503 lines
19 KiB
Scheme
503 lines
19 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2019 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages graph)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (guix build-system r)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages bioconductor)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages time)
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#:use-module (gnu packages xml))
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(define-public igraph
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(package
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(name "igraph")
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(version "0.7.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "http://igraph.org/nightly/get/c/igraph-"
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version ".tar.gz"))
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(sha256
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(base32
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"1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r"))))
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(build-system gnu-build-system)
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(arguments
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`(#:configure-flags
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(list "--with-external-glpk"
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"--with-external-blas"
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"--with-external-lapack")))
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(inputs
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`(("gmp" ,gmp)
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("glpk" ,glpk)
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("libxml2" ,libxml2)
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("lapack" ,lapack)
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("openblas" ,openblas)
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("zlib" ,zlib)))
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(home-page "http://igraph.org")
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(synopsis "Network analysis and visualization")
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(description
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"This package provides a library for the analysis of networks and graphs.
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It can handle large graphs very well and provides functions for generating
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random and regular graphs, graph visualization, centrality methods and much
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more.")
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(license license:gpl2+)))
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(define-public python-igraph
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(package (inherit igraph)
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(name "python-igraph")
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(version "0.7.1.post6")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "python-igraph" version))
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(sha256
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(base32
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"0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5"))))
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(build-system python-build-system)
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(arguments '())
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(inputs
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`(("igraph" ,igraph)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(home-page "http://pypi.python.org/pypi/python-igraph")
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(synopsis "Python bindings for the igraph network analysis library")))
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(define-public r-igraph
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(package
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(name "r-igraph")
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(version "1.2.4.1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "igraph" version))
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(sha256
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(base32
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"1074y8mvprrqlkb4vwa2qc9l03r8d7p5vaaqacj4ljjs7dvcq6l9"))))
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(build-system r-build-system)
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(native-inputs
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`(("gfortran" ,gfortran)))
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(inputs
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`(("gmp" ,gmp)
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("glpk" ,glpk)
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("libxml2" ,libxml2)
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("zlib" ,zlib)))
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(propagated-inputs
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`(("r-magrittr" ,r-magrittr)
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("r-matrix" ,r-matrix)
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("r-pkgconfig" ,r-pkgconfig)))
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(home-page "http://igraph.org")
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(synopsis "Network analysis and visualization")
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(description
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"This package provides routines for simple graphs and network analysis.
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It can handle large graphs very well and provides functions for generating
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random and regular graphs, graph visualization, centrality methods and much
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more.")
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(license license:gpl2+)))
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(define-public r-diffusionmap
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(package
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(name "r-diffusionmap")
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(version "1.1-0.1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "diffusionMap" version))
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(sha256
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(base32
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"11l4kbciawvli5nlsi4qaf8afmgk5xgqiqpdyhvaqri5mx0zhk5j"))))
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(properties `((upstream-name . "diffusionMap")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-igraph" ,r-igraph)
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("r-matrix" ,r-matrix)
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("r-scatterplot3d" ,r-scatterplot3d)))
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(home-page "https://www.r-project.org")
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(synopsis "Diffusion map")
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(description "This package implements the diffusion map method of data
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parametrization, including creation and visualization of diffusion maps,
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clustering with diffusion K-means and regression using the adaptive regression
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model.")
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(license license:gpl2)))
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(define-public r-rgraphviz
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(package
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(name "r-rgraphviz")
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(version "2.28.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "Rgraphviz" version))
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(sha256
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(base32
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"0nivz8fshaqig6ynjqbya2gmxsy4hm7jnd8fhb853z5g0ydp7g0c"))))
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(properties `((upstream-name . "Rgraphviz")))
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(build-system r-build-system)
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;; FIXME: Rgraphviz bundles the sources of an older variant of
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;; graphviz. It does not build with the latest version of graphviz, so
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;; we do not add graphviz to the inputs.
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(inputs `(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-graph" ,r-graph)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(home-page "http://bioconductor.org/packages/Rgraphviz")
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(synopsis "Plotting capabilities for R graph objects")
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(description
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"This package interfaces R with the graphviz library for plotting R graph
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objects from the @code{graph} package.")
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(license license:epl1.0)))
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(define-public r-rbiofabric
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(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
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(revision "1"))
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(package
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(name "r-rbiofabric")
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(version (string-append "0.3-" revision "." (string-take commit 7)))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/wjrl/RBioFabric.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-igraph" ,r-igraph)))
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(home-page "http://www.biofabric.org/")
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(synopsis "BioFabric network visualization")
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(description "This package provides an implementation of the function
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@code{bioFabric} for creating scalable network digrams where nodes are
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represented by horizontal lines, and edges are represented by vertical
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lines.")
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(license license:expat))))
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(define-public python-plotly
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(package
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(name "python-plotly")
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(version "2.4.1")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "plotly" version))
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(sha256
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(base32
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"0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
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(build-system python-build-system)
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(arguments
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'(#:tests? #f)) ; The tests are not distributed in the release
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(propagated-inputs
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`(("python-decorator" ,python-decorator)
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("python-nbformat" ,python-nbformat)
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("python-pandas" ,python-pandas)
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("python-pytz" ,python-pytz)
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("python-requests" ,python-requests)
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("python-six" ,python-six)))
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(home-page "https://plot.ly/python/")
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(synopsis "Interactive plotting library for Python")
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(description "Plotly's Python graphing library makes interactive,
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publication-quality graphs online. Examples of how to make line plots, scatter
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plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
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subplots, multiple-axes, polar charts, and bubble charts. ")
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(license license:expat)))
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(define-public python2-plotly
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(package-with-python2 python-plotly))
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(define-public python-louvain
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(package
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(name "python-louvain")
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(version "0.6.1")
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;; The tarball on Pypi does not include the tests.
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/vtraag/louvain-igraph.git")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0w31537sifkf65sck1iaip5i6d8g64pa3wdwad83d6p9jwkck57k"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-ddt" ,python-ddt)
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("python-igraph" ,python-igraph)))
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(inputs
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`(("igraph" ,igraph)))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("python-pytest" ,python-pytest)))
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(home-page "https://github.com/vtraag/louvain-igraph")
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(synopsis "Algorithm for methods of community detection in large networks")
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(description
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"This package provides an implementation of the Louvain algorithm for use
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with igraph. Louvain is a general algorithm for methods of community
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detection in large networks.
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This package has been superseded by the @code{leidenalg} package and should
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not be used for new projects.")
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(license license:gpl3+)))
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(define-public faiss
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(package
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(name "faiss")
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(version "1.5.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/facebookresearch/faiss.git")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(substitute* "utils.cpp"
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(("#include <immintrin.h>")
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"#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
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#t))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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(list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA.
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"-DBUILD_TUTORIAL=OFF") ; we don't need those
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'prepare-build
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(lambda _
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(let ((features (list ,@(let ((system (or (%current-target-system)
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(%current-system))))
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(cond
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((string-prefix? "x86_64" system)
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'("-mavx" "-msse2" "-mpopcnt"))
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((string-prefix? "i686" system)
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'("-msse2" "-mpopcnt"))
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(else
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'()))))))
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(substitute* "CMakeLists.txt"
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(("-m64") "")
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(("-mpopcnt") "") ; only some architectures
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(("-msse4")
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(string-append
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(string-join features)
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" -I" (getcwd)))
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;; Build also the shared library
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(("ARCHIVE DESTINATION lib")
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"LIBRARY DESTINATION lib")
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(("add_library.*" m)
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"\
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add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
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set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
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add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
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add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
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install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
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\n")))
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;; See https://github.com/facebookresearch/faiss/issues/520
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(substitute* "IndexScalarQuantizer.cpp"
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(("#define USE_AVX") ""))
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;; Make header files available for compiling tests.
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(mkdir-p "faiss")
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(for-each (lambda (file)
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(mkdir-p (string-append "faiss/" (dirname file)))
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(copy-file file (string-append "faiss/" file)))
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(find-files "." "\\.h$"))
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#t))
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(replace 'check
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(lambda _
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(invoke "make" "-C" "tests"
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(format #f "-j~a" (parallel-job-count)))))
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(add-after 'install 'remove-tests
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(lambda* (#:key outputs #:allow-other-keys)
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(delete-file-recursively
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(string-append (assoc-ref outputs "out")
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"/test"))
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#t)))))
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(inputs
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`(("openblas" ,openblas)))
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(native-inputs
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`(("googletest" ,googletest)))
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(home-page "https://github.com/facebookresearch/faiss")
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(synopsis "Efficient similarity search and clustering of dense vectors")
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(description "Faiss is a library for efficient similarity search and
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clustering of dense vectors. It contains algorithms that search in sets of
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vectors of any size, up to ones that possibly do not fit in RAM. It also
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contains supporting code for evaluation and parameter tuning.")
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(license license:bsd-3)))
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(define-public python-faiss
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(package (inherit faiss)
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(name "python-faiss")
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'chdir
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|
(lambda _ (chdir "python") #t))
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|
(add-after 'chdir 'build-swig
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(lambda* (#:key inputs #:allow-other-keys)
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(with-output-to-file "../makefile.inc"
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|
(lambda ()
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(let ((python-version ,(version-major+minor (package-version python))))
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(format #t "\
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PYTHONCFLAGS =-I~a/include/python~am/ -I~a/lib/python~a/site-packages/numpy/core/include
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LIBS = -lpython~am -lfaiss
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SHAREDFLAGS = -shared -fopenmp
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CXXFLAGS = -fpermissive -std=c++11 -fopenmp -fPIC
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CPUFLAGS = ~{~a ~}~%"
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(assoc-ref inputs "python*") python-version
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(assoc-ref inputs "python-numpy") python-version
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python-version
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|
(list ,@(let ((system (or (%current-target-system)
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(%current-system))))
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|
(cond
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((string-prefix? "x86_64" system)
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'("-mavx" "-msse2" "-mpopcnt"))
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|
((string-prefix? "i686" system)
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'("-msse2" "-mpopcnt"))
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|
(else
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'()))))))))
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(substitute* "Makefile"
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(("../libfaiss.a") ""))
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(invoke "make" "cpu"))))))
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(inputs
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`(("faiss" ,faiss)
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("openblas" ,openblas)
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|
("python*" ,python)
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|
("swig" ,swig)))
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|
(propagated-inputs
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|
`(("python-matplotlib" ,python-matplotlib)
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|
("python-numpy" ,python-numpy)))
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|
(description "Faiss is a library for efficient similarity search and
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clustering of dense vectors. This package provides Python bindings to the
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Faiss library.")))
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(define-public python-leidenalg
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(package
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(name "python-leidenalg")
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(version "0.7.0")
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(source
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|
(origin
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|
(method url-fetch)
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|
(uri (pypi-uri "leidenalg" version))
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(sha256
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(base32
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"15fwld9hdw357rd026mzcwpah5liy4f33vc9x9kwy37g71b2rjf1"))))
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(build-system python-build-system)
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(arguments '(#:tests? #f)) ; tests are not included
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(inputs
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`(("igraph" ,igraph)))
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(propagated-inputs
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`(("python-igraph" ,python-igraph)))
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(home-page "https://github.com/vtraag/leidenalg")
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(synopsis "Community detection in large networks")
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(description
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"Leiden is a general algorithm for methods of community detection in
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large networks. This package implements the Leiden algorithm in C++ and
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exposes it to Python. Besides the relative flexibility of the implementation,
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it also scales well, and can be run on graphs of millions of nodes (as long as
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they can fit in memory). The core function is @code{find_partition} which
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finds the optimal partition using the Leiden algorithm, which is an extension
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of the Louvain algorithm, for a number of different methods.")
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(license license:gpl3+)))
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(define-public edge-addition-planarity-suite
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(package
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(name "edge-addition-planarity-suite")
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(version "3.0.0.5")
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(source
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|
(origin
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|
(method git-fetch)
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|
(uri (git-reference
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|
(url (string-append "https://github.com/graph-algorithms/"
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name))
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|
(commit (string-append "Version_" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("autoconf" ,autoconf)
|
|
("automake" ,automake)
|
|
("libtool" ,libtool)))
|
|
(synopsis "Embedding of planar graphs")
|
|
(description "The package provides a reference implementation of the
|
|
linear time edge addition algorithm for embedding planar graphs and
|
|
isolating planarity obstructions.")
|
|
(license license:bsd-3)
|
|
(home-page
|
|
"https://github.com/graph-algorithms/edge-addition-planarity-suite")))
|
|
|
|
(define-public rw
|
|
(package
|
|
(name "rw")
|
|
;; There is a version 0.8, but the tarball is broken with symlinks
|
|
;; to /usr/share.
|
|
(version "0.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/rankwidth/"
|
|
"rw-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1rv2v42x2506x7f10349m1wpmmfxrv9l032bkminni2gbip9cjg0"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("igraph" ,igraph)))
|
|
(home-page "https://sourceforge.net/projects/rankwidth/")
|
|
(synopsis "Rank-width and rank-decomposition of graphs")
|
|
(description "rw computes rank-width and rank-decompositions
|
|
of graphs.")
|
|
(license license:gpl2+)))
|