diff options
Diffstat (limited to 'gnu/packages/algebra.scm')
| -rw-r--r-- | gnu/packages/algebra.scm | 586 |
1 files changed, 550 insertions, 36 deletions
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 69163a43d9..561347ad98 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -43,6 +43,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) @@ -92,6 +93,27 @@ multiplication routines such as Toom–Cook and the FFT.") (license license:lgpl3+) (home-page "http://mpfrcx.multiprecision.org/"))) +(define-public gf2x + (package + (name "gf2x") + (version "1.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-" + version ".tar.gz")) + (sha256 + (base32 + "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1")))) + (build-system gnu-build-system) + (synopsis "Arithmetic of polynomials over binary finite fields") + (description + "The gf2x library provides arithmetic of polynomials over finite fields +of characteristic 2. It implements the multiplication, squaring and +greatest common divisor operations.") + (license license:gpl3+) + (home-page "https://gforge.inria.fr/projects/gf2x/"))) + (define-public cm (package (name "cm") @@ -122,24 +144,82 @@ line applications.") (define-public fplll (package - (name "fplll") - (version "4.0.4") - (source (origin - (method url-fetch) - (uri (string-append - "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-" - version ".tar.gz")) - (sha256 (base32 - "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b")))) - (build-system gnu-build-system) - (inputs `(("gmp" ,gmp) - ("mpfr" ,mpfr))) - (synopsis "Library for LLL-reduction of euclidean lattices") - (description - "fplll LLL-reduces euclidean lattices. Since version 3, it can also -solve the shortest vector problem.") - (license license:lgpl2.1+) - (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/"))) + (name "fplll") + (version "5.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/fplll/fplll.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("gmp" ,gmp) + ("mpfr" ,mpfr))) + (home-page "https://github.com/fplll/fplll") + (synopsis "Library for LLL-reduction of euclidean lattices") + (description + "fplll contains implementations of several lattice algorithms. +The implementation relies on floating-point orthogonalization, and LLL +is central to the code, hence the name. + +It includes implementations of floating-point LLL reduction +algorithms, offering different speed/guarantees ratios. It contains +a @emph{wrapper} choosing the estimated best sequence of variants in +order to provide a guaranteed output as fast as possible. In the case +of the wrapper, the succession of variants is oblivious to the user. + +It includes an implementation of the BKZ reduction algorithm, +including the BKZ-2.0 improvements (extreme enumeration +pruning, pre-processing of blocks, early termination). Additionally, +Slide reduction and self dual BKZ are supported. + +It also includes a floating-point implementation of the +Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice +vector. For the same task, the GaussSieve algorithm is also available +in fplll. Finally, it contains a variant of the enumeration algorithm +that computes a lattice vector closest to a given vector belonging to +the real span of the lattice.") + (license license:lgpl2.1+))) + +(define-public python-fpylll + (package + (name "python-fpylll") + (version "0.4.1") + (source + (origin + ;; Pypi contains and older release, so we use a tagged release from + ;; Github instead. + (method git-fetch) + (uri (git-reference + (url "https://github.com/fplll/fpylll.git") + (commit (string-append version "dev")))) + (sha256 + (base32 + "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w")))) + (build-system python-build-system) + (inputs + `(("fplll" ,fplll) + ("gmp" ,gmp) + ("mpfr" ,mpfr) + ("pari-gp" ,pari-gp))) + (propagated-inputs + `(("cysignals" ,python-cysignals) + ("cython" ,python-cython) + ("flake8" ,python-flake8) + ("numpy" ,python-numpy) + ("pytest" ,python-pytest))) + (home-page "https://github.com/fplll/fpylll") + (synopsis "Python interface for fplll") + (description "fpylll is a Python wrapper for fplll.") + (license license:gpl2+))) (define-public pari-gp (package @@ -928,7 +1008,7 @@ xtensor provides: (define-public gap (package (name "gap") - (version "4.10.0") + (version "4.10.1") (source (origin (method url-fetch) @@ -939,7 +1019,7 @@ xtensor provides: ".tar.bz2")) (sha256 (base32 - "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird")) + "136s0zvhcw41fshj5zgsrjcy2kd58cdh2m3ddp5rdizi4rx54f10")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1))) (snippet '(begin @@ -967,20 +1047,20 @@ xtensor provides: ;; Optional packages, searched for at start, ;; and their depedencies. "alnuth-3.1.0" - "AutoDoc-2018.09.20" "autpgrp-1.10" "crisp-1.4.4" ; bsd-2 - ; "ctbllib" ; no explicit license, drop + "ctbllib" ; gpl3+ according to doc/chap0.txt "FactInt-1.6.2" "fga" "irredsol-1.4" ; bsd-2 - "laguna-3.9.0" + "laguna-3.9.2" "polenta-1.3.8" "polycyclic-2.14" "radiroot-2.8" "resclasses-4.7.1" "sophus-1.24" - ; "tomlib-1.2.7" ; no explicit license, drop + "tomlib-1.2.7" ; gpl2+, clarified in the git repository + ; and the next release "utils-0.59")))) #t)))) (build-system gnu-build-system) @@ -988,7 +1068,11 @@ xtensor provides: `(("gmp" ,gmp) ("zlib" ,zlib))) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-26) + (guix build gnu-build-system) + (guix build utils)) + #:phases (modify-phases %standard-phases (add-after 'build 'build-packages ;; Compile all packages that have not been deleted by the @@ -1004,19 +1088,16 @@ xtensor provides: (with-directory-excursion "doc" (invoke "./make_doc")) #t)) - (replace 'check - (lambda _ - ;; "make check" is expected to appear in gap-4.10.1 - (invoke "./gap" "tst/testinstall.g") - #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin")) + (lib (string-append out "/lib")) (prog (string-append bin "/gap")) (prog-real (string-append bin "/.gap-real")) (share (string-append out "/share/gap")) - (include (string-append out "/include/gap"))) + (include (string-append out "/include/gap")) + (include-hpc (string-append include "/hpc"))) ;; Install only the gap binary; the gac compiler is left ;; for maybe later. "Wrap" it in a shell script that calls ;; the binary with the correct parameter. @@ -1030,12 +1111,37 @@ xtensor provides: prog-real share))) (chmod prog #o755) - ;; Install the headers and the library, which are needed by - ;; Sage. The Makefile targets are available in gap-4.10.0, - ;; but planned to be removed in gap-4.10.1. - (invoke "make" "install-headers") - (invoke "make" "install-libgap") + ;; Install the headers, which are needed by Sage. The + ;; Makefile target "install-headers" was available in + ;; gap-4.10.0, but has been commented out in gap-4.10.1. + (mkdir-p include-hpc) (install-file "gen/config.h" include) + (let ((file-name-predicate-without-stat + (lambda (regex) + (cut (file-name-predicate regex) <> #f)))) + (with-directory-excursion "src" + (for-each + (cut install-file <> include) + (scandir "." + (file-name-predicate-without-stat ".*\\.h$")))) + (with-directory-excursion "src/hpc" + (for-each + (cut install-file <> include-hpc) + (scandir "." + (file-name-predicate-without-stat ".*\\.h$"))))) + ;; Install the library, which is needed by Sage. The + ;; Makefile target "install-libgap" was available in + ;; gap-4.10.0, but has been commented out in gap-4.10.1. + ;; Compared to the Makefile, which used libtool, the + ;; following approach of copying files and making symlinks + ;; is rather pedestrian. There is hope that some later + ;; version of gap reinstates and completes the install + ;; targets. + (invoke "make" "libgap.la") + (install-file "libgap.la" lib) + (install-file ".libs/libgap.so.0.0.0" lib) + (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so")) + (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0")) ;; Install a certain number of files and directories to ;; SHARE, where the wrapped shell script expects them. ;; Remove information on the build directory from sysinfo.gap. @@ -1068,3 +1174,411 @@ objects.") ;; means that the gpl2+ licence of GAP itself applies, but to be on the ;; safe side, we drop them for now. (license license:gpl2+))) + +(define-public givaro + (package + (name "givaro") + (version "4.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/givaro") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (propagated-inputs + `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "Algebraic computations with exact rings and fields") + (description + "Givaro is a C++ library implementing the basic arithmetic of various +algebraic objects: prime fields, extension fields, finite fields, finite +rings, polynomials, algebraic numbers, arbitrary precision integers and +rationals (C++ wrappers over gmp), fixed precision integers. It also +provides data-structures and templated classes for the manipulation of +compound objects, such as vectors, matrices and univariate polynomials.") + (license license:cecill-b) + (home-page "https://github.com/linbox-team/givaro"))) + +(define-public fflas-ffpack + (package + (name "fflas-ffpack") + (version "2.4.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/fflas-ffpack") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("openblas" ,openblas))) + (propagated-inputs + `(("givaro" ,givaro))) ; required according to the .pc file + (arguments + `(#:configure-flags + (list (string-append "--with-blas-libs=" + (assoc-ref %build-inputs "openblas") + "/lib/libopenblas.so")) + #:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "C++ library for linear algebra over finite fields") + (description + "FFLAS-FFPACK is a C++ template library for basic linear algebra +operations over a finite field. +FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation +of a subset of routines of the numerical BLAS; it also supports sparse +matrix-vector products. +FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK +library to provide functionalities of higher level, using the kernel +of a BLAS. Additionally, it provides routines specific to exact linear +algebra, such as the row echelon form.") + (license license:lgpl2.1+) + (home-page "https://linbox-team.github.io/fflas-ffpack/"))) + +(define-public linbox + (package + (name "linbox") + (version "1.6.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linbox-team/linbox") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("fflas-ffpack" ,fflas-ffpack))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "yes") + #t))))) + (synopsis "C++ library for linear algebra over exact rings") + (description + "LinBox is a C++ template library for exact linear algebra computation +with dense, sparse, and structured matrices over the integers and over +finite fields.") + (license license:lgpl2.1+) + (home-page "https://linbox-team.github.io/linbox/"))) + +(define-public m4ri + (package + (name "m4ri") + (version "20140914") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/malb/m4ri") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("libpng" ,libpng))) + (synopsis "Arithmetic of dense matrices over F_2") + (description "M4RI is a library for fast arithmetic with dense matrices +over F2. The name M4RI comes from the first implemented algorithm: The +Method of the Four Russians inversion algorithm published by Gregory Bard. +This algorithm in turn is named after the Method of the Four Russians +multiplication algorithm.") + (license license:gpl2+) + (home-page "https://bitbucket.org/malb/m4ri/"))) + +(define-public ratpoints + (package + (name "ratpoints") + (version "2.1.3") + (source (origin + (method url-fetch) + (uri (string-append + "http://www.mathe2.uni-bayreuth.de/stoll/programs/" + "ratpoints-" version ".tar.gz")) + (sha256 + (base32 + "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4")) + (patches + ;; Taken from + ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/> + (search-patches "ratpoints-sturm_and_rp_private.patch")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags + (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure) ;no configure script + (add-before 'install 'create-install-directories + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p out) + (with-directory-excursion out + (for-each (lambda (d) (mkdir-p d)) + '("bin" "include" "lib")))) + #t))))) + (inputs + `(("gmp" ,gmp))) + (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/") + (synopsis "Find rational points on hyperelliptic curves") + (description "Ratpoints tries to find all rational points within +a given height bound on a hyperelliptic curve in a very efficient way, +by using an optimized quadratic sieve algorithm.") + (license license:gpl2+))) + +(define-public symmetrica + (package + (name "symmetrica") + (version "2.0") + (source (origin + (method url-fetch/tarbomb) + (uri (let ((v (string-join (string-split version #\.) "_"))) + (string-append "http://www.algorithm.uni-bayreuth.de/" + "en/research/SYMMETRICA/" + "SYM" v "_tar.gz"))) + (sha256 + (base32 + "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz")) + ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/> + (patches (search-patches "symmetrica-bruch.patch" + "symmetrica-int32.patch" + "symmetrica-return_values.patch" + "symmetrica-sort_sum_rename.patch")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;no test + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-makefile + (lambda _ + (substitute* "makefile" + (("cc -c") "gcc -c")) + #t)) + (add-after 'fix-makefile 'turn-off-banner + (lambda _ + (substitute* "de.c" + (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE"))) + #t)) + (delete 'configure) ;no configure script + (replace 'install ;no install target + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (inc (string-append out "/include/symmetrica")) + (doc (string-append out "/share/doc/symmetrica-" ,version)) + (static "libsymmetrica.a")) + ;; Build static library. + (apply invoke "ar" "crs" static (find-files "." "\\.o$")) + (invoke "ranlib" static) + ;; Install static library and headers. + (for-each (lambda (f) (install-file f inc)) + (find-files "." "\\.h$")) + (install-file "libsymmetrica.a" lib) + ;; Install documentation. + (for-each (lambda (f) (install-file f doc)) + (find-files "." "\\.doc$")) + #t)))))) + (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/") + (synopsis "Combinatoric C Library") + (description "Symmetrica is a library for combinatorics. It has support +for the representation theory of the symmetric group and related groups, +combinatorics of tableaux, symmetric functions and polynomials, Schubert +polynomials, and the representation theory of Hecke algebras of type A_n.") + (license license:public-domain))) + +(define-public m4rie + (package + (name "m4rie") + (version "20150908") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/malb/m4rie") + (commit (string-append "release-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("m4ri" ,m4ri))) + (synopsis "Arithmetic of dense matrices over F_{2^e}") + (description "M4RI is a library for fast arithmetic with dense matrices +over finite fields of characteristic 2. So it extends the functionality +of M4RI from F_2 to F_{2^e}.") + (license license:gpl2+) + (home-page "https://bitbucket.org/malb/m4rie/"))) + +(define-public eclib + (package + (name "eclib") + (version "20190226") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JohnCremona/eclib/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (inputs + `(("gmp" ,gmp) + ("ntl" ,ntl) + ("pari-gp" ,pari-gp))) + (synopsis "Ranks of elliptic curves and modular symbols") + (description "The eclib package includes mwrank (for 2-descent on +elliptic curves over Q) and modular symbol code; it has been written by +John Cremona to compute his elliptic curve database.") + (license license:gpl2+) + (home-page (string-append "http://homepages.warwick.ac.uk/staff/" + "J.E.Cremona/mwrank/index.html")))) + +(define-public lrcalc + (package + (name "lrcalc") + (version "1.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://bitbucket.org/asbuch/lrcalc") + (commit (string-append "lrcalc-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss")))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'fix-permission + (lambda _ + (chmod "lrcalc.maple.src" #o644) + #t))))) + (synopsis "Littlewood-Richardson calculator in algebraic combinatorics") + (description "The Littlewood-Richardson Calculator (lrcalc) is a +program designed to compute Littlewood-Richardson coefficients. It computes +single Littlewood-Richardson coefficients, products of Schur functions, or +skew Schur functions. In addition it computes products in the small quantum +cohomology ring of a Grassmann variety. The software package also includes +a program that performs fast computation of the more general multiplicative +structure constants of Schubert polynomials.") + (license license:gpl2+) + (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/"))) + +(define-public iml + (package + (name "iml") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-" + version ".tar.bz2")) + (sha256 + (base32 + "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x")))) + (build-system gnu-build-system) + (inputs + `(("gmp", gmp) + ("cblas" ,openblas))) ; or any other BLAS library; the documentation + ; mentions ATLAS in particular + (arguments + `(#:configure-flags + (list + (string-append "--with-gmp-include=" + (assoc-ref %build-inputs "gmp") "/include") + (string-append "--with-gmp-lib=" + (assoc-ref %build-inputs "gmp") "/lib") + "--with-cblas=-lopenblas" + (string-append "--with-cblas-include=" + (assoc-ref %build-inputs "cblas") "/include") + (string-append "--with-cblas-lib=" + (assoc-ref %build-inputs "cblas") "/lib")))) + (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html") + (synopsis + "Solver for systems of linear equations over the integers") + (description + "IML is a C library implementing algorithms for computing exact +solutions to dense systems of linear equations over the integers. +Currently, IML provides the following functionality: + +@itemize +@item Nonsingular rational system solving: +compute the unique rational solution X to the system AX=B, where A and B +are integer matrices, A nonsingular. +@item Compute the right nullspace or kernel of an integer matrix. +@item Certified linear system solving: +compute a minimal denominator solution x to a system Ax=b, where b is an +integer vector and A is an integer matrix with arbitrary shape and +rank profile. +@end itemize + +In addition, IML provides some low level routines for a variety of mod p +matrix operations: computing the row-echelon form, determinant, rank +profile, and inverse of a mod p matrix. These mod p routines are not +general purpose; they require that p satisfy some preconditions based on +the dimension of the input matrix (usually p should be prime and should be +no more than about 20 bits long).") + (license license:bsd-3))) |