870 lines
34 KiB
Scheme
870 lines
34 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2017-2024 Ricardo Wurmus <rekado@elephly.net>
|
|
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
|
|
;;; Copyright © 2018, 2020, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
|
|
;;; Copyright © 2019, 2021, 2022, 2024 Efraim Flashner <efraim@flashner.co.il>
|
|
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
|
|
;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
|
|
;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
|
|
;;; Copyright © 2021, 2023 Vinicius Monego <monego@posteo.net>
|
|
;;; Copyright © 2021 Alexandre Hannud Abdo <abdo@member.fsf.org>
|
|
;;; Copyright © 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
|
|
;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
|
|
;;; Copyright © 2023 David Elsing <david.elsing@posteo.net>
|
|
;;;
|
|
;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages graph)
|
|
#:use-module (guix download)
|
|
#:use-module (guix gexp)
|
|
#:use-module (guix git-download)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix build-system cmake)
|
|
#:use-module (guix build-system gnu)
|
|
#:use-module (guix build-system pyproject)
|
|
#:use-module (guix build-system python)
|
|
#:use-module (guix build-system r)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages bioconductor)
|
|
#:use-module (gnu packages bioinformatics)
|
|
#:use-module (gnu packages bison)
|
|
#:use-module (gnu packages boost)
|
|
#:use-module (gnu packages c)
|
|
#:use-module (gnu packages check)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages cran)
|
|
#:use-module (gnu packages datastructures)
|
|
#:use-module (gnu packages docbook)
|
|
#:use-module (gnu packages flex)
|
|
#:use-module (gnu packages gd)
|
|
#:use-module (gnu packages graphics)
|
|
#:use-module (gnu packages graphviz)
|
|
#:use-module (gnu packages gtk)
|
|
#:use-module (gnu packages linux)
|
|
#:use-module (gnu packages machine-learning)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages multiprecision)
|
|
#:use-module (gnu packages ncurses)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages pretty-print)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-build)
|
|
#:use-module (gnu packages python-check)
|
|
#:use-module (gnu packages python-compression)
|
|
#:use-module (gnu packages python-science)
|
|
#:use-module (gnu packages python-web)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages statistics)
|
|
#:use-module (gnu packages swig)
|
|
#:use-module (gnu packages time)
|
|
#:use-module (gnu packages xml))
|
|
|
|
(define-public plfit
|
|
(package
|
|
(name "plfit")
|
|
(version "0.9.4")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/ntamas/plfit")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"042b60cnsz5wy27sz026xs0mnn9p58j46crgs78skncgkvzqyyc6"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
'(#:configure-flags (list "-DBUILD_SHARED_LIBS=ON")))
|
|
(home-page "https://github.com/ntamas/plfit")
|
|
(synopsis "Tool for fitting power-law distributions to empirical data")
|
|
(description "The @command{plfit} command fits power-law distributions to
|
|
empirical (discrete or continuous) data, according to the method of Clauset,
|
|
Shalizi and Newman (@cite{Clauset A, Shalizi CR and Newman MEJ: Power-law
|
|
distributions in empirical data. SIAM Review 51, 661-703 (2009)}).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public igraph
|
|
(package
|
|
(name "igraph")
|
|
(version "0.10.7")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/igraph/igraph")
|
|
(commit version)))
|
|
(file-name (git-file-name name version))
|
|
(patches (search-patches "igraph-fix-varargs-integer-size.patch"))
|
|
(modules '((guix build utils)
|
|
(ice-9 ftw)
|
|
(srfi srfi-26)))
|
|
(snippet '(begin
|
|
|
|
(delete-file-recursively "vendor")
|
|
(delete-file-recursively "src/isomorphism/bliss")
|
|
(substitute* '("src/CMakeLists.txt"
|
|
"etc/cmake/benchmark_helpers.cmake")
|
|
;; Remove extraneous bundling related variables.
|
|
((".*_IS_VENDORED.*") "")
|
|
((".*add_sub.*isomorphism/bliss.*") "")
|
|
(("(.*TARGETS.*)bliss(.*)cxsparse_vendored(.*)pcg(.*)"
|
|
_ part1 part2 part3 part4)
|
|
(string-append part1 part2 part3 part4))
|
|
(("cxsparse_vendored") "cxsparse")
|
|
((" pcg ") " pcg_random "))
|
|
(substitute* "CMakeLists.txt"
|
|
(("add_sub.*vendor.*") ""))))
|
|
(sha256
|
|
(base32
|
|
"025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn"))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
(list
|
|
#:configure-flags
|
|
#~(list "-DBUILD_SHARED_LIBS=ON"
|
|
;; Use the same integer width as suitesparse-cxsparse, which
|
|
;; uses int64_t in SuiteSparse v6.0.0 and later.
|
|
"-DIGRAPH_INTEGER_SIZE=64")
|
|
#:test-target "check"
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'version-file
|
|
(lambda _
|
|
(let ((port (open-file "IGRAPH_VERSION" "w")))
|
|
(display #$version port)
|
|
(close port))))
|
|
(add-after 'unpack 'patch-suitesparse
|
|
(lambda _
|
|
(substitute* '("src/core/sparsemat.c"
|
|
"include/igraph_sparsemat.h")
|
|
(("<cs/cs\\.h>") "<cs.h>")
|
|
(("cs_igraph") "cs_dl")
|
|
(("__BEGIN_DECLS.*" all)
|
|
(string-append all "\n#define CS_LONG\n")))))
|
|
(add-after 'unpack 'patch-pcg
|
|
(lambda _
|
|
(substitute* '("src/random/rng_pcg32.c"
|
|
"src/random/rng_pcg64.c")
|
|
(("#include \"pcg/(.*)\"" _ name)
|
|
(string-append "#include <" name ">")))))
|
|
(add-after 'unpack 'patch-bliss
|
|
(lambda _
|
|
(substitute* "src/isomorphism/bliss.cc"
|
|
(("#include \"bliss.*")
|
|
(string-append
|
|
"#include <bliss/graph.hh>\n"
|
|
"#include <bliss/digraph.hh>\n")))))
|
|
(add-after 'build 'build-doc
|
|
(lambda _
|
|
(invoke "cmake" "--build" "." "--target" "html")))
|
|
(add-after 'install 'install-doc
|
|
(lambda _
|
|
(copy-recursively
|
|
"doc/html"
|
|
(string-append #$output "/share/doc/"
|
|
#$name "-" #$version "/html")))))))
|
|
(native-inputs
|
|
(list bison
|
|
docbook-xml-4.3
|
|
docbook-xsl
|
|
flex
|
|
pcg-c
|
|
pkg-config
|
|
;; For the HTML documentation.
|
|
python
|
|
source-highlight
|
|
xmlto))
|
|
(inputs
|
|
(list arpack-ng
|
|
bliss
|
|
glpk
|
|
lapack
|
|
openblas
|
|
plfit
|
|
suitesparse-cxsparse))
|
|
;; libxml2 is in the 'Requires.private' of igraph.pc.
|
|
(propagated-inputs (list libxml2))
|
|
(home-page "https://igraph.org")
|
|
(synopsis "Network analysis and visualization")
|
|
(description
|
|
"This package provides a library for the analysis of networks and graphs.
|
|
It can handle large graphs very well and provides functions for generating
|
|
random and regular graphs, graph visualization, centrality methods and much
|
|
more.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public python-igraph
|
|
;; Temporarily use a precise commit, as there was a mistake in the last
|
|
;; release that was fixed by it (see:
|
|
;; https://github.com/igraph/python-igraph/issues/632).
|
|
(let ((revision "0")
|
|
(commit "b6ebd8eb277fc1d0e33340a6624629a10c638992"))
|
|
(package
|
|
(inherit igraph)
|
|
(name "python-igraph")
|
|
(version (git-version "0.10.4" revision commit))
|
|
(source (origin
|
|
(method git-fetch)
|
|
;; The PyPI archive lacks tests.
|
|
(uri (git-reference
|
|
(url "https://github.com/igraph/python-igraph")
|
|
(commit commit)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0dhrz5a6pi6vs94fm8q4nmkh6v1nmpw1sk482xls213zcbbh67hd"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-after 'unpack 'specify-libigraph-location
|
|
(lambda _
|
|
(let ((igraph #$(this-package-input "igraph")))
|
|
(substitute* "setup.py"
|
|
(("(LIBIGRAPH_FALLBACK_INCLUDE_DIRS = ).*" _ var)
|
|
(string-append
|
|
var (format #f "[~s]~%"
|
|
(string-append igraph "/include/igraph"))))
|
|
(("(LIBIGRAPH_FALLBACK_LIBRARY_DIRS = ).*" _ var)
|
|
(string-append
|
|
var (format #f "[~s]~%"
|
|
(string-append igraph "/lib")))))))))))
|
|
(inputs (list igraph))
|
|
(propagated-inputs (list python-texttable))
|
|
(native-inputs (list python-pytest))
|
|
(home-page "https://igraph.org/python/")
|
|
(synopsis "Python bindings for the igraph network analysis library"))))
|
|
|
|
(define-public r-rbiofabric
|
|
(let ((commit "666c2ae8b0a537c006592d067fac6285f71890ac")
|
|
(revision "1"))
|
|
(package
|
|
(name "r-rbiofabric")
|
|
(version (string-append "0.3-" revision "." (string-take commit 7)))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/wjrl/RBioFabric")
|
|
(commit commit)))
|
|
(file-name (string-append name "-" version "-checkout"))
|
|
(sha256
|
|
(base32
|
|
"1yahqrcrqpbcywv73y9rlmyz8apdnp08afialibrr93ch0p06f8z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
(list r-igraph))
|
|
(home-page "http://www.biofabric.org/")
|
|
(synopsis "BioFabric network visualization")
|
|
(description "This package provides an implementation of the function
|
|
@code{bioFabric} for creating scalable network digrams where nodes are
|
|
represented by horizontal lines, and edges are represented by vertical
|
|
lines.")
|
|
(license license:expat))))
|
|
|
|
(define-public python-plotly
|
|
(package
|
|
(name "python-plotly")
|
|
(version "5.20.0")
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/plotly/plotly.py")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0i22sv8p3kl84nkldbv1253kld85rbwp2pdxivxn64wwflfpqvx6"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
#~(modify-phases %standard-phases
|
|
(add-before 'build 'skip-npm
|
|
;; npm is not packaged so build without it
|
|
(lambda _
|
|
(setenv "SKIP_NPM" "T")))
|
|
(add-after 'unpack 'fix-version
|
|
;; TODO: Versioneer in Guix gets its release version from the
|
|
;; parent directory, but the plotly package is located inside a
|
|
;; depth 3 subdirectory. Try to use versioneer if possible.
|
|
(lambda _
|
|
(substitute* "packages/python/plotly/setup.py"
|
|
(("version=versioneer.get_version\\(),")
|
|
(format #f "version=~s," #$version)))
|
|
(substitute* "packages/python/plotly/plotly/version.py"
|
|
(("__version__ = get_versions\\(\\)\\[\"version\"\\]")
|
|
(format #f "__version__ = ~s" #$version)))))
|
|
(add-after 'fix-version 'chdir
|
|
(lambda _
|
|
(chdir "packages/python/plotly")))
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
(invoke "pytest" "-x" "plotly/tests/test_core")
|
|
(invoke "pytest" "-x" "plotly/tests/test_io")
|
|
;; FIXME: Add optional dependencies and enable their tests.
|
|
;; (invoke "pytest" "-x" "plotly/tests/test_optional")
|
|
(invoke "pytest" "_plotly_utils/tests")))))))
|
|
(native-inputs
|
|
(list python-ipywidgets python-pytest python-xarray))
|
|
(propagated-inputs
|
|
(list python-ipython
|
|
python-pandas
|
|
python-pillow
|
|
python-requests
|
|
python-retrying
|
|
python-six
|
|
python-tenacity
|
|
python-statsmodels))
|
|
(home-page "https://plotly.com/python/")
|
|
(synopsis "Interactive plotting library for Python")
|
|
(description "Plotly's Python graphing library makes interactive,
|
|
publication-quality graphs online. Examples of how to make line plots, scatter
|
|
plots, area charts, bar charts, error bars, box plots, histograms, heatmaps,
|
|
subplots, multiple-axes, polar charts, and bubble charts.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-plotly-2.4.1
|
|
(package (inherit python-plotly)
|
|
(version "2.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "plotly" version))
|
|
(sha256
|
|
(base32
|
|
"0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m"))))
|
|
(native-inputs '())
|
|
(propagated-inputs
|
|
(list python-decorator
|
|
python-nbformat
|
|
python-pandas
|
|
python-pytz
|
|
python-requests
|
|
python-six))
|
|
(arguments
|
|
(list
|
|
#:tests? #false ;The tests are not distributed in the release
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(add-after 'unpack 'python-compatibility
|
|
(lambda _
|
|
(substitute* "plotly/grid_objs/grid_objs.py"
|
|
(("from collections import MutableSequence")
|
|
"from collections.abc import MutableSequence")))))))))
|
|
|
|
(define-public python-louvain
|
|
(package
|
|
(name "python-louvain")
|
|
(version "0.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "python-louvain" version))
|
|
(patches (search-patches "python-louvain-fix-test.patch"))
|
|
(sha256
|
|
(base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
|
|
(build-system python-build-system)
|
|
(native-inputs
|
|
(list python-setuptools-57)) ;for use_2to3 support
|
|
(propagated-inputs
|
|
(list python-networkx python-numpy))
|
|
(home-page "https://github.com/taynaud/python-louvain")
|
|
(synopsis "Louvain algorithm for community detection")
|
|
(description
|
|
"This package provides a pure Python implementation of the Louvain
|
|
algorithm for community detection in large networks.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-vtraag-louvain
|
|
(package
|
|
(name "python-vtraag-louvain")
|
|
(version "0.8.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "louvain" version))
|
|
(sha256
|
|
(base32
|
|
"16l2zi4jwc3vpvpnz32jv7xy0g5087dp9y57wxplj1xa9r312x0i"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(add-after 'unpack 'do-not-use-bundled-igraph
|
|
(lambda _
|
|
(substitute* "setup.py"
|
|
(("self.external = False")
|
|
"self.external = True")
|
|
(("self.use_pkgconfig = False")
|
|
"self.use_pkgconfig = True")))))))
|
|
(inputs (list igraph))
|
|
(propagated-inputs (list python-igraph))
|
|
(native-inputs
|
|
(list pkg-config
|
|
python-ddt
|
|
python-setuptools-scm))
|
|
(home-page "https://github.com/vtraag/louvain")
|
|
(synopsis "Community detection in large networks")
|
|
(description
|
|
"Louvain is a general algorithm for methods of community detection in
|
|
large networks.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public python-graphtools
|
|
(package
|
|
(name "python-graphtools")
|
|
(version "1.5.3")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/KrishnaswamyLab/graphtools")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32 "1aaxhij4y5z2vvc34qnb5py6nw3ciz35a3z4lfr223f9kvfpqgak"))))
|
|
(build-system pyproject-build-system)
|
|
(arguments
|
|
(list
|
|
#:phases
|
|
'(modify-phases %standard-phases
|
|
(replace 'check
|
|
(lambda* (#:key tests? #:allow-other-keys)
|
|
(when tests?
|
|
;; Incompatibility with sklearn.
|
|
;; '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+)))
|