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, 2019–2021 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 ;;; Copyright © 2020 Marius Bakke <marius@gnu.org>
   8 ;;;
   9 ;;; This file is part of GNU Guix.
  10 ;;;
  11 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  12 ;;; under the terms of the GNU General Public License as published by
  13 ;;; the Free Software Foundation; either version 3 of the License, or (at
  14 ;;; your option) any later version.
  15 ;;;
  16 ;;; GNU Guix is distributed in the hope that it will be useful, but
  17 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  18 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  19 ;;; GNU General Public License for more details.
  20 ;;;
  21 ;;; You should have received a copy of the GNU General Public License
  22 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  23
  24 (define-module (gnu packages datastructures)
  25   #:use-module (gnu packages)
  26   #:use-module (gnu packages autotools)
  27   #:use-module (gnu packages boost)
  28   #:use-module (gnu packages build-tools)   ;for meson-0.55
  29   #:use-module (gnu packages perl)
  30   #:use-module ((guix licenses) #:prefix license:)
  31   #:use-module (guix packages)
  32   #:use-module (guix download)
  33   #:use-module (guix git-download)
  34   #:use-module (guix build-system cmake)
  35   #:use-module (guix build-system gnu)
  36   #:use-module (guix build-system meson))
  37
  38 (define-public gdsl
  39   (package
  40     (name "gdsl")
  41     (version "1.8")
  42     (source (origin
  43               (method git-fetch)
  44               (uri (git-reference
  45                     (url "https://example.org") ;only hosted on Software Heritage
  46                     (commit "6adb53be8b8f9f2e4bbfc92d357eedeefb4c7430")))
  47               (file-name (git-file-name name version))
  48               (sha256
  49                (base32
  50                 "0a52g12d9sf9hhcyvwfd7xdazj2a9i9jh97cnlqf2ymvwnvjk1g0"))))
  51     (build-system gnu-build-system)
  52     (home-page "https://web.archive.org/web/20170502005430/http://home.gna.org/gdsl/")
  53     (synopsis "Generic data structures library")
  54     (description "The Generic Data Structures Library (GDSL) is a collection
  55 of routines for generic data structures manipulation.  It is a re-entrant
  56 library fully written from scratch in pure ANSI C.  It is designed to offer
  57 for C programmers common data structures with powerful algorithms, and hidden
  58 implementation.  Available structures are lists, queues, stacks, hash tables,
  59 binary trees, binary search trees, red-black trees, 2D arrays, permutations
  60 and heaps.")
  61     (license license:gpl2+)))
  62
  63 (define-public marisa
  64   (package
  65     (name "marisa")
  66     (version "0.2.6")
  67     (source
  68      (origin
  69        (method url-fetch)
  70        (uri (string-append "https://github.com/s-yata/marisa-trie/files/"
  71                            "4832504/marisa-" version ".tar.gz"))
  72        (sha256
  73         (base32 "1pk6wmi28pa8srb4szybrwfn71jldb61c5vgxsiayxcyg1ya4qqh"))))
  74     (build-system gnu-build-system)
  75     (native-inputs
  76      `(("autoconf" ,autoconf)
  77        ("automake" ,automake)
  78        ("libtool" ,libtool)))
  79     (home-page "https://github.com/s-yata/marisa-trie")
  80     (synopsis "Trie data structure C++ library")
  81     (description "@acronym{MARISA, Matching Algorithm with Recursively
  82 Implemented StorAge} is a static and space-efficient trie data structure C++
  83 library.")
  84
  85     ;; Dual-licensed, according to docs/readme.en.html (source files lack
  86     ;; copyright/license headers.)
  87     (license (list license:bsd-2 license:lgpl2.1+))))
  88
  89 (define-public sparsehash
  90   (package
  91     (name "sparsehash")
  92     (version "2.0.4")
  93     (source (origin
  94               (method git-fetch)
  95               (uri (git-reference
  96                      (url "https://github.com/sparsehash/sparsehash")
  97                      (commit (string-append name "-" version))))
  98               (file-name (git-file-name name version))
  99               (sha256
 100                (base32
 101                 "1pf1cjvcjdmb9cd6gcazz64x0cd2ndpwh6ql2hqpypjv725xwxy7"))))
 102     (build-system gnu-build-system)
 103     (synopsis "Memory-efficient hashtable implementations")
 104     (description
 105      "This library contains several hash-map implementations, similar in API
 106 to SGI's @code{hash_map} class, but with different performance
 107 characteristics.  @code{sparse_hash_map} uses very little space overhead, 1-2
 108 bits per entry.  @code{dense_hash_map} is very fast, particularly on lookup.
 109 @code{sparse_hash_set} and @code{dense_hash_set} are the set versions of these
 110 routines.  All these implementation use a hashtable with internal quadratic
 111 probing.  This method is space-efficient -- there is no pointer overhead --
 112 and time-efficient for good hash functions.")
 113     (home-page "https://github.com/sparsehash/sparsehash")
 114     (license license:bsd-3)))
 115
 116 (define-public ssdeep
 117   (package
 118     (name "ssdeep")
 119     (version "2.14.1")
 120     (source
 121      (origin
 122        (method url-fetch)
 123        (uri (string-append "https://github.com/ssdeep-project/ssdeep/"
 124                            "releases/download/release-" version "/"
 125                            "ssdeep-" version ".tar.gz"))
 126        (sha256
 127         (base32 "04qkjc6kksxkv7xbnk32rwmf3a8czdv2vvrdzfs0kw06h73snbpz"))))
 128     (build-system gnu-build-system)
 129     (arguments
 130      `(#:configure-flags
 131        (list "--disable-static")))
 132     (home-page "https://ssdeep-project.github.io")
 133     (synopsis "Context-triggered piecewise hashing algorithm")
 134     (description "ssdeep computes and matches context triggered piecewise
 135 hashes (CTPH), also called fuzzy checksums.  It can identify similar files
 136 that have sequences of identical bytes in the same order, even though bytes
 137 in between these sequences may be different in both content and length.")
 138     (license license:gpl2+)))
 139
 140 (define-public liburcu
 141   (package
 142     (name "liburcu")
 143     (version "0.12.2")
 144     (source (origin
 145               (method url-fetch)
 146               (uri (string-append "https://www.lttng.org/files/urcu/"
 147                                   "userspace-rcu-" version ".tar.bz2"))
 148               (sha256
 149                (base32
 150                 "0yx69kbx9zd6ayjzvwvglilhdnirq4f1x1sdv33jy8bc9wgc3vsf"))))
 151     (build-system gnu-build-system)
 152     (native-inputs
 153      `(("perl" ,perl)))                 ; for tests
 154     (home-page "https://liburcu.org/")
 155     (synopsis "User-space RCU data synchronisation library")
 156     (description "liburcu is a user-space @dfn{Read-Copy-Update} (RCU) data
 157 synchronisation library.  It provides read-side access that scales linearly
 158 with the number of cores.  liburcu-cds provides efficient data structures
 159 based on RCU and lock-free algorithms.  These structures include hash tables,
 160 queues, stacks, and doubly-linked lists.")
 161     (license license:lgpl2.1+)))
 162
 163 (define-public uthash
 164   (package
 165     (name "uthash")
 166     (version "2.1.0")
 167     (source
 168      (origin
 169        (method git-fetch)
 170        (uri (git-reference
 171              (url "https://github.com/troydhanson/uthash")
 172              (commit (string-append "v" version))))
 173        (file-name (git-file-name name version))
 174        (sha256
 175         (base32 "0k80bjbb6ss5wpmfmfji6xbyjm990hg9kcshwwnhdnh73vxkcd1m"))))
 176     (build-system gnu-build-system)
 177     (native-inputs
 178      `(("perl" ,perl)))
 179     (arguments
 180      `(#:make-flags
 181        (list "CC=gcc")
 182        #:phases
 183        (modify-phases %standard-phases
 184          (delete 'configure)            ; nothing to configure
 185          (delete 'build)                ; nothing to build
 186          (replace 'check
 187            (lambda* (#:key make-flags #:allow-other-keys)
 188              (with-directory-excursion "tests"
 189                (apply invoke "make" make-flags))))
 190          (replace 'install
 191            ;; There is no top-level Makefile to do this for us.
 192            (lambda* (#:key outputs #:allow-other-keys)
 193              (let* ((out (assoc-ref outputs "out"))
 194                     (doc (string-append out "/share/doc/" ,name "-" ,version))
 195                     (include (string-append out "/include")))
 196                ;; Don't install HTML files: they're just the below .txt files
 197                ;; dolled up, can be stale, and regeneration requires asciidoc.
 198                (for-each (λ (file) (install-file file doc))
 199                          (find-files "doc" "\\.txt$"))
 200                (for-each (λ (file) (install-file file include))
 201                          (find-files "src" "\\.h$"))
 202                #t))))))
 203     (home-page "https://troydhanson.github.io/uthash/")
 204     (synopsis
 205      "Hash tables, lists, and other data structures implemented as C macros")
 206     (description
 207      "uthash implements a hash table and a few other basic data structures
 208 as C preprocessor macros.  It aims to be minimalistic and efficient: it's
 209 around 1,000 lines of code which, being macros, inline automatically.
 210
 211 Unlike function calls with fixed prototypes, macros operate on untyped
 212 arguments.  Thus, they are able to work with any type of structure and key.
 213 Any C structure can be stored in a hash table by adding @code{UT_hash_handle}
 214 to the structure and choosing one or more fields to act as the key.")
 215     (license license:bsd-2)))
 216
 217 (define-public sdsl-lite
 218   (package
 219     (name "sdsl-lite")
 220     (version "2.1.1")
 221     (source (origin
 222               (method url-fetch)
 223               (uri (string-append "https://github.com/simongog/sdsl-lite/"
 224                                   "releases/download/v" version "/"
 225                                   "sdsl-lite-" version
 226                                   ".tar.gz.offline.install.gz"))
 227               (sha256
 228                (base32
 229                 "1v86ivv3mmdy802i9xkjpxb4cggj3s27wb19ja4sw1klnivjj69g"))
 230               (modules '((guix build utils)))
 231               (snippet
 232                '(begin
 233                   (delete-file-recursively "external") #t))
 234               (patches
 235                 (list (origin
 236                         (method url-fetch)
 237                         (uri "https://salsa.debian.org/science-team/libsdsl/raw/debian/2.1.1+dfsg-2/debian/patches/0001-Patch-cmake-files.patch")
 238                         (file-name "sdsl-lite-dont-use-bundled-libraries.patch")
 239                         (sha256
 240                          (base32
 241                           "0m542xpys54bni29zibgrfpgpd0zgyny4h131virxsanixsbz52z")))))))
 242     (build-system cmake-build-system)
 243     (arguments
 244      `(#:phases
 245        (modify-phases %standard-phases
 246          (add-after 'install 'install-static-library
 247            (lambda* (#:key outputs #:allow-other-keys)
 248              (let ((out (assoc-ref outputs "out")))
 249                (copy-file "lib/libsdsl_static.a"
 250                           (string-append out "/lib/libsdsl.a")))
 251              #t))
 252         (add-after 'install 'install-pkgconfig-file
 253           (lambda* (#:key outputs #:allow-other-keys)
 254             (let* ((out (assoc-ref outputs "out"))
 255                    (lib (string-append out "/lib")))
 256               (mkdir-p (string-append lib "/pkgconfig"))
 257               (with-output-to-file (string-append lib "/pkgconfig/sdsl-lite.pc")
 258                 (lambda _
 259                   (format #t "prefix=~a~@
 260                           exec_prefix=${prefix}~@
 261                           libdir=${exec_prefix}/lib~@
 262                           includedir=${prefix}/include~@
 263                           ~@
 264                           ~@
 265                           Name: sdsl~@
 266                           Version: ~a~@
 267                           Description: SDSL: Succinct Data Structure Library~@
 268                           Libs: -L${libdir} -lsdsl -ldivsufsort -ldivsufsort64~@
 269                           Cflags: -I${includedir}~%"
 270                           out ,version)))
 271               #t))))))
 272     (native-inputs
 273      `(("libdivsufsort" ,libdivsufsort)))
 274     (home-page "https://github.com/simongog/sdsl-lite")
 275     (synopsis "Succinct data structure library")
 276     (description "The Succinct Data Structure Library (SDSL) is a powerful and
 277 flexible C++11 library implementing succinct data structures.  In total, the
 278 library contains the highlights of 40 research publications.  Succinct data
 279 structures can represent an object (such as a bitvector or a tree) in space
 280 close to the information-theoretic lower bound of the object while supporting
 281 operations of the original object efficiently.  The theoretical time
 282 complexity of an operation performed on the classical data structure and the
 283 equivalent succinct data structure are (most of the time) identical.")
 284     (license license:gpl3+)))
 285
 286 (define-public tllist
 287   (package
 288     (name "tllist")
 289     (version "1.0.5")
 290     (home-page "https://codeberg.org/dnkl/tllist")
 291     (source (origin
 292               (method git-fetch)
 293               (uri (git-reference (url home-page) (commit version)))
 294               (file-name (git-file-name name version))
 295               (sha256
 296                (base32
 297                 "061mkg6hc9x89zya3bw18ymxlzd8fbhjipxpva8x01lh2vp1d4f0"))))
 298     (build-system meson-build-system)
 299     (arguments
 300      `(#:meson ,meson-0.55))
 301     (synopsis "Typed link list for C")
 302     (description
 303      "@code{tllist} is a @dfn{typed linked list} C header file only library
 304 implemented using pre-processor macros.  It supports primitive data types as
 305 well as aggregated ones such as structs, enums and unions.")
 306     (license license:expat)))
 307
 308 (define-public libdivsufsort
 309   (package
 310     (name "libdivsufsort")
 311     (version "2.0.1")
 312     (source (origin
 313               (method git-fetch)
 314               (uri (git-reference
 315                     (url "https://github.com/y-256/libdivsufsort")
 316                     (commit version)))
 317               (file-name (git-file-name name version))
 318               (sha256
 319                (base32
 320                 "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
 321     (build-system cmake-build-system)
 322     (arguments
 323      '(#:tests? #f                      ; there are no tests
 324        #:configure-flags
 325        ;; Needed for rapmap and sailfish.
 326        '("-DBUILD_DIVSUFSORT64=ON")))
 327     (home-page "https://github.com/y-256/libdivsufsort")
 328     (synopsis "Lightweight suffix-sorting library")
 329     (description "libdivsufsort is a software library that implements a
 330 lightweight suffix array construction algorithm.  This library provides a
 331 simple and an efficient C API to construct a suffix array and a
 332 Burrows-Wheeler transformed string from a given string over a constant-size
 333 alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
 334 bytes of memory space, where n is the length of the string.")
 335     (license license:expat)))
 336
 337 (define-public robin-map
 338   (package
 339     (name "robin-map")
 340     (version "0.6.3")
 341     (source (origin
 342               (method git-fetch)
 343               (uri (git-reference
 344                     (url "https://github.com/Tessil/robin-map")
 345                     (commit (string-append "v" version))))
 346               (file-name (git-file-name name version))
 347               (sha256
 348                (base32
 349                 "1li70vwsksva9c4yly90hjafgqfixi1g6d52qq9p6r60vqc4pkjj"))))
 350     (build-system cmake-build-system)
 351     (native-inputs
 352      `(("boost" ,boost)))  ; needed for tests
 353     (arguments
 354      `(#:phases
 355        (modify-phases %standard-phases
 356          (replace 'check
 357            (lambda _
 358              (mkdir "tests")
 359              (with-directory-excursion "tests"
 360                (invoke "cmake" "../../source/tests")
 361                (invoke "cmake" "--build" ".")
 362                (invoke "./tsl_robin_map_tests")))))))
 363     (home-page "https://github.com/Tessil/robin-map")
 364     (synopsis "C++ implementation of a fast hash map and hash set")
 365     (description "The robin-map library is a C++ implementation of a fast hash
 366 map and hash set using open-addressing and linear robin hood hashing with
 367 backward shift deletion to resolve collisions.
 368
 369 Four classes are provided: tsl::robin_map, tsl::robin_set, tsl::robin_pg_map
 370 and tsl::robin_pg_set. The first two are faster and use a power of two growth
 371 policy, the last two use a prime growth policy instead and are able to cope
 372 better with a poor hash function.")
 373     (license license:expat)))