Copyright © 2020 Mark H Weaver <mhw@netris.org>
   7 ;;;
   8 ;;; This file is part of GNU Guix.
   9 ;;;
  10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  11 ;;; under the terms of the GNU General Public License as published by
  12 ;;; the Free Software Foundation; either version 3 of the License, or (at
  13 ;;; your option) any later version.
  14 ;;;
  15 ;;; GNU Guix is distributed in the hope that it will be useful, but
  16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 ;;; GNU General Public License for more details.
  19 ;;;
  20 ;;; You should have received a copy of the GNU General Public License
  21 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 (define-module (gnu packages datastructures)
  24   #:use-module (gnu packages)
  25   #:use-module (gnu packages autotools)
  26   #:use-module (gnu packages boost)
  27   #:use-module (gnu packages perl)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix packages)
  30   #:use-module (guix download)
  31   #:use-module (guix git-download)
  32   #:use-module (guix build-system cmake)
  33   #:use-module (guix build-system gnu))
  34
  35 (define-public gdsl
  36   (package
  37     (name "gdsl")
  38     (version "1.8")
  39     (source (origin
  40               (method git-fetch)
  41               (uri (git-reference
  42                     (url "https://example.org") ;only hosted on Software Heritage
  43                     (commit "6adb53be8b8f9f2e4bbfc92d357eedeefb4c7430")))
  44               (file-name (git-file-name name version))
  45               (sha256
  46                (base32
  47                 "0a52g12d9sf9hhcyvwfd7xdazj2a9i9jh97cnlqf2ymvwnvjk1g0"))))
  48     (build-system gnu-build-system)
  49     (home-page "https://web.archive.org/web/20170502005430/http://home.gna.org/gdsl/")
  50     (synopsis "Generic data structures library")
  51     (description "The Generic Data Structures Library (GDSL) is a collection
  52 of routines for generic data structures manipulation.  It is a re-entrant
  53 library fully written from scratch in pure ANSI C.  It is designed to offer
  54 for C programmers common data structures with powerful algorithms, and hidden
  55 implementation.  Available structures are lists, queues, stacks, hash tables,
  56 binary trees, binary search trees, red-black trees, 2D arrays, permutations
  57 and heaps.")
  58     (license license:gpl2+)))
  59
  60 (define-public marisa
  61   (package
  62     (name "marisa")
  63     (version "0.2.6")
  64     (source
  65      (origin
  66        (method url-fetch)
  67        (uri (string-append "https://github.com/s-yata/marisa-trie/files/"
  68                            "4832504/marisa-" version ".tar.gz"))
  69        (sha256
  70         (base32 "1pk6wmi28pa8srb4szybrwfn71jldb61c5vgxsiayxcyg1ya4qqh"))))
  71     (build-system gnu-build-system)
  72     (native-inputs
  73      `(("autoconf" ,autoconf)
  74        ("automake" ,automake)
  75        ("libtool" ,libtool)))
  76     (home-page "https://github.com/s-yata/marisa-trie")
  77     (synopsis "Trie data structure C++ library")
  78     (description "@acronym{MARISA, Matching Algorithm with Recursively
  79 Implemented StorAge} is a static and space-efficient trie data structure C++
  80 library.")
  81
  82     ;; Dual-licensed, according to docs/readme.en.html (source files lack
  83     ;; copyright/license headers.)
  84     (license (list license:bsd-2 license:lgpl2.1+))))
  85
  86 (define-public sparsehash
  87   (package
  88     (name "sparsehash")
  89     (version "2.0.4")
  90     (source (origin
  91               (method git-fetch)
  92               (uri (git-reference
  93                      (url "https://github.com/sparsehash/sparsehash")
  94                      (commit (string-append name "-" version))))
  95               (file-name (git-file-name name version))
  96               (sha256
  97                (base32
  98                 "1pf1cjvcjdmb9cd6gcazz64x0cd2ndpwh6ql2hqpypjv725xwxy7"))))
  99     (build-system gnu-build-system)
 100     (synopsis "Memory-efficient hashtable implementations")
 101     (description
 102      "This library contains several hash-map implementations, similar in API
 103 to SGI's @code{hash_map} class, but with different performance
 104 characteristics.  @code{sparse_hash_map} uses very little space overhead, 1-2
 105 bits per entry.  @code{dense_hash_map} is very fast, particularly on lookup.
 106 @code{sparse_hash_set} and @code{dense_hash_set} are the set versions of these
 107 routines.  All these implementation use a hashtable with internal quadratic
 108 probing.  This method is space-efficient -- there is no pointer overhead --
 109 and time-efficient for good hash functions.")
 110     (home-page "https://github.com/sparsehash/sparsehash")
 111     (license license:bsd-3)))
 112
 113 (define-public ssdeep
 114   (package
 115     (name "ssdeep")
 116     (version "2.14.1")
 117     (source
 118      (origin
 119        (method url-fetch)
 120        (uri (string-append "https://github.com/ssdeep-project/ssdeep/"
 121                            "releases/download/release-" version "/"
 122                            "ssdeep-" version ".tar.gz"))
 123        (sha256
 124         (base32 "04qkjc6kksxkv7xbnk32rwmf3a8czdv2vvrdzfs0kw06h73snbpz"))))
 125     (build-system gnu-build-system)
 126     (arguments
 127      `(#:configure-flags
 128        (list "--disable-static")))
 129     (home-page "https://ssdeep-project.github.io")
 130     (synopsis "Context-triggered piecewise hashing algorithm")
 131     (description "ssdeep computes and matches context triggered piecewise
 132 hashes (CTPH), also called fuzzy checksums.  It can identify similar files
 133 that have sequences of identical bytes in the same order, even though bytes
 134 in between these sequences may be different in both content and length.")
 135     (license license:gpl2+)))
 136
 137 (define-public liburcu
 138   (package
 139     (name "liburcu")
 140     (version "0.12.1")
 141     (source (origin
 142               (method url-fetch)
 143               (uri (string-append "https://www.lttng.org/files/urcu/"
 144                                   "userspace-rcu-" version ".tar.bz2"))
 145               (sha256
 146                (base32
 147                 "03nd1gy2c3fdb6xwdrd5lr1jcjxbzffqh3z91mzbjhjn6k8fmymv"))))
 148     (build-system gnu-build-system)
 149     (native-inputs
 150      `(("perl" ,perl)))                 ; for tests
 151     (home-page "https://liburcu.org/")
 152     (synopsis "User-space RCU data synchronisation library")
 153     (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data
 154 synchronisation library.  It provides read-side access that scales linearly
 155 with the number of cores.  liburcu-cds provides efficient data structures
 156 based on RCU and lock-free algorithms.  These structures include hash tables,
 157 queues, stacks, and doubly-linked lists.")
 158     (license license:lgpl2.1+)))
 159
 160 (define-public uthash
 161   (package
 162     (name "uthash")
 163     (version "2.1.0")
 164     (source
 165      (origin
 166        (method git-fetch)
 167        (uri (git-reference
 168              (url "https://github.com/troydhanson/uthash")
 169              (commit (string-append "v" version))))
 170        (file-name (git-file-name name version))
 171        (sha256
 172         (base32 "0k80bjbb6ss5wpmfmfji6xbyjm990hg9kcshwwnhdnh73vxkcd1m"))))
 173     (build-system gnu-build-system)
 174     (native-inputs
 175      `(("perl" ,perl)))
 176     (arguments
 177      `(#:make-flags
 178        (list "CC=gcc")
 179        #:phases
 180        (modify-phases %standard-phases
 181          (delete 'configure)            ; nothing to configure
 182          (delete 'build)                ; nothing to build
 183          (replace 'check
 184            (lambda* (#:key make-flags #:allow-other-keys)
 185              (with-directory-excursion "tests"
 186                (apply invoke "make" make-flags))))
 187          (replace 'install
 188            ;; There is no top-level Makefile to do this for us.
 189            (lambda* (#:key outputs #:allow-other-keys)
 190              (let* ((out (assoc-ref outputs "out"))
 191                     (doc (string-append out "/share/doc/" ,name "-" ,version))
 192                     (include (string-append out "/include")))
 193                ;; Don't install HTML files: they're just the below .txt files
 194                ;; dolled up, can be stale, and regeneration requires asciidoc.
 195                (for-each (λ (file) (install-file file doc))
 196                          (find-files "doc" "\\.txt$"))
 197                (for-each (λ (file) (install-file file include))
 198                          (find-files "src" "\\.h$"))
 199                #t))))))
 200     (home-page "https://troydhanson.github.io/uthash/")
 201     (synopsis
 202      "Hash tables, lists, and other data structures implemented as C macros")
 203     (description
 204      "uthash implements a hash table and a few other basic data structures
 205 as C preprocessor macros.  It aims to be minimalistic and efficient: it's
 206 around 1,000 lines of code which, being macros, inline automatically.
 207
 208 Unlike function calls with fixed prototypes, macros operate on untyped
 209 arguments.  Thus, they are able to work with any type of structure and key.
 210 Any C structure can be stored in a hash table by adding @code{UT_hash_handle}
 211 to the structure and choosing one or more fields to act as the key.")
 212     (license license:bsd-2)))
 213
 214 (define-public sdsl-lite
 215   (package
 216     (name "sdsl-lite")
 217     (version "2.1.1")
 218     (source (origin
 219               (method url-fetch)
 220               (uri (string-append "https://github.com/simongog/sdsl-lite/"
 221                                   "releases/download/v" version "/"
 222                                   "sdsl-lite-" version
 223                                   ".tar.gz.offline.install.gz"))
 224               (sha256
 225                (base32
 226                 "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))
 227               (modules '((guix build utils)))
 228               (snippet
 229                '(begin
 230                   (delete-file-recursively "external") #t))
 231               (patches
 232                 (list (origin
 233                         (method url-fetch)
 234                         (uri "https://salsa.debian.org/science-team/libsdsl/raw/debian/2.1.1+dfsg-2/debian/patches/0001-Patch-cmake-files.patch")
 235                         (file-name "sdsl-lite-dont-use-bundled-libraries.patch")
 236                         (sha256
 237                          (base32
 238                           "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
 239     (build-system cmake-build-system)
 240     (arguments
 241      `(#:phases
 242        (modify-phases %standard-phases
 243          (add-after 'install 'install-static-library
 244            (lambda* (#:key outputs #:allow-other-keys)
 245              (let ((out (assoc-ref outputs "out")))
 246                (copy-file "lib/libsdsl_static.a"
 247                           (string-append out "/lib/libsdsl.a")))
 248              #t))
 249         (add-after 'install 'install-pkgconfig-file
 250           (lambda* (#:key outputs #:allow-other-keys)
 251             (let* ((out (assoc-ref outputs "out"))
 252                    (lib (string-append out "/lib")))
 253               (mkdir-p (string-append lib "/pkgconfig"))
 254               (with-output-to-file (string-append lib "/pkgconfig/sdsl-lite.pc")
 255                 (lambda _
 256                   (format #t "prefix=~a~@
 257                           exec_prefix=${prefix}~@
 258                           libdir=${exec_prefix}/lib~@
 259                           includedir=${prefix}/include~@
 260                           ~@
 261                           ~@
 262                           Name: sdsl~@
 263                           Version: ~a~@
 264                           Description: SDSL: Succinct Data Structure Library~@
 265                           Libs: -L${libdir} -lsdsl -ldivsufsort -ldivsufsort64~@
 266                           Cflags: -I${includedir}~%"
 267                           out ,version)))
 268               #t))))))
 269     (native-inputs
 270      `(("libdivsufsort" ,libdivsufsort)))
 271     (home-page "https://github.com/simongog/sdsl-lite")
 272     (synopsis "Succinct data structure library")
 273     (description "The Succinct Data Structure Library (SDSL) is a powerful and
 274 flexible C++11 library implementing succinct data structures.  In total, the
 275 library contains the highlights of 40 research publications.  Succinct data
 276 structures can represent an object (such as a bitvector or a tree) in space
 277 close to the information-theoretic lower bound of the object while supporting
 278 operations of the original object efficiently.  The theoretical time
 279 complexity of an operation performed on the classical data structure and the
 280 equivalent succinct data structure are (most of the time) identical.")
 281     (license license:gpl3+)))
 282
 283 (define-public libdivsufsort
 284   (package
 285     (name "libdivsufsort")
 286     (version "2.0.1")
 287     (source (origin
 288               (method git-fetch)
 289               (uri (git-reference
 290                     (url "https://github.com/y-256/libdivsufsort")
 291                     (commit version)))
 292               (file-name (git-file-name name version))
 293               (sha256
 294                (base32
 295                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
 296     (build-system cmake-build-system)
 297     (arguments
 298      '(#:tests? #f                      ; there are no tests
 299        #:configure-flags
 300        ;; Needed for rapmap and sailfish.
 301        '("-DBUILD_DIVSUFSORT64=ON")))
 302     (home-page "https://github.com/y-256/libdivsufsort")
 303     (synopsis "Lightweight suffix-sorting library")
 304     (description "libdivsufsort is a software library that implements a
 305 lightweight suffix array construction algorithm.  This library provides a
 306 simple and an efficient C API to construct a suffix array and a
 307 Burrows-Wheeler transformed string from a given string over a constant-size
 308 alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
 309 bytes of memory space, where n is the length of the string.")
 310     (license license:expat)))
 311
 312 (define-public robin-map
 313   (package
 314     (name "robin-map")
 315     (version "0.6.3")
 316     (source (origin
 317               (method git-fetch)
 318               (uri (git-reference
 319                     (url "https://github.com/Tessil/robin-map")
 320                     (commit (string-append "v" version))))
 321               (file-name (git-file-name name version))
 322               (sha256
 323                (base32
 324                 "1li70vwsksva9c4yly90hjafgqfixi1g6d52qq9p6r60vqc4pkjj"))))
 325     (build-system cmake-build-system)
 326     (native-inputs
 327      `(("boost" ,boost)))  ; needed for tests
 328     (arguments
 329      `(#:phases
 330        (modify-phases %standard-phases
 331          (replace 'check
 332            (lambda _
 333              (mkdir "tests")
 334              (with-directory-excursion "tests"
 335                (invoke "cmake" "../../source/tests")
 336                (invoke "cmake" "--build" ".")
 337                (invoke "./tsl_robin_map_tests")))))))
 338     (home-page "https://github.com/Tessil/robin-map")
 339     (synopsis "C++ implementation of a fast hash map and hash set")
 340     (description "The robin-map library is a C++ implementation of a fast hash
 341 map and hash set using open-addressing and linear robin hood hashing with
 342 backward shift deletion to resolve collisions.
 343
 344 Four classes are provided: tsl::robin_map, tsl::robin_set, tsl::robin_pg_map
 345 and tsl::robin_pg_set. The first two are faster and use a power of two growth
 346 policy, the last two use a prime growth policy instead and are able to cope
 347 better with a poor hash function.")
 348     (license license:expat)))