870 lines
34 KiB
Scheme
870 lines
34 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017-2024 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
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;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
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;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
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;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
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;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
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;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
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;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
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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 gexp)
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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 pyproject)
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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 autotools)
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#:use-module (gnu packages base)
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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 bison)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages c)
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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 datastructures)
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#:use-module (gnu packages docbook)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages gd)
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#:use-module (gnu packages graphics)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages machine-learning)
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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 ncurses)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages pretty-print)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-check)
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#:use-module (gnu packages python-compression)
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#:use-module (gnu packages python-science)
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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 plfit
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(package
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(name "plfit")
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(version "0.9.4")
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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/ntamas/plfit")
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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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"042b60cnsz5wy27sz026xs0mnn9p58j46crgs78skncgkvzqyyc6"))))
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(build-system cmake-build-system)
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(arguments
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'(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
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(home-page "https://github.com/ntamas/plfit")
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(synopsis "Tool for fitting power-law distributions to empirical data")
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(description "The @command{plfit} command fits power-law distributions to
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empirical (discrete or continuous) data, according to the method of Clauset,
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Shalizi and Newman (@cite{Clauset A, Shalizi CR and Newman MEJ: Power-law
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distributions in empirical data. SIAM Review 51, 661-703 (2009)}).")
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(license license:gpl2+)))
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(define-public igraph
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(package
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(name "igraph")
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(version "0.10.7")
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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 "https://github.com/igraph/igraph")
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(commit version)))
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(file-name (git-file-name name version))
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(patches (search-patches "igraph-fix-varargs-integer-size.patch"))
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(modules '((guix build utils)
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(ice-9 ftw)
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(srfi srfi-26)))
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(snippet '(begin
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(delete-file-recursively "vendor")
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(delete-file-recursively "src/isomorphism/bliss")
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(substitute* '("src/CMakeLists.txt"
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"etc/cmake/benchmark_helpers.cmake")
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;; Remove extraneous bundling related variables.
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((".*_IS_VENDORED.*") "")
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((".*add_sub.*isomorphism/bliss.*") "")
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(("(.*TARGETS.*)bliss(.*)cxsparse_vendored(.*)pcg(.*)"
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_ part1 part2 part3 part4)
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(string-append part1 part2 part3 part4))
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(("cxsparse_vendored") "cxsparse")
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((" pcg ") " pcg_random "))
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(substitute* "CMakeLists.txt"
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(("add_sub.*vendor.*") ""))))
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(sha256
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(base32
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"025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn"))))
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(build-system cmake-build-system)
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(arguments
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(list
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#:configure-flags
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#~(list "-DBUILD_SHARED_LIBS=ON"
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;; Use the same integer width as suitesparse-cxsparse, which
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;; uses int64_t in SuiteSparse v6.0.0 and later.
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"-DIGRAPH_INTEGER_SIZE=64")
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#:test-target "check"
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'version-file
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(lambda _
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(let ((port (open-file "IGRAPH_VERSION" "w")))
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(display #$version port)
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(close port))))
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(add-after 'unpack 'patch-suitesparse
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(lambda _
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(substitute* '("src/core/sparsemat.c"
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"include/igraph_sparsemat.h")
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(("<cs/cs\\.h>") "<cs.h>")
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(("cs_igraph") "cs_dl")
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(("__BEGIN_DECLS.*" all)
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(string-append all "\n#define CS_LONG\n")))))
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(add-after 'unpack 'patch-pcg
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(lambda _
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(substitute* '("src/random/rng_pcg32.c"
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"src/random/rng_pcg64.c")
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(("#include \"pcg/(.*)\"" _ name)
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(string-append "#include <" name ">")))))
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(add-after 'unpack 'patch-bliss
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(lambda _
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(substitute* "src/isomorphism/bliss.cc"
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(("#include \"bliss.*")
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(string-append
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"#include <bliss/graph.hh>\n"
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"#include <bliss/digraph.hh>\n")))))
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(add-after 'build 'build-doc
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(lambda _
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(invoke "cmake" "--build" "." "--target" "html")))
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(add-after 'install 'install-doc
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(lambda _
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(copy-recursively
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"doc/html"
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(string-append #$output "/share/doc/"
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#$name "-" #$version "/html")))))))
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(native-inputs
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(list bison
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docbook-xml-4.3
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docbook-xsl
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flex
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pcg-c
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pkg-config
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;; For the HTML documentation.
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python
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source-highlight
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xmlto))
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(inputs
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(list arpack-ng
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bliss
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glpk
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lapack
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openblas
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plfit
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suitesparse-cxsparse))
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;; libxml2 is in the 'Requires.private' of igraph.pc.
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(propagated-inputs (list libxml2))
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(home-page "https://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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;; Temporarily use a precise commit, as there was a mistake in the last
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;; release that was fixed by it (see:
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;; https://github.com/igraph/python-igraph/issues/632).
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(let ((revision "0")
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(commit "b6ebd8eb277fc1d0e33340a6624629a10c638992"))
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(package
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(inherit igraph)
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(name "python-igraph")
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(version (git-version "0.10.4" revision commit))
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(source (origin
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(method git-fetch)
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;; The PyPI archive lacks tests.
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(uri (git-reference
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(url "https://github.com/igraph/python-igraph")
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(commit commit)))
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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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"0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'specify-libigraph-location
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(lambda _
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(let ((igraph #$(this-package-input "igraph")))
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(substitute* "setup.py"
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(("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var)
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(string-append
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var (format #f "[~s]~%"
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(string-append igraph "/include/igraph"))))
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(("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var)
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(string-append
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var (format #f "[~s]~%"
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(string-append igraph "/lib")))))))))))
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(inputs (list igraph))
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(propagated-inputs (list python-texttable))
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(native-inputs (list python-pytest))
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(home-page "https://igraph.org/python/")
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(synopsis "Python bindings for the igraph network analysis library"))))
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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")
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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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(list 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 "5.14.1")
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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/plotly/plotly.py")
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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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"12iy5cswn5c0590fvl87nr6vfyhvbxymrldh4c7dfm2gn6h8z8w0"))))
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(build-system python-build-system)
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(arguments
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(list
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#:phases
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#~(modify-phases %standard-phases
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(add-before 'build 'skip-npm
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;; npm is not packaged so build without it
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(lambda _
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(setenv "SKIP_NPM" "T")))
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(add-after 'unpack 'fix-version
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;; TODO: Versioneer in Guix gets its release version from the
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;; parent directory, but the plotly package is located inside a
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;; depth 3 subdirectory. Try to use versioneer if possible.
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(lambda _
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(substitute* "packages/python/plotly/setup.py"
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(("version=versioneer.get_version\\(),")
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(format #f "version=~s," #$version)))
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(substitute* "packages/python/plotly/plotly/version.py"
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(("__version__ = get_versions\\(\\)\\[\"version\"\\]")
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(format #f "__version__ = ~s" #$version)))))
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(add-after 'fix-version 'chdir
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(lambda _
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(chdir "packages/python/plotly")))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "pytest" "-x" "plotly/tests/test_core")
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(invoke "pytest" "-x" "plotly/tests/test_io")
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;; FIXME: Add optional dependencies and enable their tests.
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;; (invoke "pytest" "-x" "plotly/tests/test_optional")
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(invoke "pytest" "_plotly_utils/tests")))))))
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(native-inputs
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(list python-ipywidgets python-pytest python-xarray))
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(propagated-inputs
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(list python-ipython
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python-pandas
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python-pillow
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python-requests
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python-retrying
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python-six
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python-tenacity
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python-statsmodels))
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(home-page "https://plotly.com/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 python-plotly-2.4.1
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(package (inherit 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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(native-inputs '())
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(propagated-inputs
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(list python-decorator
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python-nbformat
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python-pandas
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python-pytz
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python-requests
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python-six))
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(arguments
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(list
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#:tests? #false ;The tests are not distributed in the release
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#:phases
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'(modify-phases %standard-phases
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(add-after 'unpack 'python-compatibility
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(lambda _
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(substitute* "plotly/grid_objs/grid_objs.py"
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(("from collections import MutableSequence")
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"from collections.abc import MutableSequence")))))))))
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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 "0.16")
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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-louvain" version))
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(patches (search-patches "python-louvain-fix-test.patch"))
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(sha256
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(base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
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(build-system python-build-system)
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(native-inputs
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(list python-setuptools-57)) ;for use_2to3 support
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(propagated-inputs
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(list python-networkx python-numpy))
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(home-page "https://github.com/taynaud/python-louvain")
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(synopsis "Louvain algorithm for community detection")
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(description
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"This package provides a pure Python implementation of the Louvain
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algorithm for community detection in large networks.")
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(license license:bsd-3)))
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(define-public python-vtraag-louvain
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(package
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(name "python-vtraag-louvain")
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(version "0.8.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "louvain" version))
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(sha256
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(base32
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"16l2zi4jwc3vpvpnz32jv7xy0g5087dp9y57wxplj1xa9r312x0i"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:phases
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|
'(modify-phases %standard-phases
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|
(add-after 'unpack 'do-not-use-bundled-igraph
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(lambda _
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(substitute* "setup.py"
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(("self.external = False")
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"self.external = True")
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(("self.use_pkgconfig = False")
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"self.use_pkgconfig = True")))))))
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(inputs (list igraph))
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(propagated-inputs (list python-igraph))
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(native-inputs
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(list pkg-config
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python-ddt
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python-setuptools-scm))
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(home-page "https://github.com/vtraag/louvain")
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(synopsis "Community detection in large networks")
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(description
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"Louvain is a general algorithm for methods of community detection in
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large networks.")
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(license license:gpl3+)))
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(define-public python-graphtools
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(package
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(name "python-graphtools")
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(version "1.5.3")
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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 "https://github.com/KrishnaswamyLab/graphtools")
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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 "1aaxhij4y5z2vvc34qnb5py6nw3ciz35a3z4lfr223f9kvfpqgak"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
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|
(list
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|
#:phases
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|
'(modify-phases %standard-phases
|
|
(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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|
(when tests?
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|
;; Incompatibility with sklearn.
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|
;; 'kNNLandmarkGraph' object has no attribute '_landmark_op'
|
|
(delete-file "test/test_landmark.py")
|
|
(setenv "LOKY_MAX_CPU_COUNT" "1")
|
|
(invoke "nose2" "-v")))))))
|
|
(propagated-inputs
|
|
(list python-deprecated
|
|
python-future
|
|
python-numpy
|
|
python-pygsp
|
|
python-scikit-learn
|
|
python-scipy
|
|
python-tasklogger))
|
|
(native-inputs
|
|
(list util-linux ;for lscpu
|
|
python-anndata
|
|
python-black
|
|
python-coverage
|
|
python-coveralls
|
|
python-nose
|
|
python-nose2
|
|
python-pandas
|
|
python-parameterized
|
|
python-igraph))
|
|
(home-page "https://github.com/KrishnaswamyLab/graphtools")
|
|
(synopsis "Tools for building and manipulating graphs in Python")
|
|
(description "This package provides tools for building and manipulating
|
|
graphs in Python.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public python-louvain-igraph
|
|
(package
|
|
(name "python-louvain-igraph")
|
|
(version "0.8.1")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/vtraag/louvain-igraph")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1j2ybihvvzggwjb9zvm829aqb5b94q10h8bw6v0h42xd9w75z9sv"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'find-igraph
|
|
(lambda _
|
|
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
|
|
(substitute* "setup.py"
|
|
(("/usr/include/igraph")
|
|
(string-append #$(this-package-input "igraph")
|
|
"/include/igraph"))))))))
|
|
(propagated-inputs (list python-igraph))
|
|
(inputs (list igraph))
|
|
(native-inputs
|
|
(list python-ddt
|
|
python-setuptools-scm
|
|
pkg-config))
|
|
(home-page "https://github.com/vtraag/louvain-igraph")
|
|
(synopsis "Implementation of the Louvain algorithm")
|
|
(description "This package implements the Louvain algorithm for community
|
|
detection in C++ and exposes it to Python. Besides the relative flexibility
|
|
of the implementation, it also scales well, and can be run on graphs of
|
|
millions of nodes (as long as they can fit in memory). The core function is
|
|
@code{find_partition} which finds the optimal partition using the louvain
|
|
algorithm for a number of different methods.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python-pygsp
|
|
(package
|
|
(name "python-pygsp")
|
|
(version "0.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "PyGSP" version))
|
|
(sha256
|
|
(base32 "002q4z3p3ka81rzhgi66qqmz1ccrg9hwch4bax7jsqixg64asx28"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:test-flags
|
|
;; These all fail due to a type error in scipy.
|
|
'(list "-k" (string-append "not test_bunny"
|
|
" and not test_lowstretchtree"
|
|
" and not test_nngraph"
|
|
" and not test_plot_graphs"
|
|
" and not test_randomregular"))
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(add-after 'unpack 'disable-doctests
|
|
(lambda _
|
|
(substitute* "pygsp/tests/test_all.py"
|
|
(("def test_docstrings.*") "def _disabled_test_docstrings():\n")
|
|
(("return doctest.DocFileSuite.*") "return False\n")
|
|
(("suites.append\\(test_docstrings.*")
|
|
"")))))))
|
|
(propagated-inputs (list python-numpy python-scikit-image python-scipy))
|
|
(native-inputs (list python-coverage python-coveralls python-flake8))
|
|
(home-page "https://github.com/epfl-lts2/pygsp")
|
|
(synopsis "Graph Signal Processing in Python")
|
|
(description "The PyGSP is a Python package to ease signal processing on
|
|
graphs.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public faiss
|
|
(package
|
|
(name "faiss")
|
|
(version "1.5.0")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/facebookresearch/faiss")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0pk15jfa775cy2pqmzq62nhd6zfjxmpvz5h731197c28aq3zw39w"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
(substitute* "utils.cpp"
|
|
(("#include <immintrin.h>")
|
|
"#ifdef __SSE__\n#include <immintrin.h>\n#endif"))
|
|
#t))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "-DBUILD_WITH_GPU=OFF" ; thanks, but no thanks, CUDA.
|
|
"-DBUILD_TUTORIAL=OFF") ; we don't need those
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'prepare-build
|
|
(lambda _
|
|
(let ((features (list ,@(let ((system (or (%current-target-system)
|
|
(%current-system))))
|
|
(cond
|
|
((string-prefix? "x86_64" system)
|
|
'("-mavx" "-msse2" "-mpopcnt"))
|
|
((string-prefix? "i686" system)
|
|
'("-msse2" "-mpopcnt"))
|
|
(else
|
|
'()))))))
|
|
(substitute* "CMakeLists.txt"
|
|
(("-m64") "")
|
|
(("-mpopcnt") "") ; only some architectures
|
|
(("-msse4")
|
|
(string-append
|
|
(string-join features)
|
|
" -I" (getcwd)))
|
|
;; Build also the shared library
|
|
(("ARCHIVE DESTINATION lib")
|
|
"LIBRARY DESTINATION lib")
|
|
(("add_library.*" m)
|
|
"\
|
|
add_library(objlib OBJECT ${faiss_cpu_headers} ${faiss_cpu_cpp})
|
|
set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
|
|
add_library(${faiss_lib}_static STATIC $<TARGET_OBJECTS:objlib>)
|
|
add_library(${faiss_lib} SHARED $<TARGET_OBJECTS:objlib>)
|
|
install(TARGETS ${faiss_lib}_static ARCHIVE DESTINATION lib)
|
|
\n")))
|
|
|
|
;; See https://github.com/facebookresearch/faiss/issues/520
|
|
(substitute* "IndexScalarQuantizer.cpp"
|
|
(("#define USE_AVX") ""))
|
|
|
|
;; Make header files available for compiling tests.
|
|
(mkdir-p "faiss")
|
|
(for-each (lambda (file)
|
|
(mkdir-p (string-append "faiss/" (dirname file)))
|
|
(copy-file file (string-append "faiss/" file)))
|
|
(find-files "." "\\.h$"))
|
|
#t))
|
|
(replace 'check
|
|
(lambda _
|
|
(invoke "make" "-C" "tests"
|
|
(format #f "-j~a" (parallel-job-count)))))
|
|
(add-after 'install 'remove-tests
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(delete-file-recursively
|
|
(string-append (assoc-ref outputs "out")
|
|
"/test"))
|
|
#t)))))
|
|
(inputs
|
|
(list openblas))
|
|
(native-inputs
|
|
(list googletest))
|
|
(home-page "https://github.com/facebookresearch/faiss")
|
|
(synopsis "Efficient similarity search and clustering of dense vectors")
|
|
(description "Faiss is a library for efficient similarity search and
|
|
clustering of dense vectors. It contains algorithms that search in sets of
|
|
vectors of any size, up to ones that possibly do not fit in RAM. It also
|
|
contains supporting code for evaluation and parameter tuning.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-faiss
|
|
(package (inherit faiss)
|
|
(name "python-faiss")
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'chdir
|
|
(lambda _ (chdir "python") #t))
|
|
(add-after 'chdir 'build-swig
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-output-to-file "../makefile.inc"
|
|
(lambda ()
|
|
(let ((python-version ,(version-major+minor (package-version python))))
|
|
(format #t "\
|
|
PYTHONCFLAGS =-I~a/include/python~a/ -I~a/lib/python~a/site-packages/numpy/core/include
|
|
LIBS = -lpython~a -lfaiss
|
|
SHAREDFLAGS = -shared -fopenmp
|
|
CXXFLAGS = -fpermissive -fopenmp -fPIC
|
|
CPUFLAGS = ~{~a ~}~%"
|
|
(assoc-ref inputs "python*") python-version
|
|
(assoc-ref inputs "python-numpy") python-version
|
|
python-version
|
|
(list ,@(let ((system (or (%current-target-system)
|
|
(%current-system))))
|
|
(cond
|
|
((string-prefix? "x86_64" system)
|
|
'("-mavx" "-msse2" "-mpopcnt"))
|
|
((string-prefix? "i686" system)
|
|
'("-msse2" "-mpopcnt"))
|
|
(else
|
|
'()))))))))
|
|
(substitute* "Makefile"
|
|
(("../libfaiss.a") ""))
|
|
(invoke "make" "cpu"))))))
|
|
(inputs
|
|
`(("faiss" ,faiss)
|
|
("openblas" ,openblas)
|
|
("python*" ,python)
|
|
("swig" ,swig)))
|
|
(propagated-inputs
|
|
(list python-matplotlib python-numpy))
|
|
(description "Faiss is a library for efficient similarity search and
|
|
clustering of dense vectors. This package provides Python bindings to the
|
|
Faiss library.")))
|
|
|
|
(define-public python-leidenalg
|
|
(package
|
|
(name "python-leidenalg")
|
|
(version "0.9.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "leidenalg" version))
|
|
(sha256
|
|
(base32
|
|
"1wvmi6ca9kf8pbxg6b18n64h82wr9a6wcdazyn82pww0dwxzwp3y"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
'(#:tests? #f ;tests are not included
|
|
#:phases (modify-phases %standard-phases
|
|
(add-after 'unpack 'fix-requirements
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("self.external = False")
|
|
"self.external = True")
|
|
(("self.use_pkgconfig = False")
|
|
"self.use_pkgconfig = True")
|
|
(("python-igraph >=")
|
|
"igraph >=")))))))
|
|
(native-inputs
|
|
(list pkg-config python-setuptools-scm))
|
|
(inputs
|
|
(list igraph))
|
|
(propagated-inputs
|
|
(list python-igraph))
|
|
(home-page "https://github.com/vtraag/leidenalg")
|
|
(synopsis "Community detection in large networks")
|
|
(description
|
|
"Leiden is a general algorithm for methods of community detection in
|
|
large networks. This package implements the Leiden algorithm in C++ and
|
|
exposes it to Python. Besides the relative flexibility of the implementation,
|
|
it also scales well, and can be run on graphs of millions of nodes (as long as
|
|
they can fit in memory). The core function is @code{find_partition} which
|
|
finds the optimal partition using the Leiden algorithm, which is an extension
|
|
of the Louvain algorithm, for a number of different methods.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public edge-addition-planarity-suite
|
|
(package
|
|
(name "edge-addition-planarity-suite")
|
|
(version "3.0.2.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url (string-append "https://github.com/graph-algorithms/"
|
|
name))
|
|
(commit (string-append "Version_" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1c7bnxgiz28mqsq3a3msznmjq629w0qqjynm2rqnnjn2qpc22h3i"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
(list autoconf automake 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 "0.9")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/rankwidth/"
|
|
"rw-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0hdlxxmlccb6fp7g58zv0rdzpbyjn9bgqlf052sgrk95zq33bq61"))
|
|
(patches (search-patches "rw-igraph-0.10.patch"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs (list pkg-config))
|
|
(inputs (list 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+)))
|
|
|
|
(define-public mscgen
|
|
(package
|
|
(name "mscgen")
|
|
(version "0.20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.mcternan.me.uk/mscgen/software/mscgen-src-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"08yw3maxhn5fl1lff81gmcrpa4j9aas4mmby1g9w5qcr0np82d1w"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
(list pkg-config))
|
|
(inputs
|
|
(list gd))
|
|
(home-page "https://www.mcternan.me.uk/mscgen/")
|
|
(synopsis "Message Sequence Chart Generator")
|
|
(description "Mscgen is a small program that parses Message Sequence Chart
|
|
descriptions and produces PNG, SVG, EPS or server side image maps (ismaps) as
|
|
the output. Message Sequence Charts (MSCs) are a way of representing entities
|
|
and interactions over some time period and are often used in combination with
|
|
SDL. MSCs are popular in Telecoms to specify how protocols operate although
|
|
MSCs need not be complicated to create or use. Mscgen aims to provide a simple
|
|
text language that is clear to create, edit and understand, which can also be
|
|
transformed into common image formats for display or printing.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public python-graph-tool
|
|
(package
|
|
(name "python-graph-tool")
|
|
(version "2.59")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://downloads.skewed.de/graph-tool/graph-tool-"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"1bmck5fcihj9lr5kd8x624bdi9xhfc13pl4mwzv74jr5lz07kr6d"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:imported-modules (,@%gnu-build-system-modules
|
|
(guix build python-build-system))
|
|
#:modules (,@%gnu-build-system-modules
|
|
((guix build python-build-system) #:select (site-packages)))
|
|
;; The build process peaks around 4GB/RAM per core.
|
|
#:parallel-build? #f
|
|
#:configure-flags
|
|
(list (string-append "--with-boost="
|
|
(assoc-ref %build-inputs "boost"))
|
|
(string-append "--with-python-module-path="
|
|
(site-packages %build-inputs %outputs)))))
|
|
(native-inputs
|
|
(list ncurses pkg-config))
|
|
(inputs
|
|
(list boost
|
|
cairomm-1.14
|
|
cgal
|
|
expat
|
|
gmp
|
|
gtk+
|
|
python-wrapper
|
|
sparsehash))
|
|
(propagated-inputs
|
|
(list python-matplotlib
|
|
python-numpy
|
|
python-pycairo
|
|
python-scipy
|
|
python-zstandard))
|
|
(synopsis "Manipulate and analyze graphs with Python efficiently")
|
|
(description "Graph-tool is an efficient Python module for manipulation
|
|
and statistical analysis of graphs (a.k.a. networks). Contrary to most other
|
|
Python modules with similar functionality, the core data structures and
|
|
algorithms are implemented in C++, making extensive use of template
|
|
metaprogramming, based heavily on the Boost Graph Library. This confers it a
|
|
level of performance that is comparable (both in memory usage and computation
|
|
time) to that of a pure C/C++ library.")
|
|
(home-page "https://graph-tool.skewed.de/")
|
|
(license license:lgpl3+)))
|