| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr> |
| 3 | ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr> |
| 4 | ;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> |
| 5 | ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> |
| 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 sagemath) |
| 23 | #:use-module ((guix licenses) #:prefix license:) |
| 24 | #:use-module (guix build-system gnu) |
| 25 | #:use-module (guix build-system python) |
| 26 | #:use-module (guix download) |
| 27 | #:use-module (guix git-download) |
| 28 | #:use-module (guix packages) |
| 29 | #:use-module (guix utils) |
| 30 | #:use-module (gnu packages) |
| 31 | #:use-module (gnu packages algebra) |
| 32 | #:use-module (gnu packages autotools) |
| 33 | #:use-module (gnu packages bdw-gc) |
| 34 | #:use-module (gnu packages boost) |
| 35 | #:use-module (gnu packages compression) |
| 36 | #:use-module (gnu packages image) |
| 37 | #:use-module (gnu packages lisp) |
| 38 | #:use-module (gnu packages multiprecision) |
| 39 | #:use-module (gnu packages pkg-config) |
| 40 | #:use-module (gnu packages python) |
| 41 | #:use-module (gnu packages python-xyz)) |
| 42 | |
| 43 | |
| 44 | (define-public python-cypari2 |
| 45 | (package |
| 46 | (name "python-cypari2") |
| 47 | (version "2.1.1") |
| 48 | (source |
| 49 | (origin |
| 50 | (method url-fetch) |
| 51 | (uri (pypi-uri "cypari2" version)) |
| 52 | (sha256 |
| 53 | (base32 |
| 54 | "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz")))) |
| 55 | (build-system python-build-system) |
| 56 | (native-inputs |
| 57 | `(("python-cython" ,python-cython))) |
| 58 | (propagated-inputs |
| 59 | `(("python-cysignals" ,python-cysignals))) |
| 60 | (inputs |
| 61 | `(("gmp" ,gmp) |
| 62 | ("pari-gp", pari-gp))) |
| 63 | (home-page "https://cypari2.readthedocs.io/") |
| 64 | (synopsis |
| 65 | "Python interface to the number theory library libpari") |
| 66 | (description |
| 67 | "Cypari2 provides a Python interface to the number theory library |
| 68 | PARI/GP. It has been spun off from the SageMath mathematics software system, |
| 69 | but it can be used independently.") |
| 70 | (license license:gpl2+))) |
| 71 | |
| 72 | (define-public python2-cypari2 |
| 73 | (package-with-python2 python-cypari2)) |
| 74 | |
| 75 | ;; The stable version of the following package is not young enough to be |
| 76 | ;; used with Sage, since it does not support cython; so we use a beta |
| 77 | ;; release. |
| 78 | (define-public python-gmpy2 |
| 79 | (package |
| 80 | (name "python-gmpy2") |
| 81 | (version "2.1.0b1") |
| 82 | (source (origin |
| 83 | (method git-fetch) |
| 84 | (uri (git-reference |
| 85 | (url "https://github.com/aleaxit/gmpy") |
| 86 | (commit (string-append "gmpy2-" version)))) |
| 87 | (file-name (git-file-name name version)) |
| 88 | (sha256 |
| 89 | (base32 |
| 90 | "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97")))) |
| 91 | (build-system python-build-system) |
| 92 | (native-inputs |
| 93 | `(("unzip" ,unzip))) |
| 94 | (inputs |
| 95 | `(("gmp" ,gmp) |
| 96 | ("mpfr" ,mpfr) |
| 97 | ("mpc" ,mpc))) |
| 98 | (home-page "https://github.com/aleaxit/gmpy") |
| 99 | (synopsis |
| 100 | "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x") |
| 101 | (description |
| 102 | "This package provides a Python interface to the GNU multiprecision |
| 103 | libraries GMO, MPFR and MPC.") |
| 104 | (license license:lgpl3+))) |
| 105 | |
| 106 | (define-public python2-gmpy2 |
| 107 | (package-with-python2 python-gmpy2)) |
| 108 | |
| 109 | (define-public cliquer |
| 110 | (package |
| 111 | (name "cliquer") |
| 112 | (version "1.21") |
| 113 | ;; The original source package is available from the home page and |
| 114 | ;; has not seen any release since 2010; it comes with only a Makefile |
| 115 | ;; without an "install" target. Instead, there is an autotoolized |
| 116 | ;; tarball available from the Sage project. |
| 117 | (source |
| 118 | (origin |
| 119 | (method url-fetch) |
| 120 | (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz") |
| 121 | (sha256 |
| 122 | (base32 |
| 123 | "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq")))) |
| 124 | (build-system gnu-build-system) |
| 125 | (synopsis "C routines for finding cliques in weighted graphs") |
| 126 | (description "Cliquer is a set of reentrant C routines for finding |
| 127 | cliques in a weighted or unweighted graph. It uses an exact |
| 128 | branch-and-bound algorithm. It can search for maximum or maximum-weight |
| 129 | cliques or cliques with size or weight within a given range, restrict the |
| 130 | search to maximal cliques, store cliques in memory and call a user-defined |
| 131 | function for every found clique.") |
| 132 | (license license:gpl2+) |
| 133 | (home-page "https://users.aalto.fi/~pat/cliquer.html"))) |
| 134 | |
| 135 | (define-public libbraiding |
| 136 | (package |
| 137 | (name "libbraiding") |
| 138 | (version "1.0") |
| 139 | (source |
| 140 | (origin |
| 141 | (method git-fetch) |
| 142 | (uri (git-reference |
| 143 | (url (string-append "https://github.com/miguelmarco/" |
| 144 | name)) |
| 145 | (commit version))) |
| 146 | (file-name (git-file-name name version)) |
| 147 | (sha256 |
| 148 | (base32 |
| 149 | "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg")))) |
| 150 | (build-system gnu-build-system) |
| 151 | (native-inputs |
| 152 | `(("autoconf" ,autoconf) |
| 153 | ("automake" ,automake) |
| 154 | ("libtool" ,libtool))) |
| 155 | (synopsis "Computations with braid groups") |
| 156 | (description "libbraiding performs computations with braid groups, |
| 157 | in particular it computes normal forms of group elements.") |
| 158 | (license license:gpl2+) |
| 159 | (home-page "https://github.com/miguelmarco/libbraiding"))) |
| 160 | |
| 161 | (define-public libhomfly |
| 162 | (package |
| 163 | (name "libhomfly") |
| 164 | (version "1.02r6") |
| 165 | (source |
| 166 | (origin |
| 167 | (method git-fetch) |
| 168 | (uri (git-reference |
| 169 | (url (string-append "https://github.com/miguelmarco/" |
| 170 | name)) |
| 171 | (commit version))) |
| 172 | (file-name (git-file-name name version)) |
| 173 | (sha256 |
| 174 | (base32 |
| 175 | "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk")))) |
| 176 | (build-system gnu-build-system) |
| 177 | (native-inputs |
| 178 | `(("autoconf" ,autoconf) |
| 179 | ("automake" ,automake) |
| 180 | ("libtool" ,libtool))) |
| 181 | (inputs |
| 182 | `(("libgc" ,libgc))) |
| 183 | (synopsis "Computation of homfly polynomials of links") |
| 184 | (description "libhomfly computes homfly polynomials of links, |
| 185 | represented as strings.") |
| 186 | (license license:public-domain) |
| 187 | (home-page "https://github.com/miguelmarco/libhomfly"))) |
| 188 | |
| 189 | ;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is |
| 190 | ;; released. See https://trac.sagemath.org/ticket/22191 |
| 191 | (define-public ecl-16 |
| 192 | (package |
| 193 | (inherit ecl) |
| 194 | (version "16.1.3") |
| 195 | (source |
| 196 | (origin |
| 197 | (method url-fetch) |
| 198 | (uri (string-append |
| 199 | "https://common-lisp.net/project/ecl/static/files/release/ecl" |
| 200 | "-" version ".tgz")) |
| 201 | (sha256 |
| 202 | (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn")) |
| 203 | (patches (search-patches |
| 204 | "ecl-16-libffi.patch" |
| 205 | "ecl-16-ignore-stderr-write-error.patch" |
| 206 | "ecl-16-format-directive-limit.patch")))) |
| 207 | ;; Current ECL uses LGPL 2.1+ |
| 208 | (license license:lgpl2.0+))) |
| 209 | |
| 210 | (define-public pynac |
| 211 | (package |
| 212 | (name "pynac") |
| 213 | (version "0.7.26") |
| 214 | (source |
| 215 | (origin |
| 216 | (method git-fetch) |
| 217 | (uri (git-reference |
| 218 | (url "https://github.com/pynac/pynac/") |
| 219 | (commit (string-append "pynac-" version)))) |
| 220 | (file-name (git-file-name name version)) |
| 221 | (sha256 |
| 222 | (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d")))) |
| 223 | (build-system gnu-build-system) |
| 224 | (native-inputs |
| 225 | `(("autoconf" ,autoconf) |
| 226 | ("automake" ,automake) |
| 227 | ("libtool" ,libtool) |
| 228 | ("pkg-config" ,pkg-config))) |
| 229 | (inputs |
| 230 | `(("flint" ,flint) |
| 231 | ("gmp" ,gmp) |
| 232 | ("python" ,python) |
| 233 | ("singular" ,singular))) |
| 234 | (synopsis "Sage fork of GiNaC") |
| 235 | (description "Pynac is a derivative of the C++ library GiNaC, which |
| 236 | allows manipulation of symbolic expressions. It currently provides the |
| 237 | backend for symbolic expressions in Sage. The main difference between |
| 238 | Pynac and GiNaC is that Pynac relies on Sage to provide the operations |
| 239 | on numerical types, while GiNaC depends on CLN for this purpose.") |
| 240 | (license license:gpl2+) |
| 241 | (home-page "http://pynac.org/"))) |
| 242 | |
| 243 | ;; Sage has become upstream of the following package. |
| 244 | (define-public zn-poly |
| 245 | (package |
| 246 | (name "zn-poly") |
| 247 | (version "0.9.2") |
| 248 | (source |
| 249 | (origin |
| 250 | (method git-fetch) |
| 251 | (uri (git-reference |
| 252 | (url (string-append "https://gitlab.com/sagemath/" |
| 253 | "zn_poly.git/")) |
| 254 | (commit version))) |
| 255 | (file-name (git-file-name "zn_poly" version)) |
| 256 | (sha256 |
| 257 | (base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0")))) |
| 258 | (build-system gnu-build-system) |
| 259 | (native-inputs |
| 260 | `(("python" ,python-2))) |
| 261 | (inputs |
| 262 | `(("gmp" ,gmp))) |
| 263 | (arguments |
| 264 | `(#:phases |
| 265 | (modify-phases %standard-phases |
| 266 | (replace 'configure |
| 267 | ;; The configure script chokes on --enable-fast-install. |
| 268 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 269 | (invoke "./configure" |
| 270 | (string-append "--prefix=" (assoc-ref outputs "out")) |
| 271 | "--cflags=-O3 -fPIC"))) |
| 272 | (add-before 'build 'prepare-build |
| 273 | (lambda _ |
| 274 | (setenv "CC" "gcc") |
| 275 | #t)) |
| 276 | (add-after 'build 'build-so |
| 277 | (lambda _ |
| 278 | (invoke "make" "libzn_poly.so"))) |
| 279 | (add-after 'install 'install-so |
| 280 | (lambda* (#:key outputs #:allow-other-keys) |
| 281 | (let* ((out (assoc-ref outputs "out")) |
| 282 | (lib (string-append out "/lib")) |
| 283 | (soname (string-append "libzn_poly-" ,version ".so")) |
| 284 | (target (string-append lib "/" soname))) |
| 285 | (install-file "libzn_poly.a" lib) |
| 286 | (install-file soname lib) |
| 287 | (symlink target |
| 288 | (string-append lib "/libzn_poly.so")) |
| 289 | (symlink target |
| 290 | (string-append lib "/libzn_poly-" |
| 291 | ,(version-major+minor version) |
| 292 | ".so"))) |
| 293 | #t))))) |
| 294 | (synopsis "Arithmetic for polynomials over Z/NZ") |
| 295 | (description "zn_poly implements the arithmetic of polynomials the |
| 296 | coefficients of which are modular integers.") |
| 297 | (license (list license:gpl2 license:gpl3)) ; dual licensed |
| 298 | (home-page "https://gitlab.com/sagemath/zn_poly"))) |
| 299 | |
| 300 | (define-public brial |
| 301 | (package |
| 302 | (name "brial") |
| 303 | (version "1.2.8") |
| 304 | (source |
| 305 | (origin |
| 306 | (method git-fetch) |
| 307 | (uri (git-reference |
| 308 | (url "https://github.com/BRiAl/BRiAl/") |
| 309 | (commit version))) |
| 310 | (file-name (git-file-name name version)) |
| 311 | (sha256 |
| 312 | (base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y")))) |
| 313 | (build-system gnu-build-system) |
| 314 | (native-inputs |
| 315 | `(("autoconf" ,autoconf) |
| 316 | ("automake" ,automake) |
| 317 | ("libtool" ,libtool) |
| 318 | ("pkg-config" ,pkg-config))) |
| 319 | (inputs |
| 320 | `(("boost" ,boost) |
| 321 | ("libpng" ,libpng) |
| 322 | ("m4ri" ,m4ri))) |
| 323 | (arguments |
| 324 | ;; We are missing the boost unit test framework. |
| 325 | `(#:tests? #f |
| 326 | #:configure-flags (list "--without-boost-unit-test-framework"))) |
| 327 | (synopsis "Arithmetic of polynomials over boolean rings") |
| 328 | (description "BRiAl is the successor to PolyBoRi maintained by the |
| 329 | Sage community. Its core is a C++ library, which provides high-level data |
| 330 | types for Boolean polynomials and monomials, exponent vectors, as well as |
| 331 | for the underlying polynomial rings and subsets of the powerset of the |
| 332 | Boolean variables. As a unique approach, binary decision diagrams are |
| 333 | used as internal storage type for polynomial structures.") |
| 334 | (license license:gpl2+) |
| 335 | (home-page "https://github.com/BRiAl/BRiAl/"))) |
| 336 | |
| 337 | (define-public lcalc |
| 338 | (package |
| 339 | (name "lcalc") |
| 340 | (version "1.23") |
| 341 | ;; The original home page of the project has disappeared, as well as |
| 342 | ;; code hosted by the original author on Google Code. The latter has |
| 343 | ;; been copied to gitlab.com/sagemath and purportedly contains patches |
| 344 | ;; for a never released version 1.3, that supposedly follows 1.23. |
| 345 | ;; We use the tarball as well as the patches hosted inside the sage |
| 346 | ;; package system distributed with the sage tarball. |
| 347 | (source |
| 348 | (origin |
| 349 | (method url-fetch) |
| 350 | (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/" |
| 351 | "upstream/lcalc/lcalc-1.23.tar.bz2")) |
| 352 | (sha256 |
| 353 | (base32 |
| 354 | "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43")) |
| 355 | (patches (search-patches "lcalc-lcommon-h.patch" |
| 356 | "lcalc-default-parameters-1.patch" |
| 357 | "lcalc-default-parameters-2.patch" |
| 358 | "lcalc-using-namespace-std.patch")))) |
| 359 | (build-system gnu-build-system) |
| 360 | (arguments |
| 361 | `(#:tests? #f ;no tests |
| 362 | #:phases |
| 363 | (modify-phases %standard-phases |
| 364 | (delete 'configure) |
| 365 | (add-before 'build 'prepare-build |
| 366 | (lambda* (#:key outputs #:allow-other-keys) |
| 367 | (chdir "src") |
| 368 | (let ((out (assoc-ref outputs "out"))) |
| 369 | (substitute* "Makefile" |
| 370 | (("^INSTALL_DIR= /usr/local") |
| 371 | (string-append "INSTALL_DIR=" out)))) |
| 372 | #t)) |
| 373 | (add-before 'install 'make-output-dirs |
| 374 | (lambda* (#:key outputs #:allow-other-keys) |
| 375 | (let* ((out (assoc-ref outputs "out")) |
| 376 | (bin (string-append out "/bin")) |
| 377 | (lib (string-append out "/lib")) |
| 378 | (include (string-append out "/include"))) |
| 379 | (mkdir-p bin) |
| 380 | (mkdir-p lib) |
| 381 | (mkdir-p include)) |
| 382 | #t))))) |
| 383 | ;; FIXME: |
| 384 | ;; We need to add pari-gp and probably pari related patches from the |
| 385 | ;; sage project, as well as uncomment the line setting PARI_DEFINE in |
| 386 | ;; the Makefile to get the full functionality of this package. |
| 387 | ;; For the time being, we hope that sage can be compiled without. |
| 388 | (synopsis "C++ library for L-functions") |
| 389 | (description "Lcalc computes L-functions, in particular the Riemann |
| 390 | zeta function and its twists by quadratic characters.") |
| 391 | (license license:gpl2+) |
| 392 | (home-page "https://gitlab.com/sagemath/sage"))) |
| 393 | |
| 394 | (define-public ratpoints |
| 395 | (package |
| 396 | (name "ratpoints") |
| 397 | (version "2.1.3") |
| 398 | (source (origin |
| 399 | (method url-fetch) |
| 400 | (uri (string-append |
| 401 | "http://www.mathe2.uni-bayreuth.de/stoll/programs/" |
| 402 | "ratpoints-" version ".tar.gz")) |
| 403 | (sha256 |
| 404 | (base32 |
| 405 | "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4")) |
| 406 | (patches |
| 407 | ;; Taken from |
| 408 | ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/> |
| 409 | (search-patches "ratpoints-sturm_and_rp_private.patch")))) |
| 410 | (build-system gnu-build-system) |
| 411 | (arguments |
| 412 | `(#:test-target "test" |
| 413 | #:make-flags |
| 414 | (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out")) |
| 415 | "CCFLAGS=-fPIC") |
| 416 | #:phases |
| 417 | (modify-phases %standard-phases |
| 418 | (delete 'configure) ;no configure script |
| 419 | (add-before 'install 'create-install-directories |
| 420 | (lambda* (#:key outputs #:allow-other-keys) |
| 421 | (let ((out (assoc-ref outputs "out"))) |
| 422 | (mkdir-p out) |
| 423 | (with-directory-excursion out |
| 424 | (for-each (lambda (d) (mkdir-p d)) |
| 425 | '("bin" "include" "lib")))) |
| 426 | #t))))) |
| 427 | (inputs |
| 428 | `(("gmp" ,gmp))) |
| 429 | (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/") |
| 430 | (synopsis "Find rational points on hyperelliptic curves") |
| 431 | (description "Ratpoints tries to find all rational points within |
| 432 | a given height bound on a hyperelliptic curve in a very efficient way, |
| 433 | by using an optimized quadratic sieve algorithm.") |
| 434 | (license license:gpl2+))) |